SEC31B

gene
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Also known as SEC31B-1DKFZP434M183

Summary

SEC31B (SEC31 homolog B, COPII component, HGNC:23197) is a protein-coding gene on chromosome 10q24.31, encoding Protein transport protein Sec31B (Q9NQW1). As a component of the coat protein complex II (COPII), may function in vesicle budding and cargo export from the endoplasmic reticulum.

This gene encodes a protein of unknown function. The protein has moderate similarity to rat VAP1 protein which is an endosomal membrane-associated protein, containing a putative Ca2+/calmodulin-dependent kinase II phosphorylation site.

Source: NCBI Gene 25956 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 214 total
  • MANE Select transcript: NM_015490

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23197
Approved symbolSEC31B
NameSEC31 homolog B, COPII component
Location10q24.31
Locus typegene with protein product
StatusApproved
AliasesSEC31B-1, DKFZP434M183
Ensembl geneENSG00000075826
Ensembl biotypeprotein_coding
OMIM610258
Entrez25956

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 9 protein_coding, 5 nonsense_mediated_decay, 5 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000370345, ENST00000462434, ENST00000469546, ENST00000469824, ENST00000479697, ENST00000480905, ENST00000482456, ENST00000484848, ENST00000485800, ENST00000490567, ENST00000492667, ENST00000494350, ENST00000498298, ENST00000883193, ENST00000883194, ENST00000955332, ENST00000955333, ENST00000955334, ENST00000955335, ENST00000955336, ENST00000955337

RefSeq mRNA: 1 — MANE Select: NM_015490 NM_015490

CCDS: CCDS7495

Canonical transcript exons

ENST00000370345 — 26 exons

ExonStartEnd
ENSE00001818448100519782100519861
ENSE00001822116100486647100487795
ENSE00003461888100516096100516219
ENSE00003468404100498705100498804
ENSE00003473355100497135100497280
ENSE00003475356100497667100497793
ENSE00003484453100499160100499258
ENSE00003486339100490008100490322
ENSE00003495877100490706100490883
ENSE00003497222100509007100509102
ENSE00003503770100509316100509511
ENSE00003515223100488027100488098
ENSE00003530384100495385100495546
ENSE00003539239100489703100489761
ENSE00003554884100498029100498207
ENSE00003565353100507908100508051
ENSE00003582771100506040100506201
ENSE00003594424100488858100488974
ENSE00003618690100489252100489398
ENSE00003625559100499524100499598
ENSE00003648471100507425100507567
ENSE00003658946100506321100506420
ENSE00003664857100502254100502484
ENSE00003671710100505361100505495
ENSE00003680641100496258100496431
ENSE00003680947100516874100516997

Expression profiles

Bgee: expression breadth ubiquitous, 191 present calls, max score 95.26.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4477 / max 23.9330, expressed in 177 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1110610.3011138
1110550.058620
1110570.057621
1110580.017214
1110560.01317

Top tissues by expression

275 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489095.26gold quality
cerebellar hemisphereUBERON:000224594.54gold quality
cerebellar cortexUBERON:000212994.34gold quality
cerebellumUBERON:000203791.52gold quality
granulocyteCL:000009491.25gold quality
apex of heartUBERON:000209891.24gold quality
adenohypophysisUBERON:000219690.58gold quality
right frontal lobeUBERON:000281090.27gold quality
mucosa of stomachUBERON:000119990.14gold quality
pituitary glandUBERON:000000789.53gold quality
small intestine Peyer’s patchUBERON:000345488.37gold quality
transverse colonUBERON:000115788.16gold quality
muscle layer of sigmoid colonUBERON:003580587.99gold quality
esophagogastric junction muscularis propriaUBERON:003584187.81gold quality
mucosa of transverse colonUBERON:000499187.68gold quality
left testisUBERON:000453387.67gold quality
lower esophagus muscularis layerUBERON:003583387.61gold quality
lower esophagusUBERON:001347387.59gold quality
tibial nerveUBERON:000132387.57gold quality
right testisUBERON:000453487.55gold quality
spleenUBERON:000210687.22gold quality
right ovaryUBERON:000211886.75gold quality
type B pancreatic cellCL:000016986.51gold quality
olfactory bulbUBERON:000226486.08gold quality
left ovaryUBERON:000211986.01gold quality
sural nerveUBERON:001548885.99gold quality
body of uterusUBERON:000985385.96gold quality
hindlimb stylopod muscleUBERON:000425285.84gold quality
right lobe of liverUBERON:000111485.74gold quality
right uterine tubeUBERON:000130285.62gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no5.14
E-GEOD-83139no3.06

