SEC24B SEC24 homolog B, COPII coat complex component [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEC24Bprovided by HGNC
Official Full Name: SEC24 homolog B, COPII coat complex componentprovided by HGNC
Primary source: HGNC:HGNC:10704
See related: Ensembl:ENSG00000138802 MIM:607184; AllianceGenome:HGNC:10704
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SEC24
Summary: The protein encoded by this gene is a member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein is thought to be a cargo-binding component of the COPII vesicle, and is thought to be involved in the transport of secretory proteins from the endoplasmic reticulum to the Golgi apparatus. Mutations in this gene have been associated with neural tube defects, and are thought to be a result of a disruption in interactions with the protein encoded by the VANGL planar cell polarity protein 2 (VANGL2) gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression: Ubiquitous expression in thyroid (RPKM 10.5), liver (RPKM 10.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q25

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (109433815..109540896)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (112735946..112843029)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (110354971..110462052)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration.
Title: Microglia ferroptosis is regulated by SEC24B and contributes to neurodegeneration.
The role of the C-terminal domain of PCSK9 and SEC24 isoforms in PCSK9 secretion.
Title: The role of the C-terminal domain of PCSK9 and SEC24 isoforms in PCSK9 secretion.
results show that functional mutations in SEC24B might contribute to the etiology of a subset of human Neural Tube Defects (NTDs).
Title: Mutations in the COPII vesicle component gene SEC24B are associated with human neural tube defects.
Observational study of gene-disease association. (HuGE Navigator)
Title: A systematic gene-based screen of chr4q22-q32 identifies association of a novel susceptibility gene, DKK2, with the quantitative trait of alcohol dependence symptom counts.
Data show that coupling of the Sec23/24 and Sec13/31 layers of the COPII coat is required to drive export of collagen from the endoplasmic reticulum, and that efficient COPII assembly is essential for normal craniofacial development during embryogenesis.
Title: Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SGC33972 (e-PCR)
- UniSTS:39937

SHGC-67946 (e-PCR)
- UniSTS:55315

SHGC-23029 (e-PCR)
- UniSTS:58412

D4S2646 (e-PCR)
- UniSTS:74549

SHGC-36718 (e-PCR)
- UniSTS:3937

SHGC-59599 (e-PCR)
- UniSTS:46965

SEC24B_1319 (e-PCR)
- UniSTS:277694

SEC24B_v400 (e-PCR)
- UniSTS:277694

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle cargo loading	IBA Inferred from Biological aspect of Ancestor more info
involved_in COPII-coated vesicle cargo loading	IDA Inferred from Direct Assay more info	PubMed
involved_in aorta morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in auditory receptor cell stereocilium organization	IEA Inferred from Electronic Annotation more info
involved_in cochlear nucleus development	IEA Inferred from Electronic Annotation more info
involved_in coronary artery morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in lung lobe morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in neural tube closure	IEA Inferred from Electronic Annotation more info
involved_in outflow tract morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in pulmonary artery morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of cargo loading into COPII-coated vesicle	IEA Inferred from Electronic Annotation more info
involved_in regulation of establishment of planar polarity involved in neural tube closure	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of COPII vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
part_of COPII vesicle coat	IDA Inferred from Direct Assay more info	PubMed
located_in ER to Golgi transport vesicle membrane	TAS Traceable Author Statement more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in endoplasmic reticulum exit site	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: protein transport protein Sec24B

Names: SEC24 related gene family, member B; secretory protein 24

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_032166.1 RefSeqGene

Range

5001..112082

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001042734.4 → NP_001036199.1 protein transport protein Sec24B isoform b

See identical proteins and their annotated locations for NP_001036199.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two in-frame exons in the 5' and central coding region, and uses an alternate in-frame splice site in the central coding region, compared to variant 3. The encoded isoform (b) is shorter, compared to isoform c.

Source sequence(s)

AC105314, BC040137, BC117135, H15283

Consensus CDS

CCDS43260.1

UniProtKB/TrEMBL

B4DTM6

Related

ENSP00000382051.2, ENST00000399100.6

Conserved Domains (6) summary

COG5028
Location:428 → 1224

COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]

cd01479
Location:640 → 883

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1105 → 1179

Gelsolin; Gelsolin repeat

pfam04810
Location:567 → 603

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:983 → 1078

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:884 → 968

Sec23_BS; Sec23/Sec24 beta-sandwich domain
NM_001300813.3 → NP_001287742.1 protein transport protein Sec24B isoform c

See identical proteins and their annotated locations for NP_001287742.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (c).

