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    Sec24d SEC24 homolog D, COPII coat complex component [ Rattus norvegicus (Norway rat) ]

    Gene ID: 310843, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Sec24dprovided by RGD
    Official Full Name
    SEC24 homolog D, COPII coat complex componentprovided by RGD
    Primary source
    RGD:1311720
    See related
    EnsemblRapid:ENSRNOG00000014872 AllianceGenome:RGD:1311720
    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 SNARE binding activity and zinc ion binding activity. Predicted to be involved in COPII-coated vesicle cargo loading. Predicted to act upstream of or within in utero embryonic development. Predicted to be located in intracellular membrane-bounded organelle. 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 Cole-Carpenter syndrome. Orthologous to human SEC24D (SEC24 homolog D, COPII coat complex component). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 137.5), Liver (RPKM 133.3) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Sec24d in Genome Data Viewer
    Location:
    2q42
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (214103138..214211155)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (211418557..211526588)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (227455704..227562801)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene adhesion molecule with Ig like domain 1, pseudogene 1 Neighboring gene synaptopodin 2 Neighboring gene uncharacterized LOC134485960 Neighboring gene methyltransferase 14, N6-adenosine-methyltransferase non-catalytic subunit Neighboring gene RNA, U6atac small nuclear

    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. CREB3L2-mediated expression of Sec23A/Sec24D is involved in hepatic stellate cell activation through ER-Golgi transport. Tomoishi S, et al. Sci Rep, 2017 Aug 11. PMID 28801610, Free PMC Article
    2. Disruption of the Sec24d gene results in early embryonic lethality in the mouse. Baines AC, et al. PLoS One, 2013. PMID 23596517, Free PMC Article
    3. Mammalian COPII coat component SEC24C is required for embryonic development in mice. Adams EJ, et al. J Biol Chem, 2014 Jul 25. PMID 24876386, Free PMC Article
    4. Selective export of human GPI-anchored proteins from the endoplasmic reticulum. Bonnon C, et al. J Cell Sci, 2010 May 15. PMID 20427317
    5. Structural basis of cargo membrane protein discrimination by the human COPII coat machinery. Mancias JD, et al. EMBO J, 2008 Nov 5. PMID 18843296, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Sec24D expression is upregulated via CREB3L2 during hepatic stellate cells activation. Sec24D knockdown abrogated the activation.
      Title: CREB3L2-mediated expression of Sec23A/Sec24D is involved in hepatic stellate cell activation through ER-Golgi transport.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables SNARE binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables SNARE binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables zinc ion binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within in utero embryonic development ISO
    Inferred from Sequence Orthology
    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
    		  
    part_of COPII vesicle coat ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    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 intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    protein transport protein Sec24D
    Names
    SEC24 family member D
    SEC24 related gene family, member D

    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_001309453.1 → NP_001296382.1  protein transport protein Sec24D

      See identical proteins and their annotated locations for NP_001296382.1

      Status: VALIDATED

      Source sequence(s)
      BC168946, JAXUCZ010000002
      UniProtKB/TrEMBL
      A6HVI6, B5DF68, G3V9S9
      Conserved Domains (6) summary
      COG5028
      Location:217 → 1029
      COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
      cd01479
      Location:439 → 698
      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:904 → 976
      Gelsolin; Gelsolin repeat
      pfam04810
      Location:362 → 399
      zf-Sec23_Sec24; Sec23/Sec24 zinc finger
      pfam04815
      Location:787 → 883
      Sec23_helical; Sec23/Sec24 helical domain
      pfam08033
      Location:688 → 772
      Sec23_BS; Sec23/Sec24 beta-sandwich domain

    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_086020.1 Reference GRCr8

      Range
      214103138..214211155
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006233272.5 → XP_006233334.1  protein transport protein Sec24D isoform X1

      See identical proteins and their annotated locations for XP_006233334.1

      UniProtKB/TrEMBL
      G3V9S9
      Related
      ENSRNOP00000059031.5, ENSRNOT00000064809.5
      Conserved Domains (6) summary
      COG5028
      Location:180 → 1028
      COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]
      cd01479
      Location:438 → 697
      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:903 → 975
      Gelsolin; Gelsolin repeat
      pfam04810
      Location:361 → 398
      zf-Sec23_Sec24; Sec23/Sec24 zinc finger
      pfam04815
      Location:786 → 882
      Sec23_helical; Sec23/Sec24 helical domain
      pfam08033
      Location:687 → 771
      Sec23_BS; Sec23/Sec24 beta-sandwich domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001107723.1: Suppressed sequence

      Description
      NM_001107723.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

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