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SEC23B SEC23 homolog B, COPII coat complex component [ Homo sapiens (human) ]

Gene ID: 10483, updated on 3-Nov-2024

Summary

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Official Symbol
SEC23Bprovided by HGNC
Official Full Name
SEC23 homolog B, COPII coat complex componentprovided by HGNC
Primary source
HGNC:HGNC:10702
See related
Ensembl:ENSG00000101310 MIM:610512; AllianceGenome:HGNC:10702
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
CWS7; CDAII; CDAN2; CDA-II; HEMPAS; hSec23B
Summary
The protein encoded by this gene is a member of the SEC23 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec23p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. The function of this gene product has been implicated in cargo selection and concentration. Multiple alternatively spliced transcript variants have been identified in this gene. [provided by RefSeq, Feb 2010]
Expression
Ubiquitous expression in thyroid (RPKM 28.7), testis (RPKM 16.8) and 25 other tissues See more
Orthologs
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Genomic context

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See SEC23B in Genome Data Viewer
Location:
20p11.23
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (18507548..18561415)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (18558602..18612485)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (18488192..18542059)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene RB binding protein 9, serine hydrolase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17586 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:18477654-18478218 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17590 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17591 Neighboring gene ribosomal protein S19 pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:18504796-18505995 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17592 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:18547927-18548209 Neighboring gene small integral membrane protein 26 Neighboring gene uncharacterized LOC124904878 Neighboring gene Sharpr-MPRA regulatory region 13138

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Homozygosity mapping reveals founder SEC23B-Y462C mutations in Indian congenital dyserythropoietic anemia type II. Singleton B, et al. Clin Genet, 2015 Aug. PMID 25418799
  2. [Analysis of genotype and phenotype of SEC23B gene in a family affected with congenital dyserythropoietic anemia type II]. Li D, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2017 Dec 10. PMID 29188620
  3. Congenital dyserythropoietic anemia type II (CDAII) is caused by mutations in the SEC23B gene. Bianchi P, et al. Hum Mutat, 2009 Sep. PMID 19621418
  4. Molecular analysis of 42 patients with congenital dyserythropoietic anemia type II: new mutations in the SEC23B gene and a search for a genotype-phenotype relationship. Iolascon A, et al. Haematologica, 2010 May. PMID 20015893, Free PMC Article
  5. CDAII presenting as hydrops foetalis: molecular characterization of two cases. Fermo E, et al. Blood Cells Mol Dis, 2010 Jun 15. PMID 20381388

See all (146) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Congenital Dyserythropoietic Anemia Type II: High Prevalence of c.1385A>G, (p.Tyr462Cys) Mutation in the Indian Population.
    Title: Congenital Dyserythropoietic Anemia Type II: High Prevalence of c.1385A>G, (p.Tyr462Cys) Mutation in the Indian Population.
  2. New Cases and Mutations in SEC23B Gene Causing Congenital Dyserythropoietic Anemia Type II.
    Title: New Cases and Mutations in SEC23B Gene Causing Congenital Dyserythropoietic Anemia Type II.
  3. A common human missense mutation of vesicle coat protein SEC23B leads to growth restriction and chronic pancreatitis in mice.
    Title: A common human missense mutation of vesicle coat protein SEC23B leads to growth restriction and chronic pancreatitis in mice.
  4. SEC23B Loss-of-Function Suppresses Hepcidin Expression by Impairing Glycosylation Pathway in Human Hepatic Cells.
    Title: SEC23B Loss-of-Function Suppresses Hepcidin Expression by Impairing Glycosylation Pathway in Human Hepatic Cells.
  5. Non-canonical role of wild-type SEC23B in the cellular stress response pathway.
    Title: Non-canonical role of wild-type SEC23B in the cellular stress response pathway.
  6. Compound heterozygosity for two novel mutations of the SEC23B gene in congenital dyserythropoietic anemia type II.
    Title: Compound heterozygosity for two novel mutations of the SEC23B gene in congenital dyserythropoietic anemia type II.
  7. [Variant analysis of SEC23B gene in 4 families with congenital dyserythropoietic anemia].
    Title: [Variant analysis of SEC23B gene in 4 families with congenital dyserythropoietic anemia].
  8. Mutations in the coat complex II component SEC23B promote colorectal cancer metastasis.
    Title: Mutations in the coat complex II component SEC23B promote colorectal cancer metastasis.
  9. RAP-011 Rescues the Disease Phenotype in a Cellular Model of Congenital Dyserythropoietic Anemia Type II by Inhibiting the SMAD2-3 Pathway.
    Title: RAP-011 Rescues the Disease Phenotype in a Cellular Model of Congenital Dyserythropoietic Anemia Type II by Inhibiting the SMAD2-3 Pathway.
  10. Here, the authors show that the F-box protein FBXW5 targets SEC23B, a component of COPII, for proteasomal degradation and that this event limits the autophagic flux in the presence of nutrients. In response to starvation, ULK1 phosphorylates SEC23B on Serine 186, preventing the interaction of SEC23B with FBXW5 and, therefore, inhibiting SEC23B degradation.
    Title: The ULK1-FBXW5-SEC23B nexus controls autophagy.
Submit: New GeneRIF Correction See all GeneRIFs (33)

