ONT Isoform Functional Annotation (superseded)

Isoform annotation — moth head+body (resubmit: pfam_collapse fix)

Download ZIP JSON-LD

Type

CWL

Status

succeeded

Engine

cwltool

Duration

0.9 h

Source Data

Study	Tissue-specific long-read transcriptome profiling of Helicoverpa armigera pupa
Sample prep	Direct cDNA library prep of Helicoverpa head and body samples for nanopore sequencing 2024-06-27
Sequencing	Nanopore sequencing of Helicoverpa head and body cDNA libraries 2024-06-28
Run Data	Run #8 (1 samples)
Run Data	Run #13 (1 samples)
Samples	body_library head_library

Pipeline

ONT Long-Read Transcriptomics (IsoQuant)

Run #35

succeeded

ONT Isoform Functional Annotation (superseded)

Run #39 (this run)

succeeded 1 sources

Combined From

#35 — ONT Long-Read Transcriptomics (IsoQuant) succeeded

Sample Provenance

Process Chain

Direct cDNA library prep of Helicoverpa head and body samples for nanopore sequencing (2024-06-27) Labbook

Protocol: Direct cDNA sequencing V14 with SQK-LSK114

2 samples produced

Nanopore sequencing of Helicoverpa head and body cDNA libraries (2024-06-28) Labbook

Workflow

ONT Isoform Functional Annotation — Moth Head+Body

#cwl

Software Tools

Tool	Version	URL
cwltool	-	https://github.com/common-workflow-language/cwltool
eldudy007_isoseq:1.0.sif	-	-

Results Summary

Unique Reads

4,589,704

from upstream transcriptomics

rRNA Reads

4,181,829 (91.1%)

mRNA Reads

407,875

used for CPM calculation

Transcripts Annotated

8,586

Pfam Hit Rate

93.4%

SwissProt Hit Rate

74.7%

High-Confidence

7,500 (87.4%)

Tier 1–2

NMD Candidates

450 (5.2%)

Evidence Tier Distribution

Novel Isoform Discovery

Total Isoforms

8,586

Reference

7,414

Novel (IsoQuant)

1,172

1,161 with ≥3 reads, 11 low-support

Novel %

13.7%

DV Genes: Novel-Created

221

Variation only from novel isoforms

DV Genes: Novel-Contributed

Novel isoforms add to existing ref variation

DV Genes: Reference-Only

136

Variation from reference annotation alone

Long-read sequencing discovered 1,172 novel isoforms (13.7%). Of 379 domain variant genes, 221 (58%) show domain architecture variation only because of novel isoforms not present in the reference annotation. In 19 DV genes, only novel isoforms produced detectable ORFs.

Isoform Read Support (CPM from upstream transcriptomics)

Novel Expression Rate

100.0%

1,172 / 1,172 (1,161 with ≥3 reads)

Reference Expression Rate

97.5%

7,231 / 7,414

Novel Median CPM

22.1

median 9 reads (mean 60.6, range 0–31,540)

Ref Median CPM

12.3

Novel (n=1,172)

Reference (n=7,414)

Box plots show median (line), IQR (box), and 1.5×IQR whiskers. Individual isoform CPM values are overlaid as jittered points. Log₁₀ scale; dashed line marks CPM = 1 expression threshold. Per-model CPM from OUT.transcript_model_counts.tsv

Novel Isoform Functional Impact

Domain Altered

7.5% of novel

NMD Candidates

340

29.0% of novel

ORF Disrupted

6.7% of novel

Conserved

400

34.1% — same protein

739 of 1172 novel isoforms (63.1%) have SwissProt protein homologs. 266 isoforms have no detectable protein homolog. Top species: Drosophila melanogaster (196), Homo sapiens (96), Mus musculus (80), Bos taurus (39), Rattus norvegicus (30).

High-Impact Novel Isoforms (150)

