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

    Gene ID: 25683, updated on 2-Nov-2024

    Summary

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    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
    human mouse all
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    Genomic context

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    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

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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. Circ_001209 aggravates diabetic retinal vascular dysfunction through regulating miR-15b-5p/COL12A1. Wang F, et al. J Transl Med, 2021 Jul 7. PMID 34233716, Free PMC Article
    2. Structural variation of type XII collagen at its carboxyl-terminal NC1 domain generated by tissue-specific alternative splicing. Kania AM, et al. J Biol Chem, 1999 Jul 30. PMID 10419532
    3. Regulation of endodermal differentiation of human embryonic stem cells through integrin-ECM interactions. Brafman DA, et al. Cell Death Differ, 2013 Mar. PMID 23154389, Free PMC Article
    4. Protein profile of exosomes from trabecular meshwork cells. Stamer WD, et al. J Proteomics, 2011 May 16. PMID 21362503, Free PMC Article
    5. Proteomic analysis of cerebrospinal fluid extracellular vesicles: a comprehensive dataset. Chiasserini D, et al. J Proteomics, 2014 Jun 25. PMID 24769233

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Circ_001209 aggravates diabetic retinal vascular dysfunction through regulating miR-15b-5p/COL12A1.
      Title: Circ_001209 aggravates diabetic retinal vascular dysfunction through regulating miR-15b-5p/COL12A1.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endodermal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    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 
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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

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

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000008
      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_039082533.2 → XP_038938461.1  collagen alpha-1(XII) chain isoform X1

      UniProtKB/TrEMBL
      A0A0G2KAJ7, A0A8I5ZRE6
      Conserved Domains (6) summary
      smart00060
      Location:1474 → 1548
      FN3; Fibronectin type 3 domain
      smart00210
      Location:2521 → 2713
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:724 → 805
      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:1198 → 1361
      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:1387 → 1465
      fn3; Fibronectin type III domain
      pfam01391
      Location:2766 → 2892
      Collagen; Collagen triple helix repeat (20 copies)

    2. XM_039082534.2 → XP_038938462.1  collagen alpha-1(XII) chain isoform X2

      UniProtKB/TrEMBL
      A6I1L5
      Conserved Domains (6) summary
      smart00060
      Location:310 → 384
      FN3; Fibronectin type 3 domain
      smart00210
      Location:1357 → 1549
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:955 → 1034
      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:34 → 197
      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:223 → 301
      fn3; Fibronectin type III domain
      pfam01391
      Location:1706 → 1734
      Collagen; Collagen triple helix repeat (20 copies)

    3. XM_063264976.1 → XP_063121046.1  collagen alpha-1(XII) chain isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P70560.1 GenPept UniProtKB/Swiss-Prot:P70560

    Gene LinkOut

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