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    Col12a1 collagen type XII alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25683, updated on 3-Dec-2024

    Summary

    Official Symbol
    Col12a1provided by RGD
    Official Full Name
    collagen type XII alpha 1 chainprovided by RGD
    Primary source
    RGD:2374
    See related
    EnsemblRapid:ENSRNOG00000058470 AllianceGenome:RGD:2374
    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 be an extracellular matrix structural constituent. Predicted to be involved in endodermal cell differentiation. Part of collagen type XII trimer. Human ortholog(s) of this gene implicated in Bethlem myopathy and Ullrich congenital muscular dystrophy 2. Orthologous to human COL12A1 (collagen type XII alpha 1 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 392.9), Adrenal (RPKM 291.6) and 7 other tissues See more
    Orthologs
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    Genomic context

    See Col12a1 in Genome Data Viewer
    Location:
    8q31
    Exon count:
    66
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 8 NC_086026.1 (89427834..89545886, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 8 NC_051343.1 (80547592..80665665, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (87042820..87150701, complement)

    Chromosome 8 - NC_086026.1Genomic Context describing neighboring genes Neighboring gene U6 spliceosomal RNA Neighboring gene ribosomal protein S3a, pseudogene 10 Neighboring gene protein transport protein Sec61 subunit gamma-like Neighboring gene Sec61 translocon subunit gamma like 1

    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

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    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
     
    Process Evidence Code Pubs
    involved_in angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endothelial cell morphogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
     
    part_of collagen type XII trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XII) chain
    Names
    collagen, type XII, alpha 1
    procollagen, type XII, alpha 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_013142.1NP_037274.1  collagen alpha-1(XII) chain precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      UniProtKB/TrEMBL
      A0A8I5ZRE6
      Related
      ENSRNOP00000075422.3, ENSRNOT00000077071.3

    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
      89427834..89545886 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039082533.2XP_038938461.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/TrEMBL
      A0A0G2KAJ7, A0A8I5ZRE6
      Conserved Domains (6) summary
      smart00060
      Location:14741548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:25212713
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724805
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:11981361
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:13871465
      fn3; Fibronectin type III domain
      pfam01391
      Location:27662892
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_039082534.2XP_038938462.1  collagen alpha-1(XII) chain isoform X2

      UniProtKB/TrEMBL
      A6I1L5
      Conserved Domains (6) summary
      smart00060
      Location:310384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:13571549
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:9551034
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      cd01482
      Location:34197
      vWA_collagen_alphaI-XII-like; Collagen: The extracellular matrix represents a complex alloy of variable members of diverse protein families defining structural integrity and various physiological functions. The most abundant family is the collagens with more than 20 different ...
      pfam00041
      Location:223301
      fn3; Fibronectin type III domain
      pfam01391
      Location:17061734
      Collagen; Collagen triple helix repeat (20 copies)
    3. XM_063264976.1XP_063121046.1  collagen alpha-1(XII) chain isoform X3

      UniProtKB/TrEMBL
      A6I1L5