Gene	Impact	Details	ORF	Reads	CPM	SwissProt
— `transcript2999.NC_087134.1.nic`	Domain altered	Lost: ApoO, CsoSCA, DBL, DUF1104, DUF2009, DUF3677, DUF4276, FAD_binding_7, HTH, HrpB2, SASP, SRP1_TIP1, Strep_SA_rep, TPR, Transpos_assoc, YbaB, tRNA_bind_arm	complete	863	2,115.8	sp\|E0X9F6\|THAP1_THAPI 53.8% — Allergen Tha p 1
— `transcript1112.NC_087142.1.nnic`	Domain altered	Gained: DUF963	complete	544	1,333.7	sp\|P80683\|CUA3A_TENMO 67.0% — Larval cuticle protein A3A
BJSP-2 `transcript485.NC_087137.1.nnic`	Domain altered	Gained: DUF5866	complete	464	1,137.6	sp\|Q06343\|BJSB2_TRINI 77.0% — Basic juvenile hormone-suppres...
BJSP-2 `transcript1819.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	338	828.7	sp\|Q06343\|BJSB2_TRINI 85.2% — Basic juvenile hormone-suppres...
— `transcript1534.NC_087132.1.nnic`	Domain altered	Lost: DUF1967	complete	333	816.4	sp\|Q24799\|MYPH_ECHGR 58.3% — Myophilin
— `transcript2067.NC_087145.1.nic`	Domain altered	Lost: EGF	complete	160	392.3	—
BJSP-2 `transcript1958.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	146	358.0	sp\|Q06343\|BJSB2_TRINI 82.7% — Basic juvenile hormone-suppres...
BJSP-2 `transcript1659.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	132	323.6	sp\|Q06343\|BJSB2_TRINI 85.7% — Basic juvenile hormone-suppres...
Spn27A `transcript1728.NC_087142.1.nic`	Domain altered	Lost: AEP	complete	125	306.5	sp\|Q9V3N1\|SP27A_DROME 40.0% — Serine protease inhibitor 27A
— `transcript1002.NC_087129.1.nic`	Domain altered	Gained: EGF	complete	113	277.1	—
BJSP-2 `transcript1967.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	105	257.4	sp\|Q06343\|BJSB2_TRINI 83.9% — Basic juvenile hormone-suppres...
BJSP-2 `transcript2032.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	105	257.4	sp\|Q06343\|BJSB2_TRINI 82.1% — Basic juvenile hormone-suppres...
BJSP-2 `transcript1956.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	92	225.6	sp\|Q06343\|BJSB2_TRINI 75.8% — Basic juvenile hormone-suppres...
BJSP-2 `transcript2093.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	79	193.7	sp\|Q06343\|BJSB2_TRINI 74.7% — Basic juvenile hormone-suppres...
Haspin `transcript2246.NC_087126.1.nnic`	Domain altered	Gained: TPR	complete	78	191.2	sp\|P83103\|HASP_DROME 40.3% — Serine/threonine-protein kinas...
BJSP-2 `transcript1964.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	77	188.8	sp\|Q06343\|BJSB2_TRINI 83.7% — Basic juvenile hormone-suppres...
BJSP-2 `transcript1990.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	62	152.0	sp\|Q06343\|BJSB2_TRINI 84.6% — Basic juvenile hormone-suppres...
BJSP-2 `transcript1988.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	60	147.1	sp\|Q06343\|BJSB2_TRINI 75.6% — Basic juvenile hormone-suppres...
CPIJ001717 `transcript1109.NC_087134.1.nnic`	Domain altered	Gained: DrsE	complete	51	125.0	sp\|B0W3H3\|GATB_CULQU 49.3% — Glutamyl-tRNA(Gln) amidotransf...
BJSP-2 `transcript1986.NC_087137.1.nnic`	Domain altered	Lost: Di-copper, Hemocyanin_N	complete	51	125.0	sp\|Q06343\|BJSB2_TRINI 76.3% — Basic juvenile hormone-suppres...
Pls3 `transcript86.NC_087145.1.nic`	Domain altered	Gained: HTH	complete	49	120.1	sp\|Q63598\|PLST_RAT 52.2% — Plastin-3
COMP `transcript629.NC_087134.1.nic`	Domain altered	Lost: Concanavalin, EGF, TSP3	complete	41	100.5	—
CtsF `transcript417.NC_087139.1.nnic`	Domain altered +NMD	Lost: DUF6699, HAD, NUC153, SPATA1_C, ScsC_N, UPF0154	complete	39	95.6	sp\|Q9VN93\|CATF_DROME 48.1% — Cathepsin F
TMEM214 `transcript1017.NC_087134.1.nnic`	Domain altered +NMD	Lost: PcfK, Polo-box	complete	36	88.3	—
— `transcript2743.NC_087144.1.nnic`	Domain altered	Lost: Tubulin_C	complete	34	83.4	sp\|O17449\|TBB1_MANSE 98.5% — Tubulin beta-1 chain
ubq-1 `transcript967.NC_087136.1.nnic`	Domain altered +NMD	Gained: 2H, CFAP298, DUF3861, DUF6393, GDYXXLXY, GHD, HTH, IT, Peptidase_CA, Phage_sheath_1N, PilZNR, ProRS-C_2, Sde2_N_Ubi, TraK, UBA	complete	33	80.9	sp\|P62972\|UBIQP_XENLA 100.0% — Polyubiquitin (Fragment)
Limd2 `transcript56.NC_087145.1.nnic`	Domain altered	Gained: P-loop_NTPase	complete	30	73.6	sp\|Q4KM31\|LIMD2_RAT 43.3% — LIM domain-containing protein ...
mknk2 `transcript964.NC_087123.1.nnic`	Domain altered	Gained: WS_DGAT_C	complete	28	68.7	sp\|Q66I46\|MKNK2_XENTR 52.9% — MAP kinase-interacting serine/...
RAB32 `transcript1194.NC_087122.1.nnic`	Domain altered	Gained: PH	complete	26	63.8	sp\|Q13637\|RAB32_HUMAN 70.7% — Ras-related protein Rab-32
PI31 `transcript1849.NC_087122.1.nnic`	Domain altered	Lost: PI31_Prot_N	complete	23	56.4	sp\|Q92530\|PSMF1_HUMAN 48.3% — Proteasome inhibitor PI31 subu...
— `transcript2760.NC_087136.1.nnic`	Domain altered	Lost: DUF2778, DUF5704, E-set	complete	23	56.4	sp\|P11733\|CU07_LOCMI 59.8% — Cuticle protein 7
r `transcript100.NC_087128.1.nic`	Domain altered	Lost: ATP-grasp, Glutaminase_I, HTH, Leu-IlvD, MGS, NADP_Rossmann, OTCace_N	complete	21	51.5	sp\|P23780\|BGAL_MOUSE 42.6% — Beta-galactosidase
pix `transcript424.NC_087142.1.nnic`	Domain altered	Lost: 4Fe-4S, RLI, VirE	complete	21	51.5	sp\|Q9VSS1\|ABCE1_DROME 87.6% — Protein Pixie
Adcy1 `transcript1559.NC_087128.1.nnic`	Domain altered	Lost: AC_N	complete	17	41.7	sp\|O88444\|ADCY1_MOUSE 66.0% — Adenylate cyclase type 1
ubq-1 `transcript971.NC_087136.1.nnic`	Domain altered	Gained: 2H, CFAP298, DUF3861, DUF6393, GDYXXLXY, GHD, HTH, IT, Peptidase_CA, Phage_sheath_1N, PilZNR, ProRS-C_2, Sde2_N_Ubi, TraK, UBA	complete	16	39.2	sp\|P0CG53\|UBB_BOVIN 100.0% — Polyubiquitin-B
Tctp `transcript1129.NC_087125.1.nnic`	Domain altered	Gained: Dim_A_B_barrel	complete	15	36.8	sp\|Q75VN3\|TCTP_BOMMO 95.0% — Translationally-controlled tum...
SERCA `transcript131.NC_087128.1.nic`	Domain altered	Lost: Peptidase_MA	complete	15	36.8	sp\|Q7PPA5\|ATC1_ANOGA 90.5% — Calcium-transporting ATPase sa...
— `transcript1031.NC_087129.1.nic`	Domain altered	Lost: UPF0564 Gained: EGF	complete	14	34.3	—
Eml2 `transcript21.NC_087135.1.nnic`	Domain altered +NMD	Lost: DUF4551	complete	14	34.3	sp\|Q6P6T4\|EMAL2_RAT 53.7% — Echinoderm microtubule-associa...
Gaa `transcript9.NC_087130.1.nnic`	Domain altered +NMD	Lost: PX, PXA, RGS	complete	14	34.3	sp\|Q6P7A9\|LYAG_RAT 41.8% — Lysosomal alpha-glucosidase
zip `transcript1198.NC_087121.1.nnic`	Domain altered	Lost: HTH	complete	12	29.4	sp\|Q99323\|MYSN_DROME 85.4% — Myosin heavy chain, non-muscle
bsdc1 `transcript281.NC_087144.1.nic`	Domain altered	Lost: DUF6449	complete	12	29.4	sp\|Q5BJ78\|BSDC1_XENTR 33.3% — BSD domain-containing protein ...
— `transcript1027.NC_087129.1.nic`	Domain altered	Lost: UPF0564 Gained: EGF	complete	11	27.0	—
— `transcript3068.NC_087142.1.nic`	Domain altered	Lost: DUF4611, OAD_gamma, PBP1_TM	complete	11	27.0	—
ARGK `transcript3079.NC_087122.1.nnic`	Domain altered	Lost: DUF3723	complete	11	27.0	sp\|Q95PM9\|KARG_PLOIN 95.2% — Arginine kinase
— `transcript170.NC_087128.1.nnic`	Domain altered +NMD	Gained: DUF3970	complete	10	24.5	sp\|P42788\|CBPZ_SIMVI 44.4% — Zinc carboxypeptidase (Fragmen...
ubq-1 `transcript2811.NC_087136.1.nnic`	Domain altered +NMD	Gained: 2H, CFAP298, DUF3861, DUF6393, GDYXXLXY, GHD, HTH, IT, Phage_sheath_1N, ProRS-C_2, Sde2_N_Ubi, TraK	complete	10	24.5	sp\|P0CG53\|UBB_BOVIN 100.0% — Polyubiquitin-B
METAP1 `transcript318.NC_087131.1.nnic`	Domain altered +NMD	Lost: TRASH	complete	10	24.5	sp\|Q5ZIM5\|MAP1_CHICK 71.3% — Methionine aminopeptidase 1
— `transcript3405.NC_087123.1.nnic`	Domain altered	Lost: E-set, Glyoxalase, SH3, Transthyretin	complete	10	24.5	sp\|P11734\|CU08_LOCMI 71.2% — Cuticle protein 8
rudhira `transcript953.NC_087129.1.nnic`	Domain altered +NMD	Lost: HC2	complete	10	24.5	sp\|Q8SY41\|BCAS3_DROME 45.0% — Breast carcinoma-amplified seq...
SERCA `transcript109.NC_087128.1.nnic`	Domain altered +NMD	Lost: Peptidase_MA	complete	9	22.1	sp\|Q7PPA5\|ATC1_ANOGA 90.5% — Calcium-transporting ATPase sa...
Dsp1 `transcript1337.NC_087129.1.nnic`	Domain altered	Gained: DUF4175, P-loop_NTPase	complete	9	22.1	sp\|Q24537\|HMG2_DROME 64.6% — High mobility group protein DS...
Fas2 `transcript28.NC_087135.1.nic`	Domain altered	Lost: Trefoil	complete	9	22.1	sp\|P34082\|FAS2_DROME 45.9% — Fasciclin-2
— `transcript3063.NC_087142.1.nnic`	Domain altered	Lost: DUF4611, OAD_gamma, PBP1_TM	complete	9	22.1	—
— `transcript3774.NC_087125.1.nic`	Domain altered	Lost: AB_hydrolase, Beta_propeller	complete	9	22.1	sp\|Q9UKV3\|ACINU_HUMAN 38.2% — Apoptotic chromatin condensati...
RpS19a `transcript4.NC_087135.1.nnic`	Domain altered	Lost: DUF5684, HTH, HTH_12	complete	9	22.1	sp\|Q98930\|SORL_CHICK 36.9% — Sortilin-related receptor (Fra...
— `transcript560.NC_087127.1.nnic`	Domain altered	Lost: BDV_P10, PAM2, Tox-GHH2	complete	9	22.1	—
Hrs `transcript1348.NC_087121.1.nic`	Domain altered	Lost: TPR	complete	8	19.6	sp\|Q960X8\|HRS_DROME 48.9% — Hepatocyte growth factor-regul...
NEGR1 `transcript181.NC_087133.1.nnic`	Domain altered	Lost: DUF1229	complete	8	19.6	sp\|Q9W6V2\|NEGR1_CHICK 30.1% — Neuronal growth regulator 1
CLIP-190 `transcript259.NC_087128.1.nic`	Domain altered	Lost: C2H2-zf, Crescentin, CwsA, Retroviral_zf, VBS-like	complete	8	19.6	sp\|Q9VJE5\|CL190_DROME 52.5% — Restin homolog
bun `transcript3296.NC_087122.1.nnic`	Domain altered	Gained: Ax_dynein_light, FtsL, Fzo_mitofusin, HTH, K-box, MIT, SNAPC5, SOGA, TIM_barrel, Wtap, bZIP	complete	8	19.6	sp\|Q24522\|BUN1_DROME 74.5% — Protein bunched, class 1/class...
smarcb1a `transcript802.NC_087141.1.nnic`	Domain altered +NMD	Gained: DUF5964	complete	8	19.6	sp\|Q5U379\|SNF5_DANRE 73.7% — SWI/SNF-related matrix-associa...
— `transcript918.NC_087122.1.nnic`	Domain altered	Lost: Zn_Beta_Ribbon	complete	8	19.6	—
ATPsyngamma `transcript564.NC_087143.1.nnic`	Domain altered	Lost: WASH_WAHD	complete	7	17.2	sp\|O01666\|ATPG_DROME 75.5% — ATP synthase subunit gamma, mi...
LDLR `transcript74.NC_087122.1.nic`	Domain altered	Lost: Calycin	complete	7	17.2	sp\|P20063\|LDLR_RABIT 38.7% — Low-density lipoprotein recept...
Osbp `transcript78.NC_087141.1.nnic`	Domain altered	Lost: DUF6522, HlyD_D23, MbeD_MobD, PH	complete	7	17.2	sp\|Q3B7Z2\|OSBP1_MOUSE 53.8% — Oxysterol-binding protein 1
— `transcript1230.NC_087137.1.nnic`	Domain altered	Lost: PET	complete	6	14.7	—
— `transcript2083.NC_087130.1.nnic`	Domain altered +NMD	Lost: E-set	complete	6	14.7	sp\|Q8MU95\|BGBP_PLOIN 56.4% — Beta-1,3-glucan-binding protei...
— `transcript3062.NC_087142.1.nnic`	Domain altered	Lost: DUF4611, OAD_gamma, PBP1_TM	complete	6	14.7	—
bun `transcript3299.NC_087122.1.nnic`	Domain altered	Gained: Ax_dynein_light, FtsL, Fzo_mitofusin, HTH, K-box, SNAPC5, TIM_barrel, Wtap, bZIP	complete	6	14.7	sp\|Q24522\|BUN1_DROME 77.9% — Protein bunched, class 1/class...
— `transcript1375.NC_087129.1.nnic`	Domain altered	Lost: FnI-like	complete	5	12.3	—
Alyref `transcript2021.NC_087127.1.nic`	Domain altered	Lost: Btz	complete	5	12.3	sp\|Q6GLW1\|THO4B_XENLA 60.8% — THO complex subunit 4-B
— `transcript294.NC_087128.1.nnic`	Domain altered	Gained: DUF3970	complete	5	12.3	sp\|P42788\|CBPZ_SIMVI 44.7% — Zinc carboxypeptidase (Fragmen...
RAB32 `transcript1199.NC_087122.1.nnic`	Domain altered	Gained: PH	complete	4	9.8	sp\|Q13637\|RAB32_HUMAN 70.7% — Ras-related protein Rab-32
SERCA `transcript132.NC_087128.1.nic`	Domain altered	Lost: Peptidase_MA	complete	4	9.8	sp\|Q7PPA5\|ATC1_ANOGA 90.2% — Calcium-transporting ATPase sa...
CG18335 `transcript2264.NC_087124.1.nnic`	Domain altered	Gained: DUF5565	complete	4	9.8	sp\|Q7JRP4\|CMIP2_DROME 48.5% — CIMIP2 protein CG18335
mettl23 `transcript3293.NC_087134.1.nnic`	Domain altered	Lost: 4H_Cytokine, NADP_Rossmann	complete	4	9.8	sp\|Q66JD7\|ACBD6_XENTR 37.0% — Acyl-CoA-binding domain-contai...
abhd11 `transcript3795.NC_087120.1.nic`	Domain altered	Lost: Chlorophyllase2	complete	4	9.8	—
— `transcript406.NC_087121.1.nic`	Domain altered +NMD	Lost: Arc_MA	complete	4	9.8	—
CLIP-190 `transcript458.NC_087128.1.nic`	Domain altered	Lost: C2H2-zf, Crescentin, CwsA, Retroviral_zf, VBS-like	complete	4	9.8	sp\|Q9VJE5\|CL190_DROME 54.3% — Restin homolog
Pkcdelta `transcript93.NC_087123.1.nnic`	Domain altered	Gained: FtrD-like, RING, zf-RING_9	complete	4	9.8	sp\|P83099\|KPC4_DROME 73.1% — Putative protein kinase C delt...
— `transcript1040.NC_087133.1.nnic`	Domain altered	Lost: PRCC	complete	3	7.4	—
Ctl2 `transcript159.NC_087124.1.nic`	Domain altered	Gained: vWF_A	complete	3	7.4	sp\|Q7PRJ0\|CTL12_ANOGA 42.9% — Choline transporter-like 2
— `transcript1674.NC_087121.1.nnic`	Domain altered	Lost: Casc1_N	complete	3	7.4	—
Csnk1g3 `transcript184.NC_087136.1.nic`	Domain altered	Lost: CK1gamma_C	complete	3	7.4	sp\|Q8C4X2\|KC1G3_MOUSE 76.5% — Casein kinase I isoform gamma-...
tns-1 `transcript2790.NC_087125.1.nnic`	Domain altered	Lost: C2, RING	complete	3	7.4	sp\|H2L045\|TENSH_CAEEL 49.8% — Tensin homolog
pik3c3 `transcript99.NC_087136.1.nnic`	Domain altered	Lost: C2	complete	3	7.4	sp\|Q6AZN6\|PK3C3_XENLA 60.6% — Phosphatidylinositol 3-kinase ...
— `transcript2073.NC_087145.1.nnic`	Domain altered	Gained: P-loop_NTPase	complete	2	4.9	—
RpS19a `transcript627.NC_087135.1.nic`	ORF disrupted	Lost: Beta_propeller, DUF5684, E-set, HTH_12, Ldl_recept_a, Sortilin_C	5prime_partial	463	1,135.2	sp\|P39018\|RS19A_DROME 66.9% — Small ribosomal subunit protei...
— `transcript1788.NC_087126.1.nnic`	ORF disrupted	Lost: ATR13, HopA1	5prime_partial	327	801.7	—
— `transcript3351.NC_087134.1.nnic`	ORF disrupted		5prime_partial	209	512.4	—
CP66 `transcript1450.NC_087125.1.nnic`	ORF disrupted		5prime_partial	185	453.6	sp\|P45590\|CU66_HYACE 78.2% — Larval/pupal rigid cuticle pro...
CP66 `transcript1638.NC_087125.1.nnic`	ORF disrupted		5prime_partial	122	299.1	—
PABPC1 `transcript3701.NC_087122.1.nic`	ORF disrupted	Lost: PABP, SLOG	3prime_partial	81	198.6	sp\|P21187\|PABP_DROME 82.5% — Polyadenylate-binding protein
BJSP-2 `transcript1944.NC_087137.1.nnic`	ORF disrupted		5prime_partial	56	137.3	sp\|Q06343\|BJSB2_TRINI 67.9% — Basic juvenile hormone-suppres...
BJSP-2 `transcript2063.NC_087137.1.nnic`	ORF disrupted		5prime_partial	52	127.5	sp\|Q06343\|BJSB2_TRINI 68.3% — Basic juvenile hormone-suppres...
RpL4 `transcript7557.NC_087150.1.nnic`	ORF disrupted	Lost: RNA_pol_Rpb5_C, Ribos_L4_asso_C, Ribosomal_L4 Gained: DUF3275, DUF3811	5prime_partial	50	122.6	—
— `transcript615.NC_087124.1.nic`	ORF disrupted		5prime_partial	36	88.3	sp\|O76485\|CSK2B_SPOFR 100.0% — Casein kinase II subunit beta
— `transcript3037.NC_087134.1.nic`	ORF disrupted		5prime_partial	29	71.1	—
— `transcript3641.NC_087122.1.nic`	ORF disrupted		3prime_partial	29	71.1	—
RpL44 `transcript2949.NC_087132.1.nnic`	ORF disrupted		5prime_partial	28	68.7	sp\|Q9NB33\|RL44_OCHTR 81.6% — Large ribosomal subunit protei...
— `transcript3108.NC_087142.1.nnic`	ORF disrupted	Lost: Mucin, Totivirus_coat	5prime_partial	26	63.8	—
— `transcript919.NC_087132.1.nnic`	ORF disrupted	Gained: DsbC, NTF2	5prime_partial	25	61.3	—
Prc1 `transcript3021.NC_087135.1.nnic`	ORF disrupted		5prime_partial	24	58.8	—
Ing2 `transcript2361.NC_087142.1.nic`	ORF disrupted	Gained: PF	5prime_partial	20	49.0	sp\|Q9ESK4\|ING2_MOUSE 35.7% — Inhibitor of growth protein 2
KAT6B `transcript2567.NC_087137.1.nnic`	ORF disrupted	Lost: Acetyltrans, C2H2-zf, HTH, RING Gained: P-loop_NTPase	5prime_partial	18	44.1	—
EIF5B `transcript2024.NC_087129.1.nic`	ORF disrupted		3prime_partial	17	41.7	—
znrf2 `transcript2804.NC_087130.1.nnic`	ORF disrupted	Lost: Bcl-2_BAD Gained: HMBD, PRP21_like_P, Rad50_zn_hook	5prime_partial	16	39.2	sp\|Q8NHG8\|ZNRF2_HUMAN 79.1% — E3 ubiquitin-protein ligase ZN...
ubq-1 `transcript3094.NC_087136.1.nnic`	ORF disrupted	Lost: DUF5450, GT-A, ORF11CD3 Gained: Bact_hydrolase, DUF3861, HTH, Sde2_N_Ubi	5prime_partial	14	34.3	sp\|P62972\|UBIQP_XENLA 97.5% — Polyubiquitin (Fragment)
nhl-1 `transcript3668.NC_087127.1.nic`	ORF disrupted	Lost: Beta_propeller, DUF5754 Gained: BBOX, Bacillus_HBL, DUF6148	3prime_partial	14	34.3	sp\|Q03601\|NHL1_CAEEL 40.5% — RING finger protein nhl-1
Ar1 `transcript446.NC_087149.1.nnic`	ORF disrupted		5prime_partial	12	29.4	sp\|M9PF61\|ALDR_DROME 65.0% — Aldo-keto reductase 1B
MAP3K7 `transcript871.NC_087137.1.nnic`	ORF disrupted	Lost: Dim_A_B_barrel, PKinase, YabA Gained: FtsL	5prime_partial	12	29.4	—
— `transcript749.NC_087126.1.nic`	ORF disrupted	Lost: ATP11, BCLiA, Borrelia_P83, CCDC71L, DDHD, LMBR1, Macoilin, Membralin, NPR, Neur_chan_memb, P-loop_NTPase, TIM_barrel, Tra1_central, V_ATPase_I Gained: DUF6479, PGA2	3prime_partial	11	27.0	sp\|C0KYB6\|DDRGK_BOMMO 77.1% — DDRGK domain-containing protei...
— `transcript1779.NC_087129.1.nnic`	ORF disrupted	Lost: Mad2, UPF0564 Gained: S4, TBD	5prime_partial	10	24.5	—
unc-22 `transcript261.NC_087145.1.nnic`	ORF disrupted	Lost: Beta_propeller, DUF3146, PKinase Gained: DUF5991	3prime_partial	10	24.5	sp\|Q23551\|UNC22_CAEEL 32.8% — Twitchin
— `transcript425.NC_087126.1.nnic`	ORF disrupted		5prime_partial	10	24.5	—
— `transcript677.NC_087126.1.nnic`	ORF disrupted		5prime_partial	10	24.5	—
MAP3K7 `transcript872.NC_087137.1.nnic`	ORF disrupted	Lost: Dim_A_B_barrel, PKinase, YabA Gained: FtsL, PRP1_N	5prime_partial	10	24.5	—
— `transcript1517.NC_087133.1.nnic`	ORF disrupted		5prime_partial	9	22.1	—
Cdk12 `transcript2168.NC_087127.1.nic`	ORF disrupted		3prime_partial	9	22.1	—
Ace `transcript2285.NC_087133.1.nic`	ORF disrupted	Gained: P-loop_NTPase	3prime_partial	9	22.1	—
Slc16a14 `transcript479.NC_087121.1.nic`	ORF disrupted	Lost: TPR Gained: NDUF_C2	3prime_partial	9	22.1	sp\|Q8K1C7\|MOT14_MOUSE 38.0% — Monocarboxylate transporter 14
— `transcript1219.NC_087129.1.nnic`	ORF disrupted	Lost: UPF0564 Gained: EGF	3prime_partial	8	19.6	—
Ctsb `transcript3446.NC_087121.1.nnic`	ORF disrupted	Gained: SLH	3prime_partial	8	19.6	sp\|P07688\|CATB_BOVIN 51.3% — Cathepsin B
Muted `transcript904.NC_087122.1.nic`	ORF disrupted	Gained: CIS_TMP, DDHD, DUF3314, DUF4229, HAD, Macoilin, Peptidase_AD, SLC12, Vma12	5prime_partial	8	19.6	sp\|Q0KI28\|BL1S5_DROME 34.9% — Biogenesis of lysosome-related...
chs-2 `transcript2022.NC_087125.1.nic`	ORF disrupted	Lost: GT-A, TMIE Gained: EhaL	3prime_partial	7	17.2	sp\|G5EBQ8\|CHS2_CAEEL 43.3% — Chitin synthase chs-2
Nadk `transcript2217.NC_087137.1.nic`	ORF disrupted		5prime_partial	7	17.2	sp\|P58058\|NADK_MOUSE 63.3% — NAD kinase
Kdm3 `transcript2239.NC_087126.1.nnic`	ORF disrupted	Lost: Cupin	3prime_partial	7	17.2	sp\|Q6ZPY7\|KDM3B_MOUSE 42.7% — Lysine-specific demethylase 3B
— `transcript3381.NC_087123.1.nic`	ORF disrupted		5prime_partial	7	17.2	—
— `transcript418.NC_087126.1.nnic`	ORF disrupted		5prime_partial	7	17.2	—
— `transcript468.NC_087124.1.nic`	ORF disrupted		5prime_partial	7	17.2	sp\|P80034\|ACH2_BOMMO 41.4% — Antichymotrypsin-2
EbpIII `transcript1106.NC_087134.1.nnic`	ORF disrupted		3prime_partial	6	14.7	sp\|E0X9F6\|THAP1_THAPI 50.9% — Allergen Tha p 1
Gnf1 `transcript2599.NC_087124.1.nic`	ORF disrupted		3prime_partial	6	14.7	—
Arglu1 `transcript3940.NC_087125.1.nnic`	ORF disrupted	Gained: SR-25	3prime_partial	6	14.7	—
CYP4C1 `transcript773.NC_087132.1.nic`	ORF disrupted		3prime_partial	6	14.7	sp\|P29981\|CP4C1_BLADI 34.5% — Cytochrome P450 4C1
unc-22 `transcript81.NC_087145.1.nnic`	ORF disrupted	Lost: Beta_propeller, DUF3146, PKinase Gained: DUF5991, Mog1p_PsbP	3prime_partial	6	14.7	sp\|O01761\|UNC89_CAEEL 24.5% — Muscle M-line assembly protein...
SMTNL1 `transcript854.NC_087127.1.nnic`	ORF disrupted	Lost: CH, Smoothelin Gained: TFIIA	3prime_partial	6	14.7	—
Pyk `transcript118.NC_087131.1.nnic`	ORF disrupted		5prime_partial	5	12.3	sp\|O62619\|KPYK_DROME 75.4% — Pyruvate kinase
YL-1 `transcript1487.NC_087133.1.nic`	ORF disrupted	Lost: Peptidase_MA, YL1_C Gained: HAD	3prime_partial	5	12.3	sp\|Q15906\|VPS72_HUMAN 39.6% — Vacuolar protein sorting-assoc...
— `transcript1652.NC_087142.1.nic`	ORF disrupted		3prime_partial	5	12.3	—
— `transcript1804.NC_087122.1.nnic`	ORF disrupted		5prime_partial	5	12.3	sp\|P35042\|TRYP_CHOFU 66.0% — Trypsin CFT-1
Ccp84Ab `transcript1936.NC_087136.1.nnic`	ORF disrupted		5prime_partial	5	12.3	sp\|Q17015\|CU01_ANOGA 50.0% — Cuticle protein
RhoL `transcript2223.NC_087124.1.nic`	ORF disrupted		3prime_partial	5	12.3	sp\|Q24192\|RHOL_DROME 65.9% — Ras-like GTP-binding protein R...
ATPsyngamma `transcript223.NC_087143.1.nnic`	ORF disrupted		5prime_partial	5	12.3	sp\|O01666\|ATPG_DROME 75.8% — ATP synthase subunit gamma, mi...
Myo9a `transcript3.NC_087136.1.nnic`	ORF disrupted	Lost: GAP, RhoGEF67_u1 Gained: DabA	3prime_partial	5	12.3	sp\|B2RTY4\|MYO9A_HUMAN 47.9% — Unconventional myosin-IXa
mnt `transcript34.NC_087141.1.nic`	ORF disrupted		5prime_partial	5	12.3	sp\|Q0VH32\|MNT_XENLA 62.4% — Max-binding protein MNT
SVIL `transcript3449.NC_087130.1.nnic`	ORF disrupted		3prime_partial	5	12.3	—
FKBP46 `transcript665.NC_087136.1.nic`	ORF disrupted	Lost: FKBP, HTH Gained: DUF4604	3prime_partial	5	12.3	sp\|Q26486\|FKBP4_SPOFR 90.2% — 46 kDa FK506-binding nuclear p...
Cir1 `transcript1454.NC_087128.1.nic`	ORF disrupted	Gained: Multiheme_cytos	3prime_partial	4	9.8	sp\|Q9DA19\|CIR1_MOUSE 50.9% — Corepressor interacting with R...
Tgs1 `transcript1606.NC_087130.1.nnic`	ORF disrupted		3prime_partial	4	9.8	—

Frame Impact Classification

Functional Diversity per Gene

Top Pfam Domains

Domain Architectures per Gene

Annotation QC: Pfam Artifact Detection

Related Pfam families are grouped into clans; proteins with anomalously high domain density (structural protein artifacts) are flagged separately. The cleaned set is used for all downstream analysis.