Source sequence(s)

AC105314, BC040137, BC143268, H15283

Consensus CDS

CCDS75179.1

UniProtKB/TrEMBL

B4DTM6

Related

ENSP00000428564.1, ENST00000504968.6

Conserved Domains (5) summary

cd01479
Location:705 → 948

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1170 → 1244

Gelsolin; Gelsolin repeat

pfam04810
Location:632 → 668

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:1048 → 1143

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:949 → 1033

Sec23_BS; Sec23/Sec24 beta-sandwich domain
NM_001318085.2 → NP_001305014.1 protein transport protein Sec24B isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an in-frame exon in the 5' coding region, compared to variant 3. The encoded isoform (d) is shorter, compared to isoform c.

Source sequence(s)

AC105314, BC040137, BC143269, H15283

UniProtKB/TrEMBL

B4DTM6

Conserved Domains (5) summary

cd01479
Location:674 → 917

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1139 → 1213

Gelsolin; Gelsolin repeat

pfam04810
Location:601 → 637

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:1017 → 1112

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:918 → 1002

Sec23_BS; Sec23/Sec24 beta-sandwich domain
NM_001318086.2 → NP_001305015.1 protein transport protein Sec24B isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) lacks two in-frame exons in the 5' and central coding region, compared to variant 3. The encoded isoform (e) is shorter, compared to isoform c.

Source sequence(s)

AC105314, AK300278, BC040137, BC143269, H15283

UniProtKB/TrEMBL

B4DTM6

Conserved Domains (5) summary

cd01479
Location:639 → 882

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1104 → 1178

Gelsolin; Gelsolin repeat

pfam04810
Location:566 → 602

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:982 → 1077

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:883 → 967

Sec23_BS; Sec23/Sec24 beta-sandwich domain
NM_006323.5 → NP_006314.2 protein transport protein Sec24B isoform a

See identical proteins and their annotated locations for NP_006314.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) lacks an in-frame exon in the 5' coding region and uses an alternate in-frame splice site in the central coding region, compared to variant 3. The encoded isoform (a) is shorter, compared to isoform c.

Source sequence(s)

AC105314, BC040137, BC143268, H15283

Consensus CDS

CCDS47124.1

UniProtKB/Swiss-Prot

B7ZKM8, B7ZKN4, O95487, Q0VG08

UniProtKB/TrEMBL

B4DTM6

Related

ENSP00000265175.4, ENST00000265175.5

Conserved Domains (6) summary

COG5028
Location:463 → 1259

COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]

cd01479
Location:675 → 918

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1140 → 1214

Gelsolin; Gelsolin repeat

pfam04810
Location:602 → 638

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:1018 → 1113

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:919 → 1003

Sec23_BS; Sec23/Sec24 beta-sandwich domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

109433815..109540896

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017007652.3 → XP_016863141.1 protein transport protein Sec24B isoform X10

UniProtKB/TrEMBL

B4DTM6
XM_047449519.1 → XP_047305475.1 protein transport protein Sec24B isoform X11
XM_011531536.4 → XP_011529838.1 protein transport protein Sec24B isoform X1

UniProtKB/TrEMBL

B4DTM6

Conserved Domains (6) summary

COG5028
Location:439 → 1235

COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]

cd01479
Location:651 → 894

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1116 → 1190

Gelsolin; Gelsolin repeat

pfam04810
Location:578 → 614

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:994 → 1089

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:895 → 979

Sec23_BS; Sec23/Sec24 beta-sandwich domain
XM_047449514.1 → XP_047305470.1 protein transport protein Sec24B isoform X5
XM_047449512.1 → XP_047305468.1 protein transport protein Sec24B isoform X3
XM_047449513.1 → XP_047305469.1 protein transport protein Sec24B isoform X4
XM_011531537.4 → XP_011529839.1 protein transport protein Sec24B isoform X2

UniProtKB/TrEMBL

B4DTM6

Conserved Domains (6) summary

COG5028
Location:436 → 1232

COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]

cd01479
Location:648 → 891

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:1113 → 1187

Gelsolin; Gelsolin repeat

pfam04810
Location:575 → 611

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:991 → 1086

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:892 → 976

Sec23_BS; Sec23/Sec24 beta-sandwich domain
XM_047449515.1 → XP_047305471.1 protein transport protein Sec24B isoform X6
XM_047449516.1 → XP_047305472.1 protein transport protein Sec24B isoform X7
XM_047449517.1 → XP_047305473.1 protein transport protein Sec24B isoform X8
XM_047449518.1 → XP_047305474.1 protein transport protein Sec24B isoform X9
XM_047449520.1 → XP_047305476.1 protein transport protein Sec24B isoform X12
XM_047449521.1 → XP_047305477.1 protein transport protein Sec24B isoform X13
XM_011531540.4 → XP_011529842.1 protein transport protein Sec24B isoform X14

UniProtKB/TrEMBL

B4E2E1

Conserved Domains (5) summary

cd01479
Location:140 → 383

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:605 → 679

Gelsolin; Gelsolin repeat

pfam04810
Location:67 → 103

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:483 → 578

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:384 → 468

Sec23_BS; Sec23/Sec24 beta-sandwich domain