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

76 targeting SEC31B, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3064-3P100.0070.091254
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-450099.9972.722367
HSA-MIR-607799.9968.042299
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-548N99.9871.944170
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-767-5P99.9570.85993
HSA-MIR-449399.9066.48977
HSA-MIR-612499.8769.783551
HSA-MIR-137-3P99.8774.742401
HSA-MIR-3180-5P99.8269.122422
HSA-MIR-3121-3P99.8271.963630

Literature-anchored findings (GeneRIF, showing 1)

  • The SEC31B protein is an orthologue of Saccharomyces cerevisiae Sec31p, a component of the COPII vesicle coat that mediates vesicular traffic from the endoplasmic reticulum. (PMID:16495487)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriosec31bENSDARG00000002916
mus_musculusSec31bENSMUSG00000051984
rattus_norvegicusSec31bENSRNOG00000025781
drosophila_melanogasterSec31FBGN0033339
caenorhabditis_elegansWBGENE00011338

Paralogs (1): SEC31A (ENSG00000138674)

Protein

Protein identifiers

Protein transport protein Sec31BQ9NQW1 (reviewed: Q9NQW1)

Alternative names: SEC31-like protein 2, SEC31-related protein B, SEC31B-1

All UniProt accessions (3): Q9NQW1, E9PKR7, F6TTE0

UniProt curated annotations — full annotation on UniProt →

Function. As a component of the coat protein complex II (COPII), may function in vesicle budding and cargo export from the endoplasmic reticulum.

Subunit / interactions. COPII is composed of at least 5 proteins: the SEC23/24 complex, the SEC13/31 complex and SAR1. SEC13 and SEC31 make a 2:2 tetramer that forms the edge element of the COPII outer coat. The tetramer self-assembles in multiple copies to form the complete polyhedral cage. Interacts (via WD 8) with SEC13. Interacts with SEC31A.

Subcellular location. Cytoplasm. Cytoplasmic vesicle. COPII-coated vesicle membrane. Endoplasmic reticulum membrane.

Tissue specificity. Ubiquitously expressed at low levels with specific expression in thymus and testis. Expressed in testis by Sertoli cells, Leydig cells and spermatogonia and in cerebellum more prominently by Purkinje and granular cells (at protein level).

Post-translational modifications. Monoubiquitinated by the BCR(KLHL12) E3 ubiquitin ligase complex, leading to regulate the size of COPII coats.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the WD repeat SEC31 family.

Isoforms (5)

UniProt IDNamesCanonical?
Q9NQW1-11, SEC31B-Fyes
Q9NQW1-22
Q9NQW1-33
Q9NQW1-44, SEC31B-t
Q9NQW1-55

RefSeq proteins (1): NP_056305* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR040251SEC31-likeFamily

Pfam: PF00400

UniProt features (28 total): sequence variant 9, repeat 8, splice variant 7, chain 1, compositionally biased region 1, sequence conflict 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NQW1-F170.080.22

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-204005COPII-mediated vesicle transport
R-HSA-199977ER to Golgi Anterograde Transport
R-HSA-199991Membrane Trafficking
R-HSA-392499Metabolism of proteins
R-HSA-446203Asparagine N-linked glycosylation
R-HSA-5653656Vesicle-mediated transport
R-HSA-597592Post-translational protein modification
R-HSA-948021Transport to the Golgi and subsequent modification

MSigDB gene sets: 152 (showing top): GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_VESICLE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_TRANSPORT, CCANNAGRKGGC_UNKNOWN, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, MYOD_01, GOBP_REGULATION_OF_CELLULAR_LOCALIZATION, GOCC_COATED_VESICLE, GOBP_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT

GO Biological Process (5): endoplasmic reticulum organization (GO:0007029), protein transport (GO:0015031), COPII-coated vesicle cargo loading (GO:0090110), endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), vesicle-mediated transport (GO:0016192)

GO Molecular Function (2): structural molecule activity (GO:0005198), protein binding (GO:0005515)

GO Cellular Component (9): endoplasmic reticulum membrane (GO:0005789), vesicle coat (GO:0030120), COPII vesicle coat (GO:0030127), endoplasmic reticulum exit site (GO:0070971), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), ER to Golgi transport vesicle membrane (GO:0012507), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-7 pathways:

CategoryPathways
ER to Golgi Anterograde Transport1
Membrane Trafficking1
Transport to the Golgi and subsequent modification1
Vesicle-mediated transport1
Post-translational protein modification1
Metabolism of proteins1
Asparagine N-linked glycosylation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
cellular anatomical structure3
transport2
intracellular transport2
coated vesicle membrane2
organelle organization1
endomembrane system organization1
intracellular protein localization1
establishment of protein localization1
vesicle cargo loading1
COPII-coated vesicle budding1
intercellular transport1
Golgi vesicle transport1
cellular process1
molecular_function1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane coat1
ER to Golgi transport vesicle membrane1
vesicle coat1
endoplasmic reticulum1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1
COPII-coated ER to Golgi transport vesicle1
transport vesicle membrane1
intracellular vesicle1