Original DV Genes

379

After QC Filtering

292

Removed (Artifacts)

Flagged Details

Flagged Artifacts (41)

Gene	Gene Name	Reason	Arch (raw)	Arch (collapsed)	Core / Variable Domains
`LOC110384212`	—	density artifact	11	0	30 / 36
`LOC110377875`	—	density artifact	4	0	31 / 3
`LOC110376902`	Iru	density artifact	2	0	30 / 0
`LOC135117277`	Cdr2	density artifact	2	0	51 / 0
`LOC110374071`	GUK1	density artifact	2	0	37 / 0
`LOC110372597`	Syx1A	density artifact	2	0	36 / 0
`Ter94`	TER94	density artifact	2	0	56 / 0
`LOC110372101`	—	density artifact	2	0	39 / 0
`LOC110372103`	Pc	clan collapse	2	1	22 / 0
`LOC110380678`	Tcjhe	clan collapse	2	1	5 / 0
`LOC110379509`	betaTub60D	clan collapse	2	1	6 / 0
`LOC110370669`	numb	clan collapse	2	1	4 / 0
`LOC110376033`	abcG23	clan collapse	2	1	9 / 0
`LOC110374423`	Usp12-46	clan collapse	2	1	5 / 0
`LOC110369716`	Traf4	clan collapse	2	1	4 / 1
`LOC110369808`	acp7	clan collapse	2	1	4 / 1
`LOC110381949`	rbm4.1	clan collapse	2	1	4 / 0
`LOC110379868`	lark	clan collapse	2	1	10 / 0
`LOC110384521`	Actn	clan collapse	2	1	11 / 0
`LOC110375316`	Oadh	clan collapse	2	1	3 / 0
`LOC110379953`	MLC1	clan collapse	2	1	4 / 0
`LOC110380328`	AIFM1	clan collapse	2	1	8 / 0
`LOC110375010`	—	clan collapse	2	1	8 / 1
`LOC110377662`	NATA1	clan collapse	2	1	9 / 0
`LOC110371964`	Tanc2	clan collapse	2	1	20 / 0
`LOC110376460`	KCNJ12	clan collapse	2	1	5 / 0
`LOC110378339`	Rho1	clan collapse	2	1	6 / 0
`LOC110375878`	Eip63F-1	clan collapse	2	1	15 / 0
`LOC110372031`	SQOR	clan collapse	2	1	8 / 0
`LOC110369940`	Mctp	clan collapse	2	1	3 / 0
`LOC110372205`	Pgant9	clan collapse	2	1	5 / 0
`LOC110383870`	Gyg1	clan collapse	2	1	3 / 0
`LOC110377229`	AnxB9	clan collapse	2	1	5 / 1
`LOC110384049`	—	clan collapse	2	1	8 / 0
`Diap1`	IAP	clan collapse	2	1	6 / 0
`LOC110376342`	DCTD	clan collapse	2	1	4 / 0
`LOC110374127`	nifk	clan collapse	2	1	2 / 0
`LOC110372702`	Ubc2	clan collapse	2	1	3 / 0
`LOC110383693`	Rala	clan collapse	2	1	9 / 0
`LOC110380619`	nas-4	clan collapse	2	1	3 / 0
`LOC110377166`	TMUB2	clan collapse	2	1	4 / 0

Domain Variants by Evidence Tier

Variable Domain Landscape

Total Variable Domains

208

Domain Loss Events

193

Domain Gain Events

Loss : Gain Ratio

9.2:1

Domain loss dominates gain ~9:1, consistent with alternative splicing predominantly removing exons encoding specific domains rather than inserting novel domain-encoding exons.

All Variable Domains (208)

Domain	DV Genes	Gain	Loss	Genes
`TFIIA`	3	1	2	AnxB11, EcR, SMTNL1
`PK_Tyr_Ser-Thr`	2	0	2	MAP3K7, unc-22
`Pkinase`	2	0	2	MAP3K7, unc-22
`Hemocyanin_N`	2	1	1	BJSP-2, BJSP-2
`Hemocyanin_M`	2	1	1	BJSP-2, BJSP-2
`SH3_2`	1	0	1	Mcf2l
`MSA-2c`	1	0	1	ZFAND6
`NDNF`	1	0	1	unc-22
`fn3_2`	1	0	1	unc-22
`DUF3146`	1	0	1	unc-22
`Kre9_KNH`	1	0	1	unc-22
`Ig_5`	1	0	1	unc-22
`fn3`	1	0	1	unc-22
`PhoD_N`	1	0	1	unc-22
`PKD_3`	1	0	1	unc-22
`Receptor_2B4`	1	0	1	unc-22
`Kelch_1`	1	0	1	unc-22
`Ig_C17orf99`	1	0	1	unc-22
`Kdo`	1	0	1	unc-22
`Pur_ac_phosph_N`	1	0	1	unc-22
`Ig_4`	1	0	1	unc-22
`Y_Y_Y`	1	0	1	unc-22
`Mog1`	1	0	1	unc-22
`Tissue_fac`	1	0	1	unc-22
`APH`	1	0	1	MAP3K7
`PRP1_N`	1	0	1	MAP3K7
`DUF3291`	1	0	1	MAP3K7
`YabA`	1	0	1	MAP3K7
`DUF3781`	1	0	1	GLG1
`DUF6215`	1	0	1	XPO5
`Snf7`	1	0	1	TMEM86B
`PspA_IM30`	1	0	1	TMEM86B
`DUF1263`	1	0	1	E75
`CRAM_rpt`	1	0	1	lfe-2
`AAA_11`	1	0	1	kay
`Cas_Csy4`	1	0	1	kay
`fvmX5`	1	0	1	ApepP
`GBP_C`	1	0	1	LOC110383740
`DUF883`	1	0	1	LOC110383740
`DUF4456`	1	0	1	LOC110383740
`DUF445`	1	0	1	LOC110383740
`ApoLp-III`	1	0	1	LOC110383740
`Mis12`	1	0	1	LOC110383740
`ApoO`	1	0	1	LOC110383740
`NIF3`	1	0	1	LOC110383740
`CAC1F_C`	1	0	1	LOC110383740
`FANCI_S3`	1	0	1	LOC110383740
`Phasin`	1	0	1	LOC110383740
`DUF2362`	1	1	0	wupA
`DUF3810`	1	0	1	SERCA
`DUF3866`	1	0	1	exd
`YbjQ_1`	1	0	1	exd
`Ribosomal_60s`	1	0	1	exd
`WS_DGAT_C`	1	0	1	mknk2
`ApoM`	1	0	1	LDLR
`EhaL`	1	0	1	chs-2
`TMIE`	1	0	1	chs-2
`UCH`	1	0	1	Usp54
`PTEN_C2`	1	0	1	GAK
`DnaJ`	1	0	1	GAK
`Mucin`	1	0	1	LOC110378652
`Totivirus_coat`	1	0	1	LOC110378652
`KxYKxGKxW_sig`	1	0	1	Tret1
`PADRE`	1	0	1	E(z)
`NPR3`	1	0	1	E(z)
`DUF2828`	1	0	1	E(z)
`SpoIIP`	1	0	1	E(z)
`RPA43_OB`	1	0	1	E(z)
`DUF4746`	1	0	1	E(z)
`TCR`	1	0	1	E(z)
`OAD_gamma`	1	0	1	LOC110378661
`PBP1_TM`	1	0	1	LOC110378661
`DUF4611`	1	0	1	LOC110378661
`DUF5866`	1	1	0	BJSP-2
`zf-MYND`	1	0	1	METAP1
`zf-C6H2`	1	0	1	METAP1
`CH`	1	0	1	SMTNL1
`CAMSAP_CH`	1	0	1	SMTNL1
`4_1_CTD`	1	0	1	SMTNL1
`OCC1`	1	0	1	Ctsb
`SLH`	1	0	1	Ctsb
`MSSP`	1	0	1	LOC110382745
`ANAPC4_WD40`	1	0	1	Ciao1
`TFIIIC_delta`	1	0	1	Ciao1
`DUF5809`	1	0	1	Ciao1
`NBCH_WD40`	1	0	1	Ciao1
`WD40`	1	0	1	Ciao1
`CTD3`	1	0	1	Ciao1
`eIF2A`	1	0	1	Ciao1
`Coatomer_WDAD`	1	0	1	Ciao1
`IKI3`	1	0	1	Ciao1
`BBS2_Mid`	1	0	1	Ciao1
`SOGA`	1	0	1	bun
`MIT`	1	0	1	bun
`FHA`	1	0	1	Phldb2
`PH_3`	1	0	1	Phldb2
`RRM_DME`	1	0	1	Phldb2
`PH_15`	1	0	1	Phldb2
`Yop-YscD_cpl`	1	0	1	Phldb2
`PH_8`	1	0	1	Phldb2
`Sublancin`	1	1	0	LOC110376808
`Porin_2`	1	0	1	LOC110376808
`EMP24_GP25L`	1	0	1	cher
`Big_3_5`	1	0	1	cher
`GDPD_2`	1	0	1	Bhmt
`ProRS-C_2`	1	0	1	ubq-1
`Bact_hydrolase`	1	1	0	ubq-1
`Transglut_core2`	1	0	1	ubq-1
`TraK`	1	0	1	ubq-1
`E3_UbLigase_EDD`	1	0	1	ubq-1
`DUF6393`	1	0	1	ubq-1
`LBP_C`	1	0	1	ubq-1
`GDYXXLXY`	1	0	1	ubq-1
`PilZNR`	1	0	1	ubq-1
`Phage_sheath_1N`	1	0	1	ubq-1
`PI3K_p85B`	1	0	1	ubq-1
`DMA`	1	0	1	ubq-1
`SAP_new25`	1	1	0	Sarm
`rve`	1	1	0	Sarm
`rve_3`	1	1	0	Sarm
`HAP1_N`	1	0	1	Cdr2
`TBD`	1	1	0	LOC110371006
`Toxin_17`	1	1	0	LOC110371006
`UPF0564`	1	0	1	LOC110371006
`S4`	1	1	0	LOC110371006
`Ribosomal_S18`	1	1	0	LOC110370162
`DUF3432`	1	0	1	LOC110370162
`7TMR-DISM_7TM`	1	1	0	LOC110370162
`DUF3377`	1	1	0	LOC110370162
`TetR_C_11`	1	0	1	LOC110370162
`Hydin_ADK`	1	0	1	CERT1
`RNA_polI_A34`	1	0	1	FKBP46
`Vfa1`	1	0	1	FKBP46
`CCD97-like_C`	1	0	1	FKBP46
`FKBP_C`	1	0	1	FKBP46
`DUF4604`	1	0	1	FKBP46
`DTHCT`	1	0	1	FKBP46
`ATG14`	1	0	1	DESI1
`RRT14`	1	0	1	DESI1
`SOTI`	1	0	1	DESI1
`Cytochrom_C`	1	0	1	DESI1
`Peptidase_C97`	1	0	1	DESI1
`HTH_IclR`	1	0	1	DESI1
`MarR_2`	1	0	1	DESI1
`PepSY_TM`	1	1	0	rtn3-b
`DUF3723`	1	0	1	ARGK
`Nexin_C`	1	0	1	Gaa
`Elf1`	1	0	1	GATA-B
`Zn-ribbon_8`	1	0	1	GATA-B
`DUF5816`	1	0	1	GATA-B
`Auto_anti-p27`	1	0	1	GATA-B
`eIF-5_eIF-2B`	1	0	1	GATA-B
`DZR`	1	0	1	GATA-B
`CYYR1`	1	0	1	GATA-B
`DZR_2`	1	0	1	GATA-B
`DUF2387`	1	0	1	GATA-B
`TDP43_N`	1	0	1	GATA-B
`OrfB_Zn_ribbon`	1	0	1	GATA-B
`HTH_24`	1	0	1	CtsF
`DnaJ-X`	1	1	0	Doa
`Presenilin`	1	0	1	Doa
`IPK`	1	1	0	Doa
`RRM_3`	1	0	1	HNRNPR
`DUF3141`	1	0	1	CP66
`CwsA`	1	0	1	CLIP-190
`HIP1_clath_bdg`	1	0	1	CLIP-190
`Crescentin`	1	0	1	CLIP-190
`zf-U1`	1	0	1	CLIP-190
`CLIP1_ZNF`	1	0	1	CLIP-190
`Nuc_H_symport`	1	0	1	LOC110379502
`Hamartin`	1	0	1	Jupiter
`VMAP-M0`	1	1	0	RAB32
`DUF5062`	1	1	0	RAB32
`DUF815`	1	0	1	RAB32
`DUF4800`	1	0	1	AnxB11
`Di19_C`	1	0	1	SYTL4
`DUF4834`	1	0	1	SYTL4
`DUF4958`	1	0	1	kug
`He_PIG`	1	0	1	kug
`RibLong`	1	0	1	kug
`EGF`	1	0	1	kug
`Kinocilin`	1	0	1	kug
`Laminin_G_2`	1	0	1	kug
`RVT_1`	1	0	1	kug
`EGF_CA`	1	0	1	kug
`Trm112p`	1	0	1	kug
`zf-C2HC_2`	1	0	1	kug
`Laminin_G_1`	1	0	1	kug
`zf-C2H2_4`	1	0	1	kug
`Methyltransf_16`	1	0	1	kug
`Zn_ribbon_recom`	1	0	1	kug
`zf-C2H2`	1	0	1	kug
`hEGF`	1	0	1	kug
`Col_cuticle_N`	1	0	1	LOC110381131
`RNA_pol_Rpb1_2`	1	0	1	LOC110372065
`DUF3306`	1	0	1	LOC110372065
`DUF4187`	1	0	1	Csrp1
`Bcl-2_BAD`	1	0	1	znrf2
`Rad50_zn_hook`	1	0	1	znrf2
`Spore_III_AB`	1	0	1	TPD52L2
`ATG17_like`	1	0	1	TPD52L2
`Erf4`	1	0	1	TPD52L2
`HTH_12`	1	0	1	RpS19a
`DUF5684`	1	0	1	RpS19a
`hNIFK_binding`	1	0	1	Jph2
`HrpB1_HrpK`	1	0	1	Fur1
`Tox-GHH2`	1	0	1	LOC110383068
`BDV_P10`	1	0	1	LOC110383068

Domain Variant Genes (292 genes, multiple architectures after QC)

All domain variant genes retaining multiple domain architectures after clan collapse and density artifact removal. Use the search box to filter by gene ID, name, function, or domain.

