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    Col5a3 collagen type V alpha 3 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 60379, updated on 9-Dec-2024

    Summary

    Official Symbol
    Col5a3provided by RGD
    Official Full Name
    collagen type V alpha 3 chainprovided by RGD
    Primary source
    RGD:70922
    See related
    EnsemblRapid:ENSRNOG00000020525 AllianceGenome:RGD:70922
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Enables proteoglycan binding activity. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell-matrix adhesion. Located in collagen-containing extracellular matrix. Orthologous to human COL5A3 (collagen type V alpha 3 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Muscle (RPKM 132.2), Heart (RPKM 94.0) and 7 other tissues See more
    Orthologs
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    Genomic context

    See Col5a3 in Genome Data Viewer
    Location:
    8q13
    Exon count:
    69
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (27580768..27626002, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (19304564..19349809, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (21786324..21831751, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 Neighboring gene olfactomedin 2 Neighboring gene retinol dehydrogenase 8 Neighboring gene angiopoietin-like 6 Neighboring gene shiftless antiviral inhibitor of ribosomal frameshifting

    Genomic regions, transcripts, and products

    Expression

    • 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

    Pathways from PubChem

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength  
    enables heparin binding  
    enables heparin binding  
    enables proteoglycan binding PubMed 
    Component Evidence Code Pubs
    part_of collagen type V trimer  
    part_of collagen type V trimer PubMed 
    is_active_in collagen-containing extracellular matrix  
    located_in collagen-containing extracellular matrix PubMed 
    is_active_in extracellular space  

    General protein information

    Preferred Names
    collagen alpha-3(V) chain
    Names
    collagen, type V, alpha 3
    collagen, type V, alpha 4
    procollagen, type V, alpha 3

    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_021760.1 → NP_068528.1  collagen alpha-3(V) chain precursor

      See identical proteins and their annotated locations for NP_068528.1

      Status: PROVISIONAL

      Source sequence(s)
      AF272661
      UniProtKB/TrEMBL
      Q9JI04
      Conserved Domains (3) summary
      pfam01391
      Location:722 → 780
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1508 → 1735
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:32 → 211
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

    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_086026.1 Reference GRCr8

      Range
      27580768..27626002 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039082051.2 → XP_038937979.1  collagen alpha-3(V) chain isoform X1

      UniProtKB/TrEMBL
      F7EVZ0
      Related
      ENSRNOP00000027897.4, ENSRNOT00000027897.6
      Conserved Domains (4) summary
      PHA03169
      Location:643 → 823
      PHA03169; hypothetical protein; Provisional
      pfam01391
      Location:724 → 779
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1506 → 1734
      COLFI; Fibrillar collagen C-terminal domain
      cl22861
      Location:31 → 210
      LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
    2. XM_039082052.2 → XP_038937980.1  collagen alpha-3(V) chain isoform X2

      Conserved Domains (3) summary
      PHA03169
      Location:333 → 513
      PHA03169; hypothetical protein; Provisional
      pfam01391
      Location:414 → 469
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1196 → 1424
      COLFI; Fibrillar collagen C-terminal domain
    3. XM_063266064.1 → XP_063122134.1  collagen alpha-3(V) chain isoform X3

    4. XM_039082054.2 → XP_038937982.1  collagen alpha-3(V) chain isoform X5

      Conserved Domains (2) summary
      pfam01391
      Location:39 → 94
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:821 → 1049
      COLFI; Fibrillar collagen C-terminal domain
    5. XM_039082053.2 → XP_038937981.1  collagen alpha-3(V) chain isoform X4

      Conserved Domains (2) summary
      pfam01391
      Location:64 → 119
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:846 → 1074
      COLFI; Fibrillar collagen C-terminal domain
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