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

    Gene ID: 10483, updated on 5-Mar-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
    mouse all
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    Genomic context

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    Location:
    20p11.23
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (18507548..18561415)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (18558602..18612485)
    105.20220307 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
    • 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. New Cases and Mutations in SEC23B Gene Causing Congenital Dyserythropoietic Anemia Type II. Musri MM, et al. Int J Mol Sci, 2023 Jun 9. PMID 37373084, Free PMC Article
    2. SEC23B Loss-of-Function Suppresses Hepcidin Expression by Impairing Glycosylation Pathway in Human Hepatic Cells. Rosato BE, et al. Int J Mol Sci, 2022 Jan 24. PMID 35163229, Free PMC Article
    3. [Variant analysis of SEC23B gene in 4 families with congenital dyserythropoietic anemia]. Feng Y, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2021 Aug 10. PMID 34365611
    4. Compound heterozygosity for two novel mutations of the SEC23B gene in congenital dyserythropoietic anemia type II. Chen S, et al. Int J Hematol, 2021 Sep. PMID 33914262
    5. Mutations in the coat complex II component SEC23B promote colorectal cancer metastasis. Yang C, et al. Cell Death Dis, 2020 Mar 2. PMID 32123160, Free PMC Article

    See all (132) 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
    		Compare labs
    Cowden syndrome 7
    MedGen: C4225179 OMIM: 616858 GeneReviews: Not available
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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_2023_10

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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