Showing 292 of 292 genes

Gene	Name	Function	Isoforms	Arch	Tier	CPM	Source	Core Domains
`LOC110384286`	ubq-1	Polyubiquitin-A	7	6	1	156.9	Novel	2_5_RNA_ligase2, Big_7, CFAP298, Crinkler, DUF2604, DUF3861, DUF5450, DUF969, Dsc3_N, FlgD_ig, HemeBinding_Shp, ORF11CD3, Plexin_RBD, Pullulanase_N2, Rad60-SLD, Rad60-SLD_2, Raf1_HTH, Sde2_N_Ubi, Staphylokinase, TBK1_ULD, TmoB, UDP-g_GGTase, UN_NPL4, Ubiquitin_2, Ubiquitin_4, Ubiquitin_5, ubiquitin
`LOC110371006`	—	—	9	6	2	56.4	Mixed	Defensin_2, EGF_Tenascin, Gamma-thionin, SLR1-BP, STOP, Toxin_2, Toxin_3, bacHORMA_2
`LOC110380881`	SMTNL1	Smoothelin-like protein 1	5	5	1	58.8	Mixed	Smoothelin
`LOC110376808`	—	Larval cuticle protein A1A	6	4	1	2.5	Novel	Chitin_bind_4, DUF963
`Rab32`	RAB32	Ras-related protein Rab-32	6	4	1	103.0	Novel	AAA_16, AAA_22, AAA_24, AAA_7, ATP_bind_1, Arf, DLIC, G-alpha, Gtr1_RagA, ISP1_C, MMR_HSR1, MMR_HSR1_Xtn, PduV-EutP, Ras, Roc, Sigma54_activat, TniB, TsaE
`LOC110375562`	znrf2	E3 ubiquitin-protein ligase znrf2	4	4	1	159.4	Novel	HMBD, PRP21_like_P, Prok-RING_1, RINGv, RNF220, zf-C3HC4, zf-C3HC4_2, zf-C3HC4_3, zf-C3HC4_4, zf-RING-like, zf-RING_11, zf-RING_16, zf-RING_2, zf-RING_5, zf-RING_UBOX, zf-rbx1
`LOC110378904`	TPD52L2	Tumor protein D54	4	4	1	76.0	Mixed	CrtO, DUF2199, HIP1_clath_bdg, HalX, Jnk-SapK_ap_N, OmpH, Peptidase_M32, PvlArgDC, TPD52
`LOC110384471`	RpS19a	Small ribosomal subunit protein eS19A	4	4	1	885.1	Mixed	BNR, BNR_6, Ldl_recept_a, Ldl_recept_b, Pur_ac_phosph_N, Ribosomal_S19e, Sortilin-Vps10, Sortilin_C, fn3
`LOC110370162`	—	—	5	4	2	7.4	Novel	—
`LOC110373907`	unc-22	Twitchin	3	3	1	193.7	Novel	C1-set, C2-set_2, DUF5991, I-set, Ig_2, Ig_3, Izumo-Ig, PKD, V-set, ig
`LOC110379538`	CtsF	Cathepsin F	3	3	1	213.3	Novel	Cathelicidins, Cystatin, DUF6699, FAM176, Inhibitor_I29, NUC153, PGP_phosphatase, Peptidase_C1, Peptidase_C1_2, SPATA1_C, SQAPI, ScsC_N, UPF0154
`LOC110382235`	MAP3K7	Mitogen-activated protein kinase kinase kinase 7	3	3	1	46.6	Novel	FtsL_2
`Wupa`	wupA	Troponin I	5	3	1	431.5	Mixed	Spc42p, Troponin
`LOC110374623`	exd	Homeobox protein extradenticle	3	3	1	46.6	Ref	CENP-B_N, DUF4878, GAIN, HTH_3, Homeobox_KN, Homeodomain, IATP, Nucleoporin_FG2, PBC, UCH, YdaS_antitoxin
`LOC110375985`	E(z)	Histone-lysine N-methyltransferase E(z)	3	3	1	27.0	Mixed	PRC2_HTH_1, SET, preSET_CXC
`LOC110376576`	Ctsb	Cathepsin B	3	3	1	1,240.6	Novel	Peptidase_C1, Peptidase_C1_2, Propeptide_C1
`LOC110370365`	FKBP46	46 kDa FK506-binding nuclear protein	3	3	1	24.5	Novel	NPL, TFIIF_alpha
`LOC110370041`	E75	Ecdysone-inducible protein E75	4	3	1	58.8	Mixed	Hormone_recep, zf-C4
`LOC110371881`	chs-2	Chitin synthase chs-2	3	3	1	88.3	Mixed	Chitin_synth_2, Glyco_tranf_2_3, Glyco_trans_2_3
`LOC110380215`	BJSP-2	Basic juvenile hormone-suppressible protein 2	5	3	1	1,380.3	Novel	Hemocyanin_C
`LOC110383815`	bun	Protein bunched, class 2/F/G isoform	4	3	1	12.3	Novel	Ax_dynein_light, CCDC106, DUF1667, DUF6262, Fzo_mitofusin, GHL13, K-box, SNAPC5, TSC22, Wtap, YabA, ZapB, bZIP_1, bZIP_2
`LOC110381191`	Phldb2	Pleckstrin homology-like domain family B member 2	3	3	1	9.8	Mixed	ACOX, HALZ, PH, PH_11
`LOC110369673`	—	Zinc carboxypeptidase (Fragment)	4	3	1	110.3	Novel	DUF3970, Peptidase_M14, Propep_M14, tRNA_deacylase
`LOC110378481`	DESI1	Desumoylating isopeptidase 1	4	3	1	19.6	Novel	DUF3670, DUF4407, PUL, TPR_MLP1_2
`LOC110376880`	rtn3-b	Reticulon-3-B	7	3	1	647.3	Ref	HisKA_3, Reticulon
`LOC110373713`	Gaa	Lysosomal alpha-glucosidase	3	3	1	17.2	Novel	DUF5110, Gal_mutarotas_2, Glyco_hydro_31, NtCtMGAM_N, PX, PXA, RGS, Trefoil
`LOC110377660`	GATA-B	Transcription factor BCFI	3	3	1	66.2	Mixed	GATA, TF_Zn_Ribbon
`Doa`	Doa	Serine/threonine-protein kinase Doa	6	3	1	120.1	Ref	PK_Tyr_Ser-Thr, Pkinase
`Kug`	kug	Fat-like cadherin-related tumor suppressor homolog	3	3	1	73.6	Novel	Big_9, Cadherin, Cadherin_2, Cadherin_3, DUF5980
`LOC110383740`	—	—	3	3	2	24.5	Novel	Apolipoprotein, DUF1663, DUF6674, Perilipin
`LOC110378652`	—	—	3	3	2	129.9	Mixed	FAP, JUPITER
`LOC110372065`	—	—	3	3	2	1,044.4	Ref	CaMBD, Citrate_synt, DUF4522, SNRNP27, Thymosin, WDCP, WH2
`LOC110383068`	—	—	3	3	2	19.6	Mixed	MIF4G, PAM2
`Zip`	zip	Myosin heavy chain, non-muscle	2	2	1	156.9	Novel	AAA_22, Hpr_kinase_C, IQ, Myosin_N, Myosin_head, Myosin_tail_1, SgrR_N
`LOC110375042`	cher	Filamin-A	5	2	1	27.0	Ref	DUF5060, DUF6801, Filamin, Y_Y_Y, YtkA
`Fhos`	Fhod3	FH1/FH2 domain-containing protein 3	2	2	1	7.4	Ref	ELMO_ARM, FH2, Formin_GBD_N
`LOC110378584`	Bin1	Myc box-dependent-interacting protein 1	2	2	1	29.4	Ref	ANIS5_cation-bd, BAR, DUF1664, GIT1_C, GPS2_interact, PIG-P, SH3_1, SH3_2, SH3_9, zf-RING_9
`LOC110375642`	Ace	Angiotensin-converting enzyme	2	2	1	78.5	Novel	Herpes_TK, Peptidase_M2
`LOC110369899`	Adcy1	Adenylate cyclase 1	2	2	1	80.9	Novel	AC_N, Adcy_cons_dom, Guanylate_cyc
`LOC110382602`	Spn27A	Serine protease inhibitor 27A	2	2	1	34.3	Novel	Diphtheria_T, PPL4, Serpin
`LOC110377274`	Ing2	Inhibitor of growth protein 2	2	2	1	2.5	Novel	CENP-U, ING, NPR3, PHD, PHD_2, SRP-alpha_N
`LOC110380713`	Obsc	Protein Obscurin	2	2	1	127.5	Novel	C2-set_2, FlgH, I-set, Ig_2, Ig_3, Izumo-Ig, Kdo, PH_10, PKD_3, PK_Tyr_Ser-Thr, Pkinase, Receptor_2B4, RhoGEF, Ribosomal_L27, SH3_1, SH3_9, V-set, fn3, ig
`LOC110369812`	CanB2	Calcineurin subunit B type 2	2	2	1	12.3	Ref	Caleosin, Dockerin_1, EF-hand_1, EF-hand_4, EF-hand_5, EF-hand_6, EF-hand_7, EF-hand_8, EF-hand_9, RecJ_OB, SPARC_Ca_bdg
`LOC110372278`	HSPB1	Heat shock protein beta-1	2	2	1	358.0	Ref	ArsA_HSP20, CTD4, HSP20
`LOC110383692`	Hdac4	Histone deacetylase 4	2	2	1	14.7	Ref	AAA_23, HDAC4_Gln, Hist_deacetyl, TFIIA
`LOC110371885`	Jph2	Junctophilin-2	3	2	2	36.8	Ref	Alanine_zipper, DUF4398, MORN
`LOC110378527`	Csrp1	Cysteine and glycine-rich protein 1	3	2	4	39.2	Novel	LIM
`LOC110378020`	ash2	Set1/Ash2 histone methyltransferase complex subunit ASH2	2	2	1	22.1	Ref	PHD, PHD_2, PHD_3, SPRY
`LOC110370040`	Tmbim6	Bax inhibitor 1	2	2	1	350.6	Novel	7TMR-DISM_7TM, ANIS5_cation-bd, Bax1-I, DHHC, DUF1140, DUF2231, DUF3381, DUF3764, DUF5366, Flavi_NS4A, FtsJ, Inhibitor_I53, Inhibitor_I69, PBP1_TM, RNA_pol_3_Rpc31, Spb1_C, Tom22
`LOC135117776`	ZFAND6	AN1-type zinc finger protein 6	4	2	1	2.5	Novel	zf-A20, zf-AN1
`LOC110370760`	Pik3ap1	Phosphoinositide 3-kinase adapter protein 1	3	2	1	58.8	Ref	Ank_2, ArgoN, DBB, FapA, Sec34, TIR_3, Zip
`LOC110380831`	NAGLU	Alpha-N-acetylglucosaminidase	2	2	1	68.6	Ref	NAGLU, NAGLU_C, NAGLU_N, Proteasome, Proteasome_A_N
`LOC110377417`	COTL1	Coactosin-like protein	2	2	1	137.3	Ref	AIP3, BLOC1_2, CAGE1, CENP-F_leu_zip, Cep57_MT_bd, Cofilin_ADF, CpG_bind_C, DUF2205, DUF3450, DUF4164, DUF4795, DivIC, FapA, Fzo_mitofusin, GAS, HemX, NPV_P10, Nsp1_C, Nuf2_DHR10-like, Phage_GP20, Seryl_tRNA_N, TMPIT, VPS11_C, YabA
`LOC110383758`	ken	Transcription factor Ken	2	2	1	29.4	Ref	BTB, DUF6431, FYVE_2, Zn-ribbon_8, Zn_ribbon_SprT, zf-C2H2, zf-C2H2_2, zf-C2H2_3rep, zf-C2H2_4, zf-C2H2_6, zf-C2H2_jaz, zf-Di19, zf-H2C2_2
`LOC110384470`	Fas2	Fasciclin-2	2	2	1	19.6	Novel	C2-set_2, I-set, Ig_2, Ig_3, Izumo-Ig, Kunitz_legume, Pur_ac_phosph_N, V-set, V-set_CD47, fn3, ig
`LOC110374080`	pnut	Protein peanut	2	2	1	12.3	Ref	AAA_16, AAA_22, AAA_23, ABC_tran, AIG1, ATG14, DUF6748, DUF87, Dynamin_N, Exonuc_VII_L, GTP_EFTU, IIGP, MMR_HSR1, Ras, Roc, RsgA_GTPase, Septin
`LOC110379393`	Vapa	Vesicle-associated membrane protein-associated protein A	2	2	1	17.2	Ref	ASH, Fez1, Motile_Sperm
`LOC110380441`	kay	Transcription factor kayak	3	2	1	76.0	Novel	BBS2_C, DUF1465, DUF3043, DUF3086, DUF3450, DUF4407, DivIC, FapA, LCD1, Macoilin, Metal_resist, UPF0242, ZapB, bZIP_1, bZIP_2, bZIP_Maf
`LOC110384311`	Myo9a	Unconventional myosin-IXa	2	2	1	46.6	Novel	C1_1, C1_2, CENP-F_leu_zip, DUF3669, DUF6409, DabA, FYVE_2, IQ, Myosin_head, PHD, PHD_2, Prok-RING_1, RA, RhoGAP, RhoGEF67_u1, zf-HC5HC2H, zf-HC5HC2H_2, zf-RING-like, zf-RING_15, zf-RING_9
`LOC110370503`	mknk2	MAP kinase-interacting serine/threonine-protein kinase 2	3	2	1	80.9	Novel	APH, Kdo, PK_Tyr_Ser-Thr, Pkinase
`LOC110384228`	Mbd3	Methyl-CpG-binding domain protein 3	2	2	1	14.7	Ref	MBD, MBD_C, MBDa, SAM_PNT
`LOC110380564`	GAK	Cyclin-G-associated kinase	3	2	1	7.4	Novel	Haspin_kinase, Kinase-like, PK_Tyr_Ser-Thr, Pkinase
`LOC110371859`	Dsp1	High mobility group protein DSP1	2	2	1	12.3	Novel	DUF4175, HMG_box, HMG_box_2, HMG_box_5, NAT_N, Protamine_like
`LOC110373455`	MAX	Protein max	2	2	1	17.2	Ref	DUF4618, DUF4763, DUF5311, DUF5595, DivIC, FapA, Frtz, HLH, JAKMIP_CC3, Jnk-SapK_ap_N, ZapB, bZIP_2
`LOC110371973`	tns-1	Tensin homolog	2	2	1	22.1	Novel	C1_1, PTB, PTEN_C2, SH2, zf-RING_15
`LOC110369696`	tio	Protein tiptop	2	2	1	7.4	Ref	Actin_micro, DUF4187, FYVE, PSI_integrin, Sgf11, Tmemb_55A, zf-C2H2, zf-C2H2_2, zf-C2H2_4, zf-C2H2_6, zf-C2H2_9, zf-C2H2_jaz, zf-C2HE, zf-met, zf_ZIC
`LOC110373303`	YL-1	Vacuolar protein sorting-associated protein 72 homolog	2	2	1	12.3	Novel	CDC45, Peptidase_M50, YL1, YL1_C
`LOC110379742`	Pls3	Plastin-3	2	2	1	53.9	Novel	CAMSAP_CH, CH, CH_2, EF-hand_1, EF-hand_5, EF-hand_6, EF-hand_7, HTH_40, RsbRD_N
`Spin`	spin	Protein spinster	2	2	1	22.1	Ref	MFS_1, OATP, Sugar_tr, TrbC
`Dnalig3`	LIG3	DNA ligase 3	2	2	1	14.7	Novel	BRCT, BRCT_2, DNA_ligase_A_C, DNA_ligase_A_M, DNA_ligase_A_N, DUF1851, LIG3_BRCT, RNA_ligase, mRNA_cap_enzyme, zf-PARP
`Lmpt`	FHL2	Four and a half LIM domains protein 2	2	2	1	36.8	Ref	LIM, PET
`LOC110370712`	—	Myophilin	2	2	1	505.1	Novel	CAMSAP_CH, CDC24, CH, Calponin, DUF1967
`LOC110380616`	smarcb1a	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1-A	2	2	1	2.5	Novel	DUF5964, SNF5
`LOC110371995`	Kdm3	Lysine-specific demethylase 3	2	2	1	117.7	Novel	C1_2, Cupin_2, FYVE, JmjC, TAF4, zf-C5HC2, zf-RING_16, zf-UBP, zf-UDP
`LOC110372410`	Limd2	LIM domain-containing protein 2	2	2	1	56.4	Novel	KdpD, LIM
`LOC110377432`	VCATH	Viral cathepsin	2	2	1	174.1	Novel	DIM, Globin, Glyco_trans_A_1, Inhibitor_I29
`LOC110372595`	lolal	Longitudinals lacking protein-like	2	2	1	7.4	Novel	BEN, BTB, Gly_kinase, zf-BED, zf-C2H2, zf-C2H2_11, zf-C2H2_3rep, zf-C2H2_4, zf-C2H2_6, zf-C2H2_jaz, zf-C2HC_2, zf-H2C2_2, zf-H2C2_5, zf-met
`LOC110375725`	Prm	Paramyosin, long form	2	2	1	225.6	Ref	Crescentin, DUF3557, ERM_helical, Filament, Myosin_tail_1, PARP, PhaP_Bmeg, T7SS_ESX_EspC
`LOC110379883`	KAT6B	Histone acetyltransferase KAT6B	2	2	1	7.4	Novel	Acetyltransf_7, HemN_C, HerA_C, Linker_histone, MOZ_SAS, PHD, zf-MYST
`LOC135117321`	Nostrin	Nostrin	2	2	1	4.9	Ref	DUF5917, FCH, Mucin15, NABP, SH3_1, SH3_2, SH3_9, betaPIX_CC
`LOC110372844`	HMG20A	High mobility group protein 20A	2	2	1	12.3	Ref	Exonuc_VII_L, HMG_box, HMG_box_2
`LOC110379998`	Sdc	Syndecan	2	2	2	12.3	Novel	Cytomega_TRL10, DUF2207, Glycophorin_A, Myc_target_1, RunxI, Syndecan
`LOC110384210`	PDLIM3	PDZ and LIM domain protein 3	5	2	4	22.1	Novel	DUF4749, PDZ, PDZ_2, PDZ_6
`LOC110372681`	Cd63	CD63 antigen	3	2	1	152.0	Mixed	AC_N, DUF1600, DUF2892, DUF3185, DUF373, DUF6057, DUF6750, FtsX, PHO4, Tetraspanin
`LOC110383845`	Mcf2l	Guanine nucleotide exchange factor DBS	3	2	1	14.7	Novel	CRAL_TRIO, CRAL_TRIO_2, DUF4201, PH, PH_10, RhoGEF, SH3_1, SH3_9, Spectrin
`LOC110380390`	Trmt13	tRNA:m(4)X modification enzyme TRM13 homolog	2	2	1	7.4	Novel	Methyltransf_32, TRM13, zf-TRM13_CCCH, zf-U11-48K
`LOC126056716`	—	Beta-1,3-glucan-binding protein	3	2	1	44.1	Novel	CBM39, Glyco_hydro_16
`LOC110372928`	Rab6	Ras-related protein Rab6	3	2	1	51.5	Mixed	Arf, DUF6581, FeoB_N, GTP_EFTU, Gtr1_RagA, MMR_HSR1, Ras, Roc, RsgA_GTPase, SRPRB, TetR_C_16
`Glg1`	GLG1	Golgi apparatus protein 1	3	2	1	34.3	Ref	Cys_rich_FGFR
`LOC110375684`	Cir1	Corepressor interacting with RBPJ 1	2	2	1	53.9	Novel	Cir_N, NapB, zf-CCHC_6
`LOC110377756`	bwa	Alkaline ceramidase	2	2	1	98.1	Novel	Ceramidase, DUF2484, DUF3927, DUF6007, Toxin_YhaV
`LOC110383466`	GF21161	Ubiquitin-conjugating enzyme E2 S	2	2	1	7.4	Novel	MIP, UQ_con
`LOC110380340`	MYOCD	Myocardin	2	2	1	7.4	Ref	DUF3584, DUF4140, RPEL, SAP, SAP_new25
`LOC110369850`	plxna3	Plexin A3	2	2	1	66.2	Ref	Acyltransf_C, Acyltransferase, Delta_lysin, HcgF, PSI, Plexin_RBD, Plexin_cytopl, Sema, TIG, TIG_2, TIG_SUH, TIG_plexin
`LOC110377643`	Odc1	Ornithine decarboxylase	2	2	1	73.6	Novel	Orn_Arg_deC_N, Orn_DAP_Arg_deC, rRNA_processing
`LOC110374389`	XPO5	Exportin-5	3	2	1	14.7	Novel	DUF3437, Exportin-5, IBN_N, Xpo1