Protein interactions and networks

STRING

948 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
SEC31BSEC13P55735918
SEC31BSEC24BO95487743
SEC31BSEC24DO94855673
SEC31BSEC23BQ15437607
SEC31BSEC24AO95486585
SEC31BSEC16AO15027559
SEC31BSEC24CP53992523
SEC31BSAR1AQ9NR31494
SEC31BPREBQ9HCU5477
SEC31BSAR1BQ9Y6B6471
SEC31BSEC31AO94979455
SEC31BCOPB1P53618414
SEC31BCOPB2P35606414
SEC31BUSO1O60763401
SEC31BSTPG4Q8N801400

IntAct

11 interactions, top by confidence:

ABTypeScore
YBX1HNRNPRpsi-mi:“MI:0915”(physical association)0.770
SF3A2SEC31Bpsi-mi:“MI:0915”(physical association)0.400
DND1RPSA2psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
MYCPDZD2psi-mi:“MI:0914”(association)0.350
KIF2Apsi-mi:“MI:0914”(association)0.350
SEC31BTCP1psi-mi:“MI:0914”(association)0.350
SNW1psi-mi:“MI:0914”(association)0.350
RUNX1SEC31Bpsi-mi:“MI:0915”(physical association)0.000

BioGRID (37): SEC31B (Affinity Capture-MS), CCT7 (Affinity Capture-MS), CCT3 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), CCT6A (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT4 (Affinity Capture-MS), TCP1 (Affinity Capture-MS), SEC31B (Co-fractionation), SEC31B (Affinity Capture-MS), CCT7 (Affinity Capture-MS), CCT6B (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), TCP1 (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8QPS5, A0A571BF63, A0A8M9QN10, A1A535, A1A5P5, A2BID5, A4D1P6, A9JRI0, B2RYI0, D3YVL2, F1QNV4, P97874, Q05B30, Q0WV90, Q15291, Q1LUT1, Q1LXR6, Q27GK7, Q2HJE1, Q32PH0, Q3TZ89, Q3U0M1, Q3UMY5, Q4V9P9, Q5NBT9, Q5PQS3, Q5R5R2, Q5R6T6, Q5ZLL7, Q6AI08, Q6DTM3, Q6PA97, Q6TEN6, Q7TMQ7, Q7Z3E5, Q7ZVL2, Q84JM4, Q8BL99, Q8CFJ9, Q8N957

Diamond homologs: A1C6X5, A1DHK2, A2QBZ0, F4ICD9, O94979, Q0CYG9, Q0ULF5, Q2GVT8, Q2UF60, Q3TZ89, Q3UPL0, Q4P2B6, Q4X0M4, Q55CT5, Q5AZM3, Q5F3X8, Q5R4F4, Q5S580, Q7SYD5, Q873A1, Q8L611, Q9NQW1, Q9Z2Q1, A3GFK8, A4RD35, A5DB75, A5DTX3, O13637, Q1DX43, Q5AAU3, Q5RHI5, Q6BRR2, Q6C414, Q9R1K5, Q9SU78, Q9UM11, A6ZN74, B3LIS9, C7GV13, C8ZHH9

SIGNOR signaling

4 interactions.

AEffectBMechanism
SEC31B“form complex”“COPII vesicle”binding
KLHL12“up-regulates activity”SEC31Bbinding
“Cullin 3-RBX1-Skp1”“up-regulates activity”SEC31Bmonoubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

214 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance175
Likely benign17
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4063 predictions. Top by Δscore:

VariantEffectΔscore
10:100488025:A:ACdonor_gain1.0000
10:100488025:ACTGT:Adonor_gain1.0000
10:100488026:C:CCdonor_gain1.0000
10:100488026:CTGT:Cdonor_gain1.0000
10:100488026:CTGTC:Cdonor_gain1.0000
10:100488099:C:CCacceptor_gain1.0000
10:100488854:TTA:Tdonor_loss1.0000
10:100488855:TA:Tdonor_loss1.0000
10:100488856:A:ACdonor_gain1.0000
10:100488856:AC:Adonor_loss1.0000
10:100488857:C:CCdonor_gain1.0000
10:100488857:CT:Cdonor_gain1.0000
10:100488857:CTA:Cdonor_gain1.0000
10:100488857:CTAA:Cdonor_gain1.0000
10:100488857:CTAAG:Cdonor_gain1.0000
10:100488975:CTG:Cacceptor_gain1.0000
10:100488976:TG:Tacceptor_gain1.0000
10:100488978:C:CCacceptor_gain1.0000
10:100489698:TTGAC:Tdonor_loss1.0000
10:100489699:TGACC:Tdonor_loss1.0000
10:100489700:GACCT:Gdonor_loss1.0000
10:100489702:C:CTdonor_loss1.0000
10:100496253:CTTA:Cdonor_loss1.0000
10:100496254:TTA:Tdonor_loss1.0000
10:100496255:TACCT:Tdonor_loss1.0000
10:100496256:A:ATdonor_loss1.0000
10:100496257:C:Adonor_loss1.0000
10:100496429:GTCC:Gacceptor_loss1.0000
10:100496430:TCCTG:Tacceptor_loss1.0000
10:100496432:C:CCacceptor_gain1.0000

AlphaMissense

7648 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
10:100502482:A:CF394L0.972
10:100502482:A:TF394L0.972
10:100502484:A:GF394L0.972
10:100505364:A:CF392L0.965
10:100505364:A:TF392L0.965
10:100505366:A:GF392L0.965
10:100509057:A:GW149R0.963
10:100509057:A:TW149R0.963
10:100516165:A:TI45K0.961
10:100509495:A:GW74R0.954
10:100509495:A:TW74R0.954
10:100496289:G:TA760D0.952
10:100495521:C:GR779P0.950
10:100487667:G:CF1163L0.948
10:100487667:G:TF1163L0.948
10:100487669:A:GF1163L0.948
10:100509344:A:TV124D0.946
10:100497730:A:GW643R0.941
10:100497730:A:TW643R0.941
10:100509089:G:TA138D0.940
10:100516165:A:CI45R0.940
10:100502471:A:GL398P0.936
10:100502268:A:GW466R0.935
10:100502268:A:TW466R0.935
10:100497265:C:GR669P0.932
10:100497728:C:AW643C0.929
10:100497728:C:GW643C0.929
10:100502260:G:CF468L0.928
10:100502260:G:TF468L0.928
10:100502262:A:GF468L0.928

dbSNP variants (sampled 300 via entrez): RS1000017998 (10:100495123 G>A,C), RS1000088032 (10:100493648 TC>T), RS1000095580 (10:100489125 G>A,C), RS1000161061 (10:100488490 T>C), RS1000240469 (10:100515760 A>G), RS1000292564 (10:100508608 C>A,G,T), RS1000299461 (10:100488767 G>A,T), RS1000405951 (10:100502000 T>C), RS1000534964 (10:100507163 G>T), RS1000758371 (10:100500368 A>G,T), RS1000940729 (10:100514774 C>A), RS1001026005 (10:100513903 G>A), RS1001093881 (10:100520558 C>A,G,T), RS1001123153 (10:100508318 A>G), RS1001209662 (10:100495827 C>T)

Disease associations

OMIM: gene MIM:610258 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001841_4Palmitoleic acid (16:1n-7) levels6.000000e-09
GCST010703_13Brain morphology (MOSTest)1.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation2
Cisplatindecreases expression, affects cotreatment, increases expression2
Tobacco Smoke Pollutiondecreases expression2
aristolochic acid Iincreases expression1
methylmercuric chloridedecreases expression1
alpha-pineneaffects cotreatment, decreases expression, increases abundance1
tris(2-butoxyethyl) phosphateaffects expression1
beta-lapachonedecreases expression1
tris(1,3-dichloro-2-propyl)phosphateaffects expression1
butyraldehydedecreases expression1
methacrylaldehydeaffects cotreatment, decreases expression, increases abundance1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
abrineincreases expression1
jinfukangaffects cotreatment, increases expression1
Acroleinaffects cotreatment, decreases expression, increases abundance1
Air Pollutantsincreases abundance, affects cotreatment, decreases expression1
Diethylhexyl Phthalatedecreases expression1
Doxorubicindecreases expression1
Fluorouracilaffects reaction, decreases expression1
Methotrexateincreases expression1
Ozoneaffects cotreatment, decreases expression, increases abundance1
Polychlorinated Biphenylsaffects expression1
Tetrachlorodibenzodioxinincreases expression1
Vincristinedecreases expression1
Aflatoxin B1decreases expression, increases expression1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1
Volatile Organic Compoundsaffects cotreatment, decreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B5KUHAP1 SEC31B (-) 2Cancer cell lineMale
CVCL_XS55HAP1 SEC31B (-) 1Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.