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    Col11a2 collagen type XI alpha 2 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 294279, updated on 27-Nov-2024

    Summary

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    Symbol
    Col11a2provided by RGD
    Full Name
    collagen type XI alpha 2 chainprovided by RGD
    Primary source
    RGD:2373
    