`Tweek`	bltp1	Bridge-like lipid transfer protein family member 1	2	2	1	31.9	Novel	FSA_C, Kiaa1109_N
`LOC110379319`	Klp10A	Kinesin-like protein Klp10A	2	2	1	24.5	Ref	DUF4140, DivIC, Kinesin, Microtub_bd
`LOC110376519`	692975	Serine hydroxymethyltransferase	2	2	1	56.4	Ref	Beta_elim_lyase, DUF4200, DUF6376, SHMT
`LOC110380384`	TMEM86B	Lysoplasmalogenase TMEM86B	3	2	1	27.0	Novel	YhhN
`LOC110369917`	lfe-2	Inositol-trisphosphate 3-kinase homolog	3	2	1	66.2	Ref	IPK
`LOC110373235`	Clic	Chloride intracellular channel Clic	2	2	1	31.9	Ref	GST_C_2, GST_N, GST_N_3, Sec23_helical
`LOC110370077`	GLMN	Glomulin	2	2	1	4.9	Novel	COQ9, Kinetochor_Ybp2
`LOC110378939`	CYP4C1	Cytochrome P450 4C1	2	2	1	56.4	Novel	FAD_binding_1, PalH, RhoGEF, SKN1_KRE6_Sbg1, p450
`LOC135118096`	—	Serine protease inhibitor dipetalogastin (Fragment)	2	2	1	228.0	Novel	Kazal_1, Kazal_2, PET
`LOC126055869`	—	Cuticle protein 7	2	2	1	34.3	Novel	Cadherin_5, Chitin_bind_4, DUF2778, DUF5704
`LOC110376117`	GSPT1	Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	2	2	1	51.5	Ref	G-alpha, GTP_EFTU, GTP_EFTU_D2, GTP_EFTU_D3, MMR_HSR1, PAM2
`LOC110379208`	GART	Trifunctional purine biosynthetic protein adenosine-3	2	2	1	46.6	Ref	AIRS, AIRS_C, ATP-grasp, ATP-grasp_2, ATP-grasp_3, ATP-grasp_4, CPSase_L_D2, DUF389, Formyl_trans_N, GARS_A, GARS_C, GARS_N, LAL_C2, RimK
`Smash`	CG43427	Uncharacterized protein CG43427	2	2	1	56.4	Novel	ATP-synt_E_2, DUF4757, LIM
`LOC110383591`	ApepP	Xaa-Pro aminopeptidase ApepP	3	2	1	46.6	Novel	Creatinase_N, Creatinase_N_2, DUF6635, Peptidase_M24, Peptidase_M24_C
`LOC110377474`	Hrs	Hepatocyte growth factor-regulated tyrosine kinase substrate	2	2	1	95.6	Novel	CID, DZR, FYVE, FYVE_2, Hrs_helical, UIM, VHS
`Gish`	Csnk1g3	Casein kinase I isoform gamma-3	3	2	1	12.3	Novel	CK1gamma_C, PK_Tyr_Ser-Thr, Pkinase, Pkinase_fungal, YrbL-PhoP_reg
`LOC110383804`	Muted	Biogenesis of lysosome-related organelles complex 1 subunit 5	2	2	1	7.4	Novel	CDC45, CIS_TMP, DDHD, DUF3314, DUF4229, DUF4931, LMBR1, Macoilin, Muted, Presenilin, Prominin, SLC12, TMF_TATA_bd, Vma12
`LOC110376864`	Mlc-c	Myosin-2 essential light chain	2	2	1	497.7	Ref	Caleosin, DUF3349, EF-hand_1, EF-hand_5, EF-hand_6, EF-hand_7, EF-hand_8, EF-hand_9, UPF0154
`Stac`	stac	Protein unc-13 homolog 4B	2	2	1	7.4	Novel	C2, MUN
`Serca`	SERCA	Calcium-transporting ATPase sarcoplasmic/endoplasmic reticulum type	7	2	1	365.3	Mixed	Cation_ATPase, Cation_ATPase_C, Cation_ATPase_N, E1-E2_ATPase, HAD, Hydrolase, Hydrolase_3
`LOC110370539`	AGGF1	Angiogenic factor with G patch and FHA domains 1	2	2	1	4.9	Ref	BSMAP, FHA, FHA_2, G-patch, G-patch_2, OCRE, Stomoxyn, Yop-YscD_cpl
`LOC110378448`	OtopLc	Proton channel OtopLc	2	2	1	4.9	Ref	DUF2828, MAP17, Otopetrin, SpoIIIAH, UPF0242, VIT1, V_ATPase_I, Vfa1, Zip
`LOC110383871`	LDLR	Low-density lipoprotein receptor (Fragment)	4	2	1	17.2	Mixed	DUF5050, EGF_CA, FXa_inhibition, Ldl_recept_a, Ldl_recept_b, SGL, cEGF
`LOC110380778`	Nlp	Nucleoplasmin-like protein	2	2	1	142.2	Ref	DNA_pol_phi, GCIP, NPL, Nucleoplasmin, RRN3
`LOC110379520`	—	Tubulin beta-1 chain	2	2	1	1,010.1	Novel	Misat_Tub_SegII, Tubulin, Tubulin_2, Tubulin_3, Tubulin_C
`LOC110380545`	Eif4g3	Eukaryotic translation initiation factor 4 gamma 3	2	2	1	9.8	Ref	Condensin2nSMC, FeoB_Cyto, Fib_alpha, MA3, MIF4G, TAFH, W2
`LOC110375907`	REXO1L1	Exonuclease GOR	2	2	1	328.5	Ref	ANAPC4_WD40, DPPIV_N, Ge1_WD40, NBCH_WD40, PAM2, Rv2179c-like, SGL, WD40
`LOC110371071`	LMO4	LIM domain transcription factor LMO4	2	2	1	4.9	Ref	LIM, TNFR_c6, YhfH, zf-HYPF, zf-IS66, zf-dskA_traR
`Step`	CYTH1	Cytohesin-1	2	2	1	17.2	Ref	FlgN, PH, PH_11, PH_20, PH_3, PH_6, PH_8, Sec7, Sialidase
`LOC110378331`	RAB23	Ras-related protein Rab-23	2	2	1	17.2	Novel	AAA_16, AAA_7, Arf, DUF2528, MMR_HSR1, PduV-EutP, Ras, Roc, RsgA_GTPase
`LOC110370769`	Osbp	Oxysterol-binding protein 1	2	2	1	66.2	Novel	DUF6522, HlyD_D23, MbeD_MobD, Oxysterol_BP, PH, PH_11, PH_20, PH_6, PH_8
`LOC110383912`	Usp54	Ubiquitin carboxyl-terminal hydrolase 54	3	2	1	12.3	Ref	C1_2
`LOC110374408`	Clc	Clathrin light chain	2	2	1	274.6	Ref	Ax_dynein_light, Clathrin_lg_ch, EMG1
`Prp19`	PRPF19	Pre-mRNA-processing factor 19	2	2	1	7.4	Novel	ANAPC4_WD40, Coatomer_WDAD, Cytochrom_D1, Ge1_WD40, Glyphos_transf, HPS3_N, NBCH_WD40, Nup160, PAS_11, Prp19, U-box, WD40, WD40_like, eIF2A
`LOC110374119`	Tret1	Facilitated trehalose transporter Tret1	3	2	1	132.4	Novel	FAM210A-B_dom, MFS_1, Mntp, SelK_SelG, Sugar_tr
`LOC110372925`	PI31	Proteasome inhibitor PI31 subunit	2	2	1	95.6	Novel	PI31_Prot_C, PI31_Prot_N
`LOC110373102`	SmydA-8	SET domain-containing protein SmydA-8, isoform A	2	2	1	9.8	Ref	SET, zf-HIT
`LOC110377634`	RpS7	Small ribosomal subunit protein eS7	2	2	1	1,088.6	Ref	DUF5613, DUF5678, PCuAC, Ribosomal_S7e
`LOC110376357`	—	Allergen Tha p 1	2	2	1	51.5	Novel	ApoO, CsoSCA, DUF1104, DUF1133, DUF2009, DUF3677, DUF4276, DUF5302, FAD_binding_7, GET4, HrpB2, OS-D, PFEMP, SRP1_TIP1, Seryl_tRNA_N, Strep_SA_rep, Transpos_assoc, Urb2, YbaB_DNA_bd
`LOC110380709`	NEGR1	Neuronal growth regulator 1	2	2	1	166.7	Novel	Adeno_E3_CR1, BTD, C2-set_2, DUF1229, I-set, Ig_2, Ig_3, Ig_4, Ig_6, Ig_C17orf99, V-set, ig
`LOC110374492`	syd	JNK-interacting protein 3	2	2	1	4.9	Ref	ATG14, CENP-F_leu_zip, JIP_LZII, Jnk-SapK_ap_N, Reg_prop, TPR_MLP1_2, WD40_2, WD40_alt, bZIP_1
`LOC110380423`	Lims2	LIM and senescent cell antigen-like-containing domain protein 2	2	2	1	34.3	Ref	DZR_2, LIM, NinD, zf-C4pol, zinc-ribbons_6
`LOC110372709`	SOD1	Superoxide dismutase [Cu-Zn]	3	2	1	353.0	Ref	DUF4148, Sod_Cu
`LOC110379889`	zdhhc2	Palmitoyltransferase ZDHHC2	2	2	1	22.1	Ref	DHHC, SecY
`LOC110379084`	pik3c3	Phosphatidylinositol 3-kinase catalytic subunit type 3	3	2	1	134.8	Novel	DUF4135, DUF928, PI3K_C2, PI3Ka, PI3_PI4_kinase
`Tn`	nhl-1	RING finger protein nhl-1	4	2	1	80.9	Novel	Bacillus_HBL, Baculo_PEP_C, DUF5128, DUF5711, DUF5754, DUF6148, DUF641, NHL, Phytase-like, SBBP, SGL, TolB_like, zf-B_box, zf-C3HC4, zf-C3HC4_2, zf-C3HC4_3, zf-RING_2, zf-RING_5, zf-RING_UBOX
`LOC110370466`	NSMCE2	E3 SUMO-protein ligase NSE2	2	2	1	4.9	Novel	Dna2, Stevor, U-box, zf-Nse, zf-RING_16, zf-RING_UBOX
`LOC110383951`	METAP1	Methionine aminopeptidase 1	3	2	1	22.1	Mixed	Peptidase_M24
`LOC126053519`	Ddx17	Probable ATP-dependent RNA helicase DDX17	2	2	1	61.3	Novel	AAA_19, Apt1, DEAD, DUF4050, Helicase_C, NPR3, ResIII
`LOC110382601`	Rlip	RalA-binding protein 1	2	2	1	7.4	Ref	DUF3915, RhoGAP, Trans_reg_C, Vfa1
`LOC135118639`	ATPsyngamma	ATP synthase subunit gamma, mitochondrial	2	2	1	103.0	Novel	ATP-synt, WASH_WAHD
`LOC110373924`	YIPF1	Protein YIPF1	2	2	1	2.5	Novel	DUF2070, LisH_2, Yip1
`Pabp`	PABPC1	Polyadenylate-binding protein 1	2	2	1	642.4	Novel	Lysine_decarbox, MARF1_RRM1, Nup35_RRM_2, OB_RNB, PABP, RRM_1, RRM_3, RRM_5, RRM_7, RRM_occluded, SET_assoc
`LOC110370967`	rudhira	Breast carcinoma-amplified sequence 3 homolog	2	2	1	103.0	Novel	BCAS3, DUF326, HC2
`LOC110375677`	Ciao1	Probable cytosolic iron-sulfur protein assembly protein Ciao1	3	2	1	7.4	Ref	NIF3
`LOC110372369`	Haspin	Serine/threonine-protein kinase haspin homolog	2	2	1	164.3	Novel	APH, DUF3856, Haspin_kinase, PK_Tyr_Ser-Thr, Pkinase
`LOC110381839`	cops2	COP9 signalosome complex subunit 2	2	2	1	7.4	Ref	DUF4570, PCI, RPN6_N, TPR_1, TPR_2, TPR_7
`LOC110376307`	cactin	Splicing factor Cactin	2	2	1	17.2	Ref	CactinC_cactus, Cactin_mid, CoV_nucleocap, TFIIA
`LOC110374024`	dod	Putative peptidyl-prolyl cis-trans isomerase dodo	2	2	1	14.7	Ref	DUF5671, Phage_TAC_6, RBD-FIP, Rotamase, Rotamase_2, Rotamase_3, TilS, WW, zf_CopZ
`LOC110374093`	fundc1	FUN14 domain-containing protein 1	2	2	1	159.4	Ref	Birna_RdRp_C, DUF1798, FUN14, Halogen_Hydrol, ISG65-75, Osmo_CC, Prefoldin, SCAB_CC, TipAS
`LOC126053458`	Tbca	Tubulin-specific chaperone A	2	2	1	49.0	Novel	DUF5938, DUF6681, DinB, PDCD7, PRIMA1, Peptidase_S46, RabGAP-TBC, TBCA, UPF0242
`LOC110379118`	AGAP003331	Enolase-phosphatase E1	2	2	1	56.4	Novel	ATPgrasp_N, Abhydrolase_7, HAD_2, Hydrolase, Hydrolase_like
`LOC110376123`	COMP	Cartilage oligomeric matrix protein	2	2	1	73.6	Novel	COMP, EGF_3, EGF_CA, SlyX, TSP_3, TSP_C, cEGF
`LOC110371122`	—	Venom dipeptidyl peptidase 4	2	2	1	7.4	Novel	BD-FAE, DPPIV_N, Esterase, PAF-AH_p_II, Peptidase_S9, RRM_1, RSB_motif
`LOC110373585`	Anp32a	Acidic leucine-rich nuclear phosphoprotein 32 family member A	2	2	1	24.5	Ref	BUD22, LRR_4, LRR_5, LRR_6, LRR_8, LRR_9, RPC5, SURF2
`LOC110381057`	CG18335	CIMIP2 protein CG18335	2	2	1	12.3	Novel	DUF2475, DUF5565
`LOC110380363`	Bhmt	Betaine-homocysteine S-methyltransferase	3	2	1	291.8	Novel	S-methyl_trans, SprT-like
`LOC110377169`	EIF2B1	Translation initiation factor eIF2B subunit alpha	2	2	1	17.2	Novel	DNAJ_related, DUF3539, IF-2B
`LOC110369777`	SRRM2	Serine/arginine repetitive matrix protein 2	2	2	1	29.4	Ref	DUF6074, SieB, cwf21
`LOC110382063`	bsdc1	BSD domain-containing protein 1	2	2	1	9.8	Novel	BSD, DUF6449
`LOC110375379`	spen	Protein split ends	2	2	1	218.2	Novel	HTH_47, RRM_1, RRM_7, RRM_occluded, SPOC
`LOC110378624`	RpL4	Large ribosomal subunit protein uL4	2	2	1	2,066.8	Novel	DUF3275, DUF3811, RNA_pol_Rpb5_C, Ribos_L4_asso_C, Ribosomal_L4
`S6kl`	S6KL	Serine/threonine-protein kinase S6KL	2	2	1	2.5	Novel	ABC1, APH, ATG101, FTA2, Haspin_kinase, Kdo, PK_Tyr_Ser-Thr, Pkinase, Pkinase_fungal, RIO1
`LOC110375237`	—	Cuticle protein 8	2	2	1	58.8	Novel	Chitin_bind_4, Glyoxalase_8, PAZ_3, SpaA_2, T2SS-T3SS_pil_N
`Sarm`	Sarm	NAD(+) hydrolase sarm1	5	2	1	41.7	Novel	Arm, SAM_1, SAM_2, SAM_3, TIR_2
`LOC110374985`	—	27 kDa hemolymph protein	2	2	1	39.2	Ref	DUF1397, DUF2277, DUF2481, DUF4230, SurA_N_3, TetR_C_34
`LOC110371499`	Cdr2	Cerebellar degeneration-related protein 2	3	2	1	29.4	Ref	KASH_CCD, Prefoldin, SlyX
`Pix`	pix	Protein Pixie	2	2	1	274.6	Novel	AAA, AAA_14, AAA_15, AAA_16, AAA_21, AAA_22, AAA_23, AAA_24, AAA_28, AAA_29, AAA_30, AAA_33, AAA_5, AAA_7, ABC_tran, DLIC, DUF5906, Fer4, Fer4_10, Fer4_16, Fer4_2, Fer4_21, Fer4_4, Fer4_6, Fer4_7, Fer4_8, Fer4_9, Gemini_AC4_5, MMR_HSR1, NACHT, NB-ARC, RLI, RNA_helicase, Rad17, Roc, RsgA_GTPase, SMC_N, SRP54, Septin, TsaE, VirE
`LOC110379977`	mettl23	Histone-arginine methyltransferase METTL23	2	2	1	4.9	Novel	ACBP, Ank, Ank_2, Ank_3, Ank_4, Ank_5, IL2, MTS, Methyltransf_16, Methyltransf_23, Methyltransf_25, T3SS_ATPase_C
`LOC110378594`	Nanp	N-acylneuraminate-9-phosphatase	2	2	1	19.6	Novel	DUF6690, HAD, HAD_2, Hydrolase, Hydrolase_like, PGP_phosphatase, PNK3P, PqqD
`LOC110373700`	DHX38	Pre-mRNA-splicing factor ATP-dependent RNA helicase PRP16	2	2	1	19.6	Ref	AAA_14, AAA_19, AAA_22, AAA_23, AAA_30, AAA_33, AAA_7, ABC_tran, ATPase, DEAD, DUF4398, DinB, Flavi_DEAD, FtsK_SpoIIIE, HA2, Helicase_C, OB_NTP_bind, PhoH, Sigma54_activ_2, Sigma54_activat, T2SSE, cobW
`LOC110376069`	—	DDRGK domain-containing protein 1	2	2	1	49.0	Novel	AAA_11, ATG14, ATP11, Borrelia_P83, CCDC71L, DDHD, DDRGK, DUF6479, FeoC, LMBR1, Macoilin, Membralin, NPR3, Neur_chan_memb, PGA2, PMSI1, Tra1_central, V_ATPase_I, hDGE_amylase
`LOC110380216`	BJSP-2	Basic juvenile hormone-suppressible protein 2	9	2	1	5,455.1	Novel	Hemocyanin_C
`LOC126055753`	—	Cuticle protein 7	2	2	1	22.1	Novel	Chitin_bind_4, DUF2486
`LOC110369847`	Eml2	Echinoderm microtubule-associated protein-like 2	2	2	1	7.4	Novel	ANAPC4_WD40, CPSF_A, DUF4551, HELP, NBCH_WD40, WD40
`LOC110375153`	eEF1delta	Probable elongation factor 1-delta	4	2	1	139.7	Mixed	BLOC1_2, CCD48, Cwf_Cwc_15, DUF1664, DUF4407, DivIC, EF-1_beta_acid, EF1_GNE, FlaC_arch, OAD_gamma, Ribosomal_60s, Shugoshin_N, Spc24, Syntaxin-6_N, TMF_DNA_bd, TSC22, Wtap, bZIP_1
`LOC110375960`	lola	Longitudinals lacking protein, isoforms H/M/V	2	2	1	71.1	Ref	BTB, CpXC, Trm112p, VIR_N, Zn_Tnp_IS1595, zf-AN1, zf-C2H2, zf-C2H2_2, zf-C2H2_4, zf-C2H2_7, zf-C6H2, zf-Di19, zf-H2C2_2, zf-H2C2_5, zf-Mss51, zf_C2H2_10, zf_C2H2_ZHX, zinc_ribbon_5
`LOC110371224`	CERT1	Ceramide transfer protein	3	2	1	68.6	Novel	CCDC74_C, PH, PH_11, PH_8, START
`LOC126053617`	shf	Protein shifted	2	2	1	2.5	Novel	EGF, EGF_2, Laminin_EGF, WIF, cEGF, hEGF
`LOC110379722`	TMEM214	Transmembrane protein 214	2	2	1	51.5	Novel	PcfK, Plk4_PB1, TMEM214
`LOC110377829`	bab2	Protein bric-a-brac 2	2	2	1	9.8	Ref	BTB, HTH_Tnp_1, HTH_Tnp_IS630, HTH_psq, MerR, SspB
`LOC110374451`	Ctl2	Choline transporter-like 2	2	2	1	41.7	Novel	Choline_transpo, TgpA_N, vWF_A