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

Associated conditions

Description Tests
Congenital dyserythropoietic anemia, type II
MedGen: C1306589 OMIM: 224100 GeneReviews: Not available
not available
Cowden syndrome 7
MedGen: C4225179 OMIM: 616858 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in COPII-coated vesicle cargo loading IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in intracellular protein transport 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
  
located_in cytosol IEA
Inferred from Electronic Annotation
more info
  
located_in endomembrane system IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in endoplasmic reticulum exit site IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
protein transport protein Sec23B
Names
SEC23 homolog B, coat complex II component
SEC23-like protein B
SEC23-related protein B
transport protein SEC23B

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

  1. NG_016281.2 RefSeqGene

    Range
    5459..58934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_1134

mRNA and Protein(s)

  1. NM_001172745.3 → NP_001166216.1  protein transport protein Sec23B isoform 1

    See identical proteins and their annotated locations for NP_001166216.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) has an alternate 5' UTR exon, as compared to variant 2. Variants 1, 2, 3 and 4 encode the same isoform (1).
    Source sequence(s)
    AL121893, AL121900, BC005032, BC005404, DC351945
    Consensus CDS
    CCDS13137.1
    UniProtKB/Swiss-Prot
    D3DW33, Q15437, Q503A9, Q5W183, Q9BS15, Q9BSI2, Q9H1D7
    UniProtKB/TrEMBL
    B4DJW8
    Related
    ENSP00000366685.1, ENST00000377465.6
    Conserved Domains (1) summary
    PLN00162
    Location:12 → 765
    PLN00162; transport protein sec23; Provisional

  2. NM_001172746.3 → NP_001166217.1  protein transport protein Sec23B isoform 2

    See identical proteins and their annotated locations for NP_001166217.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternative splice site and lacks an in-frame segment in the 5' CDS, as compared to variant 2. The resulting isoform (2) lacks an internal segment, as compared to isoform 1.
    Source sequence(s)
    AK296270, AL121900, BC005032
    Consensus CDS
    CCDS86935.1
    UniProtKB/TrEMBL
    A0A2R8YFH5, B4DJW8
    Related
    ENSP00000496460.1, ENST00000643747.1
    Conserved Domains (6) summary
    cd11287
    Location:594 → 714
    Sec23_C; C-terminal Actin depolymerization factor-homology domain of Sec23
    PLN00162
    Location:12 → 747
    PLN00162; transport protein sec23; Provisional
    cd01478
    Location:123 → 372
    Sec23-like; Sec23-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 ...
    pfam04810
    Location:58 → 97
    zf-Sec23_Sec24; Sec23/Sec24 zinc finger
    pfam04815
    Location:506 → 599
    Sec23_helical; Sec23/Sec24 helical domain
    pfam08033
    Location:385 → 488
    Sec23_BS; Sec23/Sec24 beta-sandwich domain

  3. NM_006363.6 → NP_006354.2  protein transport protein Sec23B isoform 1

    See identical proteins and their annotated locations for NP_006354.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) uses an alternative splice site and lacks a segment in the 5' UTR, as compared to variant 2. Variants 1, 2, 3 and 4 encode the same isoform (1).
    Source sequence(s)
    BC001151, BC095404, CA307855, X97065
    Consensus CDS
    CCDS13137.1
    UniProtKB/Swiss-Prot
    D3DW33, Q15437, Q503A9, Q5W183, Q9BS15, Q9BSI2, Q9H1D7
    UniProtKB/TrEMBL
    B4DJW8
    Related
    ENSP00000497473.1, ENST00000650089.1
    Conserved Domains (1) summary
    PLN00162
    Location:12 → 765
    PLN00162; transport protein sec23; Provisional

  4. NM_032985.6 → NP_116780.1  protein transport protein Sec23B isoform 1

    See identical proteins and their annotated locations for NP_116780.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) represents the longest transcript. Variants 1, 2, 3 and 4 encode the same isoform (1).
    Source sequence(s)
    BC005032, BC095404, BM925053, CA307855, EC528189
    Consensus CDS
    CCDS13137.1
    UniProtKB/Swiss-Prot
    D3DW33, Q15437, Q503A9, Q5W183, Q9BS15, Q9BSI2, Q9H1D7
    UniProtKB/TrEMBL
    B4DJW8
    Related
    ENSP00000338844.3, ENST00000336714.8
    Conserved Domains (1) summary
    PLN00162
    Location:12 → 765
    PLN00162; transport protein sec23; Provisional

  5. NM_032986.5 → NP_116781.1  protein transport protein Sec23B isoform 1

    See identical proteins and their annotated locations for NP_116781.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site and lacks a segment in the 5' UTR, as compared to variant 2. Variants 1, 2, 3 and 4 encode the same isoform (1).
    Source sequence(s)
    AL540773, BC001151, BC095404, CA307855, DC401693
    Consensus CDS
    CCDS13137.1
    UniProtKB/Swiss-Prot
    D3DW33, Q15437, Q503A9, Q5W183, Q9BS15, Q9BSI2, Q9H1D7
    UniProtKB/TrEMBL
    B4DJW8
    Related
    ENSP00000262544.2, ENST00000262544.6
    Conserved Domains (1) summary
    PLN00162
    Location:12 → 765
    PLN00162; transport protein sec23; Provisional

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

  1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    18507548..18561415
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    18558602..18612485
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15437.2 GenPept UniProtKB/Swiss-Prot:Q15437

Gene LinkOut

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