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    Col5a2 collagen type V alpha 2 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 85250, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Col5a2provided by RGD
    Official Full Name
    collagen type V alpha 2 chainprovided by RGD
    Primary source
    RGD:70921
    See related
    EnsemblRapid:ENSRNOG00000003736 AllianceGenome:RGD:70921
    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 SMAD binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in ossification. Predicted to be part of collagen type V trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in Ehlers-Danlos syndrome and Ehlers-Danlos syndrome classic type 2. Orthologous to human COL5A2 (collagen type V alpha 2 chain). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in Lung (RPKM 592.9), Uterus (RPKM 552.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col5a2 in Genome Data Viewer
    Location:
    9q22
    Exon count:
    54
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 9 NC_086027.1 (54940768..55090151, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 9 NC_051344.1 (47448741..47598134, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 9 NC_005108.4 (52091088..52238735, complement)

    Chromosome 9 - NC_086027.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein S3, pseudogene 8 Neighboring gene collagen type III alpha 1 chain Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC134480367 Neighboring gene CTP synthase 1, pseudogene 2 Neighboring gene WD repeat domain 75

    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 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. Mutations of the alpha2(V) chain of type V collagen impair matrix assembly and produce ehlers-danlos syndrome type I. Michalickova K, et al. Hum Mol Genet, 1998 Feb. PMID 9425231
    2. A single base mutation in COL5A2 causes Ehlers-Danlos syndrome type II. Richards AJ, et al. J Med Genet, 1998 Oct. PMID 9783710, Free PMC Article
    3. Development of a functional skin matrix requires deposition of collagen V heterotrimers. Chanut-Delalande H, et al. Mol Cell Biol, 2004 Jul. PMID 15199158, Free PMC Article
    4. Col V siRNA engineered tenocytes for tendon tissue engineering. Lu P, et al. PLoS One, 2011. PMID 21713001, Free PMC Article
    5. Identification of the shared gene signatures between pulmonary fibrosis and pulmonary hypertension using bioinformatics analysis. Zhao H, et al. Front Immunol, 2023. PMID 37731513, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    Function Evidence Code Pubs
    enables SMAD binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables extracellular matrix structural constituent TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cellular response to amino acid stimulus ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in eye morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ossification IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within skeletal system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in skin development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skin development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of collagen type V trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen type V trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of collagen type V trimer TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    collagen alpha-2(V) chain
    Names
    collagen, type V, alpha 2
    procollagen, type V, alpha 2

    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_001399195.1 → NP_001386124.1  collagen alpha-2(V) chain precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000009
      UniProtKB/TrEMBL
      A0A8I6GEX8, A6INT3
      Related
      ENSRNOP00000086427.1, ENSRNOT00000099326.2
      Conserved Domains (5) summary
      smart00214
      Location:40 → 95
      VWC; von Willebrand factor (vWF) type C domain
      PHA03307
      Location:745 → 1145
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam09606
      Location:282 → 643
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal
      pfam01391
      Location:1043 → 1099
      Collagen; Collagen triple helix repeat (20 copies)
      pfam01410
      Location:1264 → 1497
      COLFI; Fibrillar collagen C-terminal 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_086027.1 Reference GRCr8

      Range
      54940768..55090151 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_053488.1: Suppressed sequence

      Description
      NM_053488.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

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