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    Sec23b Sec23 homolog B, COPII coat complex component [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362226, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Sec23bprovided by RGD
    Official Full Name
    Sec23 homolog B, COPII coat complex componentprovided by RGD
    Primary source
    RGD:1310699
    See related
    EnsemblRapid:ENSRNOG00000008411 AllianceGenome:RGD:1310699
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable GTPase activator activity. Predicted to be involved in COPII-coated vesicle cargo loading. Predicted to be located in endoplasmic reticulum and perinuclear region of cytoplasm. Predicted to be part of COPII vesicle coat. Predicted to be active in endoplasmic reticulum exit site. Human ortholog(s) of this gene implicated in Cowden syndrome 7 and congenital dyserythropoietic anemia type II. Orthologous to human SEC23B (SEC23 homolog B, COPII coat complex component). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 187.2), Kidney (RPKM 183.8) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sec23b in Genome Data Viewer
    Location:
    3q41
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (152392340..152434813)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (131939011..131981489)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (138715118..138757111)

    Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene RNA polymerase III subunit F Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene RB binding protein 9, serine hydrolase Neighboring gene small integral membrane protein 26 Neighboring gene D-aminoacyl-tRNA deacylase 1 Neighboring gene uncharacterized LOC134486168 Neighboring gene receptor for activated C kinase 1, pseudogene 3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Germline Heterozygous Variants in SEC23B Are Associated with Cowden Syndrome and Enriched in Apparently Sporadic Thyroid Cancer. Yehia L, et al. Am J Hum Genet, 2015 Nov 5. PMID 26522472, Free PMC Article
    2. Codanin-1 mutations in congenital dyserythropoietic anemia type 1 affect HP1{alpha} localization in erythroblasts. Renella R, et al. Blood, 2011 Jun 23. PMID 21364188
    3. Yeast two-hybrid screens imply that GGNBP1, GGNBP2 and OAZ3 are potential interaction partners of testicular germ cell-specific protein GGN1. Zhang J, et al. FEBS Lett, 2005 Jan 17. PMID 15642376
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein transport protein Sec23B
    Names
    Sec23 homolog B, coat complex II component

    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.

    mRNA and Protein(s)

    1. NM_001277235.1 → NP_001264164.1  protein transport protein Sec23B

      See identical proteins and their annotated locations for NP_001264164.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000003
      UniProtKB/TrEMBL
      A0A8I5ZKS5, D3ZCT7
      Related
      ENSRNOP00000062590.3, ENSRNOT00000064723.5
      Conserved Domains (1) summary
      PLN00162
      Location:12 → 765
      PLN00162; transport protein sec23; Provisional

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086021.1 Reference GRCr8

      Range
      152392340..152434813
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006235126.5 → XP_006235188.1  protein transport protein Sec23B isoform X1

      See identical proteins and their annotated locations for XP_006235188.1

      UniProtKB/TrEMBL
      A0A8I5ZKS5, D3ZCT7
      Related
      ENSRNOP00000078374.2, ENSRNOT00000095527.2
      Conserved Domains (1) summary
      PLN00162
      Location:12 → 765
      PLN00162; transport protein sec23; Provisional

    2. XM_063284169.1 → XP_063140239.1  protein transport protein Sec23B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZKS5, D3ZCT7

    3. XM_063284168.1 → XP_063140238.1  protein transport protein Sec23B isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZKS5, D3ZCT7

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108593.1: Suppressed sequence

      Description
      NM_001108593.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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