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

    Gene ID: 25683, updated on 18-Apr-2019

    Summary

    Official Symbol
    Col12a1provided by RGD
    Official Full Name
    collagen type XII alpha 1 chainprovided by RGD
    Primary source
    RGD:2374
    See related
    Ensembl:ENSRNOG00000058470
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    may mediate interactions between extracellular matrix molecules and cells [RGD, Feb 2006]
    Expression
    Biased expression in Kidney (RPKM 392.9), Adrenal (RPKM 291.6) and 7 other tissues See more
    Orthologs

    Genomic context

    See Col12a1 in Genome Data Viewer
    Location:
    8q31
    Exon count:
    64
    Annotation release Status Assembly Chr Location
    106 current Rnor_6.0 (GCF_000001895.5) 8 NC_005107.4 (87042820..87150701, complement)
    104 previous assembly Rnor_5.0 (GCF_000001895.4) 8 NC_005107.3 (86584555..86701809, complement)

    Chromosome 8 - NC_005107.4Genomic Context describing neighboring genes Neighboring gene dynein light chain 1-like Neighboring gene similar to 40S ribosomal protein S3a (V-fos transformation effector protein) Neighboring gene uncharacterized LOC103690438 Neighboring gene protein transport protein Sec61 subunit gamma pseudogene

    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

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    extracellular matrix structural constituent TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    cell adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    collagen fibril organization IEA
    Inferred from Electronic Annotation
    more info
     
    endodermal cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    PubMed 
    Component Evidence Code Pubs
    collagen type XII trimer IDA
    Inferred from Direct Assay
    more info
    PubMed 
    collagen type XII trimer IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    collagen alpha-1(XII) chain; LOW QUALITY PROTEIN: collagen alpha-1(XII) chain
    Names
    collagen, type XII, alpha 1
    procollagen, type XII, alpha 1

    NCBI Reference Sequences (RefSeq)

    RefSeqs of Annotated Genomes: Rattus norvegicus Annotation Release 106 details...Open this link in a new tab

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference Rnor_6.0 Primary Assembly

    Genomic

    1. NC_005107.4 Reference Rnor_6.0 Primary Assembly

      Range
      87042820..87150701 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017596099.1XP_017451588.1  LOW QUALITY PROTEIN: collagen alpha-1(XII) chain isoform X1

      Related
      ENSRNOP00000075422.1, ENSRNOT00000077071.1

    Alternate Rn_Celera

    Genomic

    1. AC_000076.1 Alternate Rn_Celera

      Range
      80273757..80389987 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_001060689.6XP_001060689.2  collagen alpha-1(XII) chain isoform X2

      Conserved Domains (6) summary
      pfam01391
      Location:27652892
      Collagen; Collagen triple helix repeat (20 copies)
      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:17561836
      fn3; Fibronectin type III domain
    2. XM_008757826.2XP_008756048.1  collagen alpha-1(XII) chain isoform X3

      Conserved Domains (6) summary
      pfam01391
      Location:17061734
      Collagen; Collagen triple helix repeat (20 copies)
      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:592672
      fn3; Fibronectin type III domain
    3. XM_008757825.2XP_008756047.1  collagen alpha-1(XII) chain isoform X1

      Conserved Domains (6) summary
      pfam01391
      Location:28032930
      Collagen; Collagen triple helix repeat (20 copies)
      smart00060
      Location:15121586
      FN3; Fibronectin type 3 domain
      smart00210
      Location:25592751
      TSPN; Thrombospondin N-terminal -like domains
      cd00063
      Location:762843
      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:12361399
      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:17941874
      fn3; Fibronectin type III domain
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