`LOC110371237`	Tssk4	Testis-specific serine/threonine-protein kinase 4	2	2	1	7.4	Ref	ABC1, Aida_N, Kdo, Kinase-like, PK_Tyr_Ser-Thr, Pkinase, QPE
`LOC110382429`	TRIP11	Thyroid receptor-interacting protein 11	2	2	1	9.8	Ref	CC149, CENP-F_leu_zip, Crescentin, Csm1_N, DUF3138, Docking, GRAB, GRIP, KASH_CCD, SHE3, TSC22, TolA_bind_tri
`LOC110372825`	Alyref	THO complex subunit 4	2	2	1	83.4	Novel	Btz, FoP_duplication, RRM_1
`LOC110375686`	Erp44	Endoplasmic reticulum resident protein 44	2	2	1	7.4	Novel	Calsequestrin, OST3_OST6, Thioredoxin, Thioredoxin_6, UPAR_LY6_2
`LOC110376508`	Slc16a14	Monocarboxylate transporter 14	2	2	1	58.8	Novel	MFS_1, NDUF_C2, Not1, Rce1-like, Sugar_tr
`Hwt`	Shf	SH2 domain-containing adapter protein F	2	2	1	41.7	Novel	DUF4551, NigD_C, SH2
`LOC110380571`	Pkcdelta	Putative protein kinase C delta type homolog	2	2	1	24.5	Novel	APH, C1_1, C1_2, FtrD-like, Haspin_kinase, Kdo, Kinase-like, PHD, PHD_2, PK_Tyr_Ser-Thr, Pkinase, Pkinase_C, Pkinase_fungal, zf-RING_15, zf-RING_9
`LOC110372888`	ARGK	Arginine kinase	3	2	1	286.9	Mixed	ATP-gua_Ptrans, ATP-gua_PtransN, Ac76
`LOC110380469`	14-3-3zeta	14-3-3 protein zeta	5	2	1	483.0	Mixed	14-3-3, DUF4518, DUF4710, NPFF
`LOC110370733`	PPAE1	Phenoloxidase-activating enzyme 1	2	2	1	93.2	Novel	CLIP, DUF1986, PT, Trypsin, Trypsin_2
`LOC110369974`	EcR	Ecdysone receptor	4	2	1	22.1	Ref	Hormone_recep, zf-C4
`LOC110372358`	—	97 kDa heat shock protein	2	2	1	29.4	Ref	HSP70, Ketoacyl-synt_C, MreB_Mbl, Peptidase_S49_N, Vta1
`LOC110376053`	Odad1	Outer dynein arm-docking complex subunit 1	2	2	1	0.0	Novel	BLOC1S3, Caudo_TAP, DUF3376, DUF848, Exonuc_VII_L, FlaC_arch, Med9, Mod_r, NYD-SP28_assoc, Nup88, Vert_HS_TF, Vip3A_N
`LOC110371441`	Vps26	Vacuolar protein sorting-associated protein 26	2	2	1	93.2	Novel	Arrestin_C, Arrestin_N, Mannosyl_trans, PIG-U, Vps26
`Vari`	PALS2	Protein PALS2	2	2	1	14.7	Ref	Colicin_E5, Exo_endo_phos_2, Guanylate_kin, IL1_propep, PDZ, PDZ_2, PDZ_6, Peptidase_M50, SH3_1, SH3_2, SH3_9, Tricorn_PDZ
`LOC110370085`	LOC113510063	Phenoloxidase-activating factor 2 (Fragment)	2	2	1	31.9	Ref	CLIP_1, DUF316, Trypsin, Trypsin_2
`LOC110379433`	TMEM165	Putative divalent cation/proton antiporter TMEM165	2	2	1	9.8	Novel	CobD_Cbib, DUF6584, Mntp, OFeT_1, Pet100, Strabismus, UPF0016
`LOC110378362`	rab11fip4a	Rab11 family-interacting protein 4A	2	2	1	7.4	Novel	BRI3BP, CENP-K, DUF1664, DUF4554, DUF5660, EMP24_GP25L, FapA, Fez1, Fib_alpha, FlxA, Halogen_Hydrol, Lzipper-MIP1, Mce4_CUP1, NPV_P10, RBD-FIP, Ribosomal_L29, Vac_Fusion, phiKZ_IP
`LOC110373174`	SCP2	Sterol carrier protein 2	2	2	1	470.7	Novel	ACP_syn_III, Alkyl_sulf_C, Ketoacyl-synt_C, SCP2, SCP2_2, SpoVAD, Thiolase_C, Thiolase_N, ketoacyl-synt
`LOC110372477`	abhd11	sn-1-specific diacylglycerol lipase ABHD11	2	2	1	4.9	Novel	Abhydrolase_1, Abhydrolase_11, Abhydrolase_3, Abhydrolase_5, Abhydrolase_6, Chlorophyllase, Chlorophyllase2, DLH, DUF1057, DUF676, DUF915, Esterase, Hydrolase_4, Lipase_3, Ndr, PAF-AH_p_II, PGAP1, Thioesterase
`LOC110369956`	MLXIP	MLX-interacting protein	2	2	1	4.9	Ref	DivIC, HLH, MAP65_ASE1, Macoilin, NPV_P10, bZIP_1
`LOC110380874`	GILT1	GILT-like protein 1	2	2	1	12.3	Novel	GILT, Phage_tail_U, Thioredoxin_4
`LOC110371057`	Arglu1	Arginine and glutamate-rich protein 1	2	2	1	34.3	Novel	ARGLU, SR-25
`LOC110372790`	CG32795	Transmembrane protein 120 homolog	2	2	1	9.8	Ref	DUF4765, DUF641, Rx_N, SPC25, TMPIT
`LOC110381581`	Ubxn4	UBX domain-containing protein 4	2	2	1	0.0	Novel	DUF3526, ORC3_N, UBX
`LOC110376350`	CPIJ001717	Glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrial	2	2	1	134.8	Novel	DrsE, GatB_N, GatB_Yqey
`LOC110378990`	GPN2	GPN-loop GTPase 2	2	2	1	9.8	Ref	AAA, AAA_16, AAA_17, AAA_18, AAA_22, AAA_24, AAA_30, AAA_31, AAA_33, AAA_5, ATP_bind_1, ArsA_ATPase, CbiA, Fer4_NifH, KTI12, MeaB, NTPase_1, PAC3, RNA_helicase, RuvB_N, SRP54, Zeta_toxin
`LOC126056620`	marchf2	E3 ubiquitin-protein ligase MARCHF2	2	2	1	14.7	Ref	MHC2-interact, RINGv, Transmemb_17, zf-C3HC4_3, zf-RING_16, zf-RING_2, zf-rbx1
`LOC110375328`	HNRNPR	Heterogeneous nuclear ribonucleoprotein R	4	2	1	63.7	Novel	DUF1707, DUF1866, MARF1_RRM1, PHM7_cyt, RRM_1, RRM_5, RRM_7, RRM_occluded, SET_assoc, hnRNP_Q_AcD
`LOC110380880`	Marchf2	E3 ubiquitin-protein ligase MARCHF2	2	2	1	2.5	Ref	Hpre_diP_synt_I, RINGv, malic, zf-RING_2
`LOC110382272`	CP66	Larval/pupal rigid cuticle protein 66	3	2	1	10,809.7	Novel	Chitin_bind_4
`Psn`	Psn	Presenilin homolog	2	2	1	14.7	Ref	ABC2_membrane_2, DUF2109, Pox_A14, Presenilin
`LOC110372605`	CLIP-190	Restin homolog	3	2	1	12.3	Novel	CAP_GLY
`LOC110377255`	Jupiter	Microtubule-associated protein Jupiter	3	2	1	41.7	Ref	JUPITER
`LOC110375794`	porin	Voltage-dependent anion-selective channel	2	2	1	171.6	Novel	DUF6733, EKAL, Porin_3, Tcp10_C
`LOC110371905`	DGAT1	Diacylglycerol O-acyltransferase 1	4	2	1	9.8	Ref	ABC2_membrane_5, MBOAT, MBOAT_2
`LOC110370025`	r	Multifunctional protein r	2	2	1	27.0	Novel	ATP-grasp, ATP-grasp_3, ATPgrasp_Ter, Amidohydro_1, BetaGal_dom4_5, CPSase_L_D2, CPSase_L_D3, CPSase_sm_chain, Cellulase, DJ-1_PfpI, Dala_Dala_lig_C, GARS_A, GATase, Glyco_hydro_35, Glyco_hydro_42, MGS, OTCace, OTCace_N, Peptidase_C26, RimK
`LOC110378703`	AnxB11	Annexin B11	3	2	1	68.6	Ref	Annexin, DUF1678, DUF2179, Myb_DNA-bind_7
`LOC110383954`	SYTL4	Synaptotagmin-like protein 4	3	2	1	17.2	Novel	C2
`Su(tpl)`	Ell	RNA polymerase II elongation factor Ell	2	2	1	9.8	Ref	BRF1, ELL, Occludin_ELL, RAP1
`LOC110370376`	RABAC1	Prenylated Rab acceptor protein 1	2	2	1	12.3	Ref	DUF6057, Osmo_MPGsynth, PRA1
`LOC110381278`	NCOA7	Nuclear receptor coactivator 7	2	2	1	51.5	Ref	LysM, TLD
`LOC110379761`	ARHGEF1	Rho guanine nucleotide exchange factor 1	2	2	1	44.1	Novel	C1_1, C1_2, Hemerythrin, PDZ, PDZ_2, PDZ_6, PH_16, Peptidase_M50, RGS-like, RhoGEF
`LOC110371268`	Ctdp1	RNA polymerase II subunit A C-terminal domain phosphatase	2	2	1	17.2	Novel	BRCT, BRCT_2, Biotin_lipoyl, Biotin_lipoyl_2, CDC45, FCP1_C, HAD, HlyD_3, LIG3_BRCT, NIF, PTCB-BRCT
`LOC110383103`	Vars1	Valine--tRNA ligase	2	2	1	12.3	Ref	ABC_tran_CTD, Anticodon_1, DASH_Spc19, DUF1664, Val_tRNA-synt_C, tRNA-synt_1, tRNA-synt_1_2, tRNA-synt_1e, tRNA-synt_1g
`LOC126055824`	Fur1	Furin-like protease 1, isoforms 1/1-X/2	3	2	1	34.3	Ref	Furin-like_2, GF_recep_IV, P_proprotein, Peptidase_S8, S8_pro-domain
`LOC110377970`	lsm14a	Protein LSM14 homolog A	2	2	1	14.7	Ref	DUF4551, FDF, G_path_suppress, LSM14, SM-ATX, TFIIA
`LOC110375177`	nmd3	60S ribosomal export protein NMD3	2	2	1	14.7	Novel	AAA, AAA_16, AAA_19, AAA_30, ABC_tran, ATP-synt_ab, ATP-synt_ab_N, ATPase, ATPase_2, CttA_N, DUF2075, FUSC-like, NACHT, NB-ARC, NMD3, Nif11, RNA_helicase, RsgA_GTPase
`LOC110381267`	Tctp	Translationally-controlled tumor protein homolog	2	2	1	1,784.9	Novel	DUF4286, TCTP
`LOC110372667`	—	—	2	2	2	286.9	Novel	Adenylsucc_synt, DNA_ligase_C, GramPos_pilinBB, Hexapep, Hexapep_2, S1-like
`LOC110381137`	—	—	2	2	2	22.1	Ref	AmyA-gluTrfs_C, DUF3520, DUF6201
`LOC110380693`	—	—	2	2	2	46.6	Ref	AroM, DUF6759, DUF6791, zf-AD, zf-BED, zf-C2H2, zf-C2H2_11, zf-C2H2_2, zf-C2H2_3rep, zf-C2H2_4, zf-C2H2_6, zf-C2H2_8, zf-C2H2_9, zf-C2H2_jaz, zf-Di19, zf-H2C2_2, zf-met
`LOC110371340`	—	—	2	2	2	39.2	Novel	Casc1_N, Colicin_Pyocin, DUF6308, HHH
`LOC110379263`	—	—	2	2	2	14.7	Ref	COX_ARM, HIND, YjbR, YqzH
`LOC110374458`	—	—	2	2	2	600.7	Ref	DUF2452, DUF4571, LRR_1, LRR_4, LRR_6, LRR_8, LRR_9
`LOC110382218`	—	—	2	2	2	2.5	Novel	ATG17_like, Baculo_PEP_C, JAKMIP_CC3, Mobilization_B, Surfac_D-trimer
`LOC110370034`	—	—	2	2	2	4.9	Ref	AIMP2_LysRS_bd, GST_C, GST_C_2, GST_C_3, Prefoldin, Snapin_Pallidin, Thioredoxin_16, XhlA
`LOC110380173`	—	—	2	2	2	12.3	Novel	ADIP, CCDC92, CENP-H, Cnn_1N, DUF3807, DUF4407, End3, Filament, Mto2_bdg, UPF0242
`LOC110380491`	—	—	2	2	2	0.0	Novel	DZR, FAM194
`LOC110382068`	—	—	2	2	2	0.0	Ref	DUF6353, MADF_DNA_bdg, Myb_DNA-bind_3, Myb_DNA-bind_4, Myb_DNA-bind_5
`LOC110373722`	—	—	2	2	2	24.5	Ref	Amnionless, DUF5305, DUF6458, LapA_dom, Shisa, TMEM171
`LOC110379210`	—	—	2	2	2	2.5	Novel	DUF2576, DUF5082, RRF, Tropomyosin_1
`LOC110378473`	—	—	2	2	2	56.4	Novel	ADIP, Apolipoprotein, Baculo_PEP_C, Claudin_2, DUF2975, DUF4131, DUF898, Prominin, RmuC, TPR_MLP1_2, Tetraspanin
`LOC110371384`	—	—	2	2	2	27.0	Ref	Actin_micro, zf-BED
`LOC110377188`	—	—	2	2	2	12.3	Novel	Arc_MA, SpecificRecomb
`LOC135117166`	—	—	2	2	2	13,553.2	Novel	ATR13, Cuticle_3, HopA1
`LOC110377265`	—	—	2	2	2	61.3	Novel	CiPC, Hormone_3
`LOC110372639`	—	—	2	2	2	12.3	Novel	K1377, Kazal_1, Kazal_2
`LOC110378661`	—	—	6	2	2	539.4	Mixed	DEC-1_N
`LOC110376454`	—	—	2	2	2	12.3	Ref	DUF4497, DUF4776
`LOC110382745`	—	—	3	2	2	49.0	Novel	Collagen
`LOC110382347`	—	—	2	2	2	105.4	Novel	Atrophin-1, PPP4R2, RNA_pol_3_Rpc31
`LOC110383835`	—	—	2	2	2	205.9	Novel	BamHI, DUF3421, DUF5010_C, Methyltransf_FA
`LOC110376464`	—	—	2	2	2	12.3	Ref	CDC45, CENP-B_dimeris, CobT, Conotoxin, DUF4746, FAM176, Nop14, PBP1_TM, QVR, S-antigen, Sporozoite_P67, VID27_N
`LOC110374641`	—	—	3	2	2	36.8	Ref	CCDC53, DUF1330, DUF4860, HisK_sensor, Nup35_RRM, RL, RRM_1, RRM_3
`LOC110383792`	—	—	2	2	2	845.8	Novel	CDC45, CobT, DNA_pol_phi, LRR_1, LRR_3, LRR_4, LRR_5, LRR_6, LRR_8, LRR_9, Nop14, Sigma70_ner
`LOC110383215`	—	—	2	2	2	7.4	Ref	ApoO, DUF3138, GP41, HEF_HK, UPF0231
`LOC110377174`	—	—	2	2	2	166.7	Novel	MPS2, PRCC, Phage_sheath_1C, bZIP_1, bZIP_2
`LOC110378860`	—	—	2	2	2	44.1	Novel	CBM26, DUF6216, Glyco_hydro_127, PHtD_u1
`LOC110375908`	—	—	3	2	2	115.2	Ref	Comm, DUF6114, DUF6724, TMEM52, WBP-1
`LOC110375613`	—	—	2	2	2	12.3	Ref	Acyltransf_C, C1_1, DUF5810, DZR_2, HTH_18, PyrI_C, zf-C2H2, zf-C2H2_2, zf-C2H2_4, zf-C2H2_6, zf-C2H2_jaz, zf-Di19, zf-FCS, zf-H2C2_2, zf-TRAF, zf-met, zinc_ribbon_15
`LOC110383442`	—	—	2	2	2	7.4	Novel	DUF2322, LRR_1, LRR_4, LRR_6, LRR_8, LRR_9, Peptidase_C25_C, RUN, UB2H
`LOC110372666`	—	—	2	2	2	284.4	Novel	DUF4758, EGF, EGF_3, EGF_CA, EGF_MSP1_1, Plasmod_Pvs28, cEGF, hEGF
`LOC110380700`	—	—	2	2	2	29.4	Ref	ADK_lid, AT_hook, DUF629, PyrI_C, Thioredoxin_3, Trm112p, Vps36-NZF-N, Zn-ribbon_8, zf-AD, zf-BED, zf-C2H2, zf-C2H2_12, zf-C2H2_2, zf-C2H2_3rep, zf-C2H2_4, zf-C2H2_6, zf-C2H2_jaz, zf-Di19, zf-H2C2_2, zf-met, zinc_ribbon_15, zinc_ribbon_9
`LOC110373581`	—	—	2	2	2	12.3	Ref	ADIP, APG6_N, Crescentin, DUF4200, DUF4349, DUF724, DivIC, Exo84_C, EzrA, F-box-like_2, Fib_alpha, HAUS6_N, Nuf2_DHR10-like, Prefoldin_2, Prominin, SKA2, SlyX, TMF_DNA_bd, TMF_TATA_bd, UPF0242, Uds1
`LOC110377332`	—	—	3	2	2	68.6	Novel	PSP94, SHIPPO-rpt
`LOC110382815`	—	—	2	2	2	9.8	Ref	Cwf_Cwc_15, DUF3083, DUF5383
`LOC110370009`	—	—	2	2	2	51.5	Ref	DIM, Dickkopf_N, EB, FOG_N, PCSK9_C1, Secapin, zf_CCCH_4
`LOC110370740`	—	—	2	2	2	505.1	Novel	Chorion_2, DsbC, T4BSS_DotI_IcmL
`LOC110373833`	—	—	2	2	2	144.7	Novel	AT_hook, DUF1318, DUF4749, TFIIA
`LOC135116808`	Edg84A	Pupal cuticle protein Edg-84A	2	2	3	73.6	Novel	Chitin_bind_4, DUF1796, Hid1
`novel_gene_NC_087130.1_1765`	—	—	2	2	3	0.0	Novel	DUF22, eIF-3_zeta
`LOC110383216`	—	—	2	2	4	36.8	Ref	CCDC22, DUF4525
`LOC110378016`	—	—	2	2	4	4.9	Novel	DCC1-like, DUF3798, DUF5332, DUF5693, DeoC, DraK_HK_N, Fin, GAD, Glrx-like, Glutaredoxin, HyaE, Ins134_P3_kin_N, Redoxin, TMP-TENI, Thioredoxin, Thioredoxin_2, Thioredoxin_3, Thioredoxin_5, Thioredoxin_6, Thioredoxin_8, Toxin-deaminase, TraF, UPF0180, W2, zf-HC3
`LOC110373584`	—	—	2	2	4	7.4	Ref	DUF1676, Pacs-1, Rota_NSP4
`LOC110374487`	FPR2	FK506-binding protein 2	2	2	4	159.4	Ref	EF-hand_1, EF-hand_10, EF-hand_5, EF-hand_6, EF-hand_7, EF-hand_8, FKBP_C, M20_dimer, RelB_N, SPARC_Ca_bdg
`novel_gene_NC_087139.1_2706`	—	—	2	2	4	0.0	Novel	ApoO, Baculo_PEP_C, DUF3584, DUF4407, Fez1, HrpB7, Mitovir_RNA_pol, NPV_P10, Peptidase_S46, Prominin, Tweety, XhlA
`LOC110370179`	—	—	2	2	4	492.8	Novel	Adeno_shaft, Lamprin, Retinin_C
`LOC110380900`	APY	Apyrase	5	2	4	71.1	Novel	5_nucleotid_C, MFS_1_like, Metallophos, PGA_cap
`LOC110377194`	RGN	Regucalcin	2	2	4	220.7	Novel	DUF5074, DUF839, NHL, Peptidase_S9_N, Reg_prop, SGL
`LOC135117096`	—	—	2	2	4	15,955.9	Novel	ATR13, Cuticle_3, EPTP, HopA1, Retinin_C
`LOC110379502`	—	—	3	2	4	205.9	Novel	DUF6491
`LOC110372973`	Hmcn2	Hemicentin-2	2	2	4	36.8	Novel	Adeno_E3_CR1, C2-set, C2-set_2, Endonuclease_NS, Herpes_gE_N, I-set, Ig_2, Ig_3, Ig_4, Ig_5, Ig_6, Ig_C17orf99, Izumo-Ig, V-set, V-set_CD47, VWA_2, ig, zf-RRN7
`LOC110381131`	—	—	3	2	4	490.3	Novel	DUF3611, TMEM82, TgpA_N

GO Term Enrichment (QC-filtered domain variant genes, FDR < 0.05)

Overrepresented GO terms in genes with genuine domain architecture variants (after artifact removal). These terms indicate which biological processes, molecular functions, and cellular compartments are enriched for alternative splicing that alters protein domain composition.

All Significant GO Terms

Namespace	GO ID	Term	DV Genes	Background	FDR	Genes
BP	`GO:0045214`	sarcomere organization	8/235	21/5001	`0.002405`	CanB2, Csrp1, Fhod3, Obsc, cher, unc-22, wupA, zip
BP	`GO:0034142`	toll-like receptor 4 signaling pathway	3/235	0/5001	`0.003713`	MAP3K7, NAGLU, Pik3ap1
BP	`GO:0048149`	behavioral response to ethanol	5/235	10/5001	`0.008998`	Adcy1, Fas2, Kdm3, Spn27A, cher
BP	`GO:2001234`	negative regulation of apoptotic signaling pathway	3/235	2/5001	`0.016138`	HSPB1, Ing2, Tmbim6
MF	`GO:0051015`	actin filament binding	10/235	48/5001	`0.006190`	Bin1, COTL1, Fhod3, LOC110370712, Limd2, Myo9a, Pls3, cher, pnut, zip
MF	`GO:0005516`	calmodulin binding	7/235	33/5001	`0.030570`	Ace, Adcy1, CanB2, SMTNL1, mknk2, unc-22, zip
MF	`GO:0008234`	cysteine-type peptidase activity	3/235	4/5001	`0.041242`	CtsF, Ctsb, VCATH
MF	`GO:0003677`	DNA binding	21/235	223/5001	`0.041242`	Dsp1, E(z), FKBP46, HMG20A, Hdac4, Ing2, Jph2, KAT6B, LIG3, MAX, Mbd3, Nostrin, YL-1, ZFAND6, ash2, exd, kay, ken, lolal, smarcb1a, tio
CC	`GO:0030018`	Z disc	10/235	32/5001	`0.001973`	Bin1, Csrp1, FHL2, Fhod3, HSPB1, Hdac4, Jph2, PDLIM3, cher, zip
CC	`GO:0098595`	perivitelline space	3/235	0/5001	`0.003713`	CtsF, Sdc, Spn27A
CC	`GO:0031430`	M band	5/235	7/5001	`0.003713`	Obsc, Prm, SMTNL1, tns-1, unc-22
CC	`GO:0031982`	vesicle	5/235	11/5001	`0.011037`	Ace, Bin1, GAK, Vapa, spin

DV Enrichment by Expression Level (CPM from upstream transcriptomics)

Baseline DV Rate

4.1%

292 / 7,082 genes

Peak DV Rate

9.8%

Very high (>=200) bin

Peak Enrichment

2.4×

vs baseline

Chi-square trend

p < 0.001

Expression Bin	Total Genes	DV Genes	DV %	Fold vs Baseline
Silent (<1) CPM	380	6	1.6%	0.4×
Low (1-10) CPM	2,649	57	2.2%	0.5×
Moderate (10-50) CPM	2,682	107	4.0%	1.0×
High (50-200) CPM	933	79	8.5%	2.1×
Very high (>=200) CPM	438	43	9.8%	2.4×

Bar height shows the percentage of genes that are domain-variant within each expression bin. Dashed line = overall DV rate (4.1%). If DV enrichment increases monotonically with expression, ascertainment bias (more reads = more isoform discovery) is the dominant driver. Enrichment above baseline at specific expression tiers may indicate biological enrichment beyond the detection effect. CPM from 407,875 mRNA reads (91.1% rRNA excluded).

ORF Type Distribution

NMD Prediction by ORF Type

NMD Candidates by Evidence Tier

NMD Expression Validation (CPM from upstream transcriptomics)

NMD Expression Rate

99.8%

449 / 450

Non-NMD Expression Rate

97.8%

7,954 / 8,136

Fold Difference

1.0×

non-NMD / NMD

Tier 1 NMD Expression

100.0%

274 / 274

NMD Candidates (n=450)

Non-NMD (n=8,136)

Box plots show median (line), IQR (box), and 1.5×IQR whiskers. Individual transcript CPM values are overlaid as jittered points. NMD candidates are expressed at 99.8% (median 19.6 CPM) vs 97.8% (median 14.7 CPM) for non-NMD — no evidence of NMD-mediated degradation.

Output Files

blastp.with_title.tsv HPC 1 MB gene_functional_summary.tsv HPC 242.4 KB isoform_annotations.tsv HPC 1.6 MB job.yml HPC 608 B pfam.domtblout HPC 18.6 MB results_summary.json HPC 2.6 KB

Provenance

Execution	Expression quantification summary
Completed	2026-02-28T03:20:58+00:00

RO-Crate 1.1 Workflow RO-Crate 1.0 FAIR

This analysis is packaged as a Research Object Crate with machine-readable provenance and FAIR metadata.

RO-Crate Metadata (JSON-LD)

Show/hide raw JSON-LD

{
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        "https://w3id.org/ro/crate/1.1/context",
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                    "@id": "https://w3id.org/ro/crate/1.1"
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                {
                    "@id": "https://w3id.org/workflowhub/workflow-ro-crate/1.0"
                }
            ]
        },
        {
            "@id": "./",
            "@type": "Dataset",
            "name": "ONT Isoform Functional Annotation \u2014 Moth Head+Body \u2014 Run #39",
            "description": "Pfam domain search, SwissProt homology, NMD prediction, and functional diversity classification for ONT transcript isoforms.",
            "datePublished": "2026-02-28",
            "license": {
                "@id": "https://creativecommons.org/licenses/by/4.0/"
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                    "@id": "gene_functional_summary.tsv"
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                    "@id": "blastp.with_title.tsv"
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        {
            "@id": "isoform_annotations.tsv",
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        {
            "@id": "pfam.domtblout",
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            "name": "pfam.domtblout",
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        {
            "@id": "#execution",
            "@type": "CreateAction",
            "name": "ONT Isoform Functional Annotation \u2014 Moth Head+Body execution",
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                "@id": "ont_isoform_annotation.cwl"
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                {
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                {
                    "@id": "pfam.domtblout"
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            ]
        },
        {
            "@id": "results_summary.json",
            "@type": "File",
            "name": "results_summary.json",
            "description": "Derived summary statistics from pipeline outputs (CPM >= 1, uniquely mapped reads)",
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        {
            "@id": "summary_extractor.py",
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            "name": "Summary extraction script",
            "description": "Python script that computed results_summary.json from pipeline outputs",
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                "@id": "#python3"
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        },
        {
            "@id": "#python3",
            "@type": "ComputerLanguage",
            "name": "Python",
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            "version": "3"
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        {
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            "@type": "CreateAction",
            "name": "Expression quantification summary",
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            "endTime": "2026-02-28T03:20:58+00:00",
            "object": [
                {
                    "@id": "OUT.read_assignments.tsv.gz"
                },
                {
                    "@id": "OUT.gene_counts.tsv"
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                {
                    "@id": "OUT.transcript_counts.tsv"
                },
                {
                    "@id": "OUT.extended_annotation.gtf"
                },
                {
                    "@id": "OUT.transcript_models.gtf"
                }
            ],
            "result": [
                {
                    "@id": "results_summary.json"
                }
            ]
        },
        {
            "@id": "#protocol-19",
            "@type": "LabProtocol",
            "name": "Direct cDNA sequencing V14 with SQK-LSK114",
            "description": "This protocol describes how to carry out sequencing of cDNA using a reverse transcription and strand-switching method and the Ligation Sequencing Kit V14 (SQK-LSK114) This protocol is recommended for users who:\r\n\r\n- Are interested in exploring novel RNA biology.\r\n- Are looking for splice variant and fusion transcript analysis.\r\n- Do not wish to use PCR.\r\n- Wish to preserve quantitative information in samples likely to be impacted by PCR bias.\r\n- Would like full-length cDNA strands.\r\n- Want to achieve median raw read accuracy of Q20+ (99%) and above.\r\n- Want to optimise their sequencing experiment for output.\r\n",
            "version": "1",
            "category": "sample_prep",
            "step": [
                {
                    "@type": "HowToStep",
                    "position": 1,
                    "text": "Thaw the following reagents and spin down briefly using a microfuge, before mixing as indicated in the table below, and place on ice.\r\n\r\nReagent \t                                            1. Thaw at room temperature \t2. Briefly spin down \t3. Mix well by pipetting\r\nUser-supplied VN Primer diluted to 2 \u00b5M \t                          \u2713 \t                           \u2713 \t                     \u2713\r\nUser-supplied Strand-Switching Primer diluted to 10 \u00b5M \t                  \u2713 \t                           \u2713 \t                     \u2713\r\n10 mM dNTP solution \t                                                  \u2713 \t                           \u2713 \t                     \u2713\r\nRNaseOUT \t                                                      Not frozen \t                   \u2713 \t                     \u2713\r\nMaxima H Minus Reverse Transcriptase \t                              Not frozen \t                   \u2713 \t                     \u2713\r\nMaxima H Minus 5x RT Buffer \t                                          \u2713 \t                           \u2713 \t              Mix by vortexing"
                },
                {
                    "@type": "HowToStep",
                    "position": 2,
                    "text": "Prepare the RNA in nuclease-free water\r\n\r\n- Transfer 100 ng Poly(A)+ RNA or 1 \u03bcg of total RNA into a 0.2 ml PCR tube\r\n- Adjust the volume to up to 7.5 \u03bcl with nuclease-free water\r\n- Mix by flicking the tube to avoid unwanted shearing\r\n- Spin down briefly in a microfuge"
                },
                {
                    "@type": "HowToStep",
                    "position": 3,
                    "text": "Prepare the following reaction in the 0.2 ml PCR tube containing the prepared RNA input:\r\n\r\nReagent \t                                                            Volume\r\nRNA input (100 ng Poly(A)+ RNA or 1 \u03bcg of total RNA) from step above \t    7.5 \u03bcl\r\nVN Primer diluted to 2 \u03bcM \t                                            2.5 \u03bcl\r\n10 mM dNTPs \t                                                            1 \u03bcl\r\nTotal volume \t                                                            11 \u03bcl         "
                },
                {
                    "@type": "HowToStep",
                    "position": 4,
                    "text": "Mix gently by flicking the tube, and spin down."
                },
                {
                    "@type": "HowToStep",
                    "position": 5,
                    "text": "Incubate at 65\u00b0C for 5 minutes and then snap cool on a pre-chilled freezer block for 1 minute."
                },
                {
                    "@type": "HowToStep",
                    "position": 6,
                    "text": "In a separate tube, mix together the following:\r\n\r\nReagent \t                               Volume\r\n5x RT Buffer \t                                4 \u03bcl\r\nRNaseOUT \t                                1 \u03bcl\r\nNuclease-free water \t                        1 \u03bcl\r\nStrand-Switching Primer diluted to 10 \u00b5M \t2 \u03bcl\r\nTotal \t                                        8 \u03bcl     "
                },
                {
                    "@type": "HowToStep",
                    "position": 7,
                    "text": "Mix gently by flicking the tube, and spin down."
                },
                {
                    "@type": "HowToStep",
                    "position": 8,
                    "text": "Add the 8 \u03bcl of strand-switching reagents (prepared in steps 6-7) to the 11 \u03bcl of snap-cooled mRNA (from steps 2-5). Mix by flicking the tube and spin down."
                },
                {
                    "@type": "HowToStep",
                    "position": 9,
                    "text": "Incubate at 42\u00b0C for 2 minutes in the thermal cycler."
                },
                {
                    "@type": "HowToStep",
                    "position": 10,
                    "text": "Add 1 \u00b5l of Maxima H Minus Reverse Transcriptase. The total volume is now 20 \u00b5l."
                },
                {
                    "@type": "HowToStep",
                    "position": 11,
                    "text": "Mix gently by flicking the tube, and spin down."
                },
                {
                    "@type": "HowToStep",
                    "position": 12,
                    "text": "Incubate using the following protocol using a thermal cycler:\r\n\r\nCycle step \t                              Temperature \tTime \t    No. of cycles\r\nReverse transcription and strand-switching    42\u00b0C \t        90 mins \t  1\r\nHeat inactivation \t                      85\u00b0C \t        5 mins \t          1\r\nHold \t                                      4\u00b0C \t        \u221e \t                    "
                },
                {
                    "@type": "HowToStep",
                    "position": 13,
                    "text": "Thaw the following reagents and spin down briefly using a microfuge, before mixing as indicated in the table below, and place on ice.\r\n\r\nReagent \t                             1. Thaw at room temperature \t2. Briefly spin down \t3. Mix well by pipetting\r\nUser-supplied PR2 Primer diluted to 10 \u00b5M \t           \u2713 \t                           \u2713 \t                    \u2713\r\nRNase Cocktail Enzyme Mix \t                       Not frozen \t                   \u2713 \t                    \u2713\r\nLongAmp Taq 2X Master Mix \t                           \u2713 \t                           \u2713 \t                    \u2713   "
                },
                {
                    "@type": "HowToStep",
                    "position": 14,
                    "text": "Thaw the AMPure XP Beads (AXP) at room temperature and mix by vortexing. Keep the beads at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 15,
                    "text": "Add 1 \u00b5l RNase Cocktail Enzyme Mix (ThermoFisher, cat # AM2286) to the reverse transcription reaction. "
                },
                {
                    "@type": "HowToStep",
                    "position": 16,
                    "text": "Incubate the reaction for 10 minutes at 37\u00b0 C in a thermal cycler."
                },
                {
                    "@type": "HowToStep",
                    "position": 17,
                    "text": "Resuspend the AMPure XP beads (AXP) by vortexing."
                },
                {
                    "@type": "HowToStep",
                    "position": 18,
                    "text": "Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 19,
                    "text": "Add 17 \u00b5l of resuspended AMPure XP beads (AXP) to the reaction and mix by flicking the tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 20,
                    "text": "Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 21,
                    "text": "Prepare 500 \u03bcl of fresh 80% ethanol in nuclease-free water."
                },
                {
                    "@type": "HowToStep",
                    "position": 22,
                    "text": "Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernatant."
                },
                {
                    "@type": "HowToStep",
                    "position": 23,
                    "text": "Keep the tubes on the magnet and wash the beads with 200 \u00b5l of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard. If the pellet was disturbed, wait for beads to pellet again before removing the ethanol."
                },
                {
                    "@type": "HowToStep",
                    "position": 24,
                    "text": "Repeat the previous step."
                },
                {
                    "@type": "HowToStep",
                    "position": 25,
                    "text": "Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking."
                },
                {
                    "@type": "HowToStep",
                    "position": 26,
                    "text": "Remove the tube from the magnetic rack and resuspend pellet in 20 \u00b5l nuclease-free water."
                },
                {
                    "@type": "HowToStep",
                    "position": 27,
                    "text": "Incubate on a Hula mixer (rotator mixer) for 10 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 28,
                    "text": "Briefly spin down the tube and pellet the beads on the magnet until the eluate is clear and colourless, for at least 1 minute."
                },
                {
                    "@type": "HowToStep",
                    "position": 29,
                    "text": "Remove and retain 20 \u00b5l of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 30,
                    "text": "Prepare the following reaction in a 0.2 ml thin-walled PCR tube:\r\n\r\nReagent \t                           Volume\r\n2x LongAmp Taq Master Mix \t           25 \u03bcl\r\nPR2 Primer diluted to 10 \u03bcM \t           2 \u03bcl\r\nReverse-transcribed sample from above \t   20 \u03bcl\r\nNuclease-free water \t                   3 \u03bcl\r\nTotal \t                                   50 \u03bcl           "
                },
                {
                    "@type": "HowToStep",
                    "position": 31,
                    "text": "Incubate using the following protocol:\r\n\r\nCycle step \tTemperature \tTime \t    No. of cycles\r\nDenaturation \t94 \u00b0C \t        1 mins \t    1\r\nAnnealing \t50 \u00b0C \t        1 mins \t    1\r\nExtension \t65 \u00b0C \t        15 mins     1\r\nHold \t        4 \u00b0C \t        \u221e \t        "
                },
                {
                    "@type": "HowToStep",
                    "position": 32,
                    "text": "Resuspend the AMPure XP beads (AXP) by vortexing.  "
                },
                {
                    "@type": "HowToStep",
                    "position": 33,
                    "text": "Transfer the sample to a clean 1.5 ml Eppendorf DNA LoBind tube. "
                },
                {
                    "@type": "HowToStep",
                    "position": 34,
                    "text": "Add 40 \u00b5l of resuspended AMPure XP beads (AXP) to the reaction and mix by flicking the tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 35,
                    "text": "Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 36,
                    "text": "Prepare 500 \u03bcl of fresh 80% ethanol in nuclease-free water."
                },
                {
                    "@type": "HowToStep",
                    "position": 37,
                    "text": "Spin down the sample and pellet on a magnet. Keep the tube on the magnet, and pipette off the supernatant."
                },
                {
                    "@type": "HowToStep",
                    "position": 38,
                    "text": "Keep the tubes on the magnet and wash the beads with 200 \u00b5l of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard.\r\n\r\nIf the pellet was disturbed, wait for beads to pellet again before removing the ethanol.  "
                },
                {
                    "@type": "HowToStep",
                    "position": 39,
                    "text": "Repeat the previous step. "
                },
                {
                    "@type": "HowToStep",
                    "position": 40,
                    "text": "Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking."
                },
                {
                    "@type": "HowToStep",
                    "position": 41,
                    "text": "Remove the tube from the magnetic rack and resuspend pellet in 21 \u00b5l nuclease-free water."
                },
                {
                    "@type": "HowToStep",
                    "position": 42,
                    "text": "Incubate on a Hula mixer (rotator mixer) for 10 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 43,
                    "text": "Briefly spin down the tube and pellet the beads on the magnet until the eluate is clear and colourless, for at least 1 minute."
                },
                {
                    "@type": "HowToStep",
                    "position": 44,
                    "text": "Remove and retain 21 \u00b5l of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 45,
                    "text": "Analyse 1 \u00b5l of the strand-switched DNA for size, quantity and quality using an Agilent Bioanalyzer and Qubit fluorometer (or equivalent)."
                },
                {
                    "@type": "HowToStep",
                    "position": 46,
                    "text": "Prepare the NEBNext Ultra II End Repair / dA-tailing Module reagents in accordance with manufacturer's instructions, and place on ice:\r\n\r\nFor optimal perfomance, NEB recommend the following:\r\n\r\n1. Thaw all reagents on ice.\r\n2. Flick and/or invert the reagent tubes to ensure they are well mixed.\r\n     Note: Do not vortex the Ultra II End Prep Enzyme Mix.\r\n3. Always spin down tubes before opening for the first time each day.\r\n4. The Ultra II End Prep Buffer may have a little precipitate. Allow the mixture to come to room temperature and pipette the buffer up and down several times to break up the precipitate, followed by vortexing the tube for 30 seconds to solubilise any precipitate."
                },
                {
                    "@type": "HowToStep",
                    "position": 47,
                    "text": "Combine the following reagents in a 0.2 ml PCR tube:\r\n\r\nReagent \t                       Volume\r\ncDNA sample \t                       20 \u00b5l\r\nNuclease-free water \t               30 \u00b5l\r\nUltra II End-prep reaction buffer      7 \u00b5l\r\nUltra II End-prep enzyme mix \t       3 \u00b5l\r\nTotal \t                               60 \u00b5l        "
                },
                {
                    "@type": "HowToStep",
                    "position": 48,
                    "text": "Thoroughly mix the reaction by gently pipetting and briefly spinning down."
                },
                {
                    "@type": "HowToStep",
                    "position": 49,
                    "text": "Using a thermal cycler, incubate at 20\u00b0C for 5 minutes and 65\u00b0C for 5 minutes."
                },
                {
                    "@type": "HowToStep",
                    "position": 50,
                    "text": "Resuspend the AMPure XP Beads (AXP) by vortexing."
                },
                {
                    "@type": "HowToStep",
                    "position": 51,
                    "text": "Transfer the DNA sample to a clean 1.5 ml Eppendorf DNA LoBind tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 52,
                    "text": "Add 60 \u00b5l of resuspended the AMPure XP Beads (AXP) to the end-prep reaction and mix by flicking the tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 53,
                    "text": "Incubate on a Hula mixer (rotator mixer) for 5 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 54,
                    "text": "Prepare 500 \u03bcl of fresh 80% ethanol in nuclease-free water."
                },
                {
                    "@type": "HowToStep",
                    "position": 55,
                    "text": "Spin down the sample and pellet on a magnet until supernatant is clear and colourless. Keep the tube on the magnet, and pipette off the supernatant. "
                },
                {
                    "@type": "HowToStep",
                    "position": 56,
                    "text": "Keep the tube on the magnet and wash the beads with 200 \u00b5l of freshly prepared 80% ethanol without disturbing the pellet. Remove the ethanol using a pipette and discard."
                },
                {
                    "@type": "HowToStep",
                    "position": 57,
                    "text": "Repeat the previous step."
                },
                {
                    "@type": "HowToStep",
                    "position": 58,
                    "text": "Spin down and place the tube back on the magnet. Pipette off any residual ethanol. Allow to dry for ~30 seconds, but do not dry the pellet to the point of cracking."
                },
                {
                    "@type": "HowToStep",
                    "position": 59,
                    "text": "Remove the tube from the magnetic rack and resuspend pellet in 61 \u00b5l nuclease-free water. Incubate for 2 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 60,
                    "text": "Pellet the beads on a magnet until the eluate is clear and colourless, for at least 1 minute."
                },
                {
                    "@type": "HowToStep",
                    "position": 61,
                    "text": "Remove and retain 61 \u00b5l of eluate into a clean 1.5 ml Eppendorf DNA LoBind tube."
                },
                {
                    "@type": "HowToStep",
                    "position": 62,
                    "text": "Quantify 1 \u00b5l of eluted sample using a Qubit fluorometer.\r\n\r\nTake forward the 60 \u00b5l of repaired and end-prepped cDNA into the adapter ligation step. However, at this point it is also possible to store the sample at 4\u00b0C overnight.                  "
                },
                {
                    "@type": "HowToStep",
                    "position": 63,
                    "text": "Spin down the Ligation Adapter (LA) and Quick T4 Ligase, and place on ice."
                },
                {
                    "@type": "HowToStep",
                    "position": 64,
                    "text": "Thaw Ligation Buffer (LNB) at room temperature, spin down and mix by pipetting. Due to viscosity, vortexing this buffer is ineffective. Place on ice immediately after thawing and mixing. "
                },
                {
                    "@type": "HowToStep",
                    "position": 65,
                    "text": "Thaw the Elution Buffer (EB) at room temperature and mix by vortexing. Then spin down and place on ice."
                },
                {
                    "@type": "HowToStep",
                    "position": 66,
                    "text": "Thaw the Short Fragment Buffer (SFB) at room temperature and mix by vortexing. Then spin down and place on ice."
                },
                {
                    "@type": "HowToStep",
                    "position": 67,
                    "text": "In a 1.5 ml Eppendorf DNA LoBind tube, mix in the following order:\r\n\r\nBetween each addition, pipette mix 10-20 times.\r\n\r\nReagent \t                        Volume\r\ncDNA sample from the previous step \t60 \u00b5l\r\nLigation Buffer (LNB) \t                25 \u00b5l\r\nNEBNext Quick T4 DNA Ligase \t        10 \u00b5l\r\nLigation Adapter (LA) \t                5 \u00b5l\r\nTotal \t                                100 \u00b5l      "
                },
                {
                    "@type": "HowToStep",
                    "position": 68,
                    "text": "Thoroughly mix the reaction by gently pipetting and briefly spinning down."
                },
                {
                    "@type": "HowToStep",
                    "position": 69,
                    "text": "Incubate the reaction for 10 minutes at room temperature."
                },
                {
                    "@type": "HowToStep",
                    "position": 70,
                    "text": "Resuspend the AMPure XP Beads (AXP) by vortexing."
                },
                {
                    "@type": "HowToStep",
                    "position": 71,
                    "text": ""
                }
            ]
        },
        {
            "@id": "#protocol-35",
            "@type": "LabProtocol",
            "name": "Sequencing Submission",
            "description": "Submit samples for sequencing at the genomics facility. Links kevlab samples to QC app runs after sequencing is complete.",
            "version": "1.0",
            "category": "sequencing"
        },
        {
            "@id": "#sample-352",
            "@type": "BioSample",
            "name": "body_library",
            "materialType": "sample",
            "isBasedOn": [
                {
                    "@id": "#sample-274"
                },
                {
                    "@id": "#sample-317"
                },
                {
                    "@id": "#sample-338"
                }
            ]
        },
        {
            "@id": "#sample-353",
            "@type": "BioSample",
            "name": "head_library",
            "materialType": "sample",
            "isBasedOn": [
                {
                    "@id": "#sample-276"
                },
                {
                    "@id": "#sample-312"
                },
                {
                    "@id": "#sample-334"
                }
            ]
        },
        {
            "@id": "#instrument-gridion",
            "@type": "Thing",
            "name": "Oxford Nanopore GridION Mk1",
            "additionalType": "http://purl.obolibrary.org/obo/OBI_0002751"
        },
        {
            "@id": "#process-81",
            "@type": "CreateAction",
            "name": "Direct cDNA library prep of Helicoverpa head and body samples for nanopore sequencing",
            "instrument": {
                "@id": "#protocol-19"
            },
            "startTime": "2024-06-27",
            "category": "sample_prep",
            "description": "Three body samples were pooled and three head (tail?) samples were pooled prior to library prep using the LSK114 kit.",
            "result": [
                {
                    "@id": "#sample-352"
                },
                {
                    "@id": "#sample-353"
                }
            ]
        },
        {
            "@id": "#process-82",
            "@type": "CreateAction",
            "name": "Nanopore sequencing of Helicoverpa head and body cDNA libraries",
            "instrument": [
                {
                    "@id": "#protocol-35"
                },
                {
                    "@id": "#instrument-gridion"
                }
            ],
            "startTime": "2024-06-28",
            "category": "sequencing",
            "object": [
                {
                    "@id": "#sample-352"
                },
                {
                    "@id": "#sample-353"
                }
            ]
        }
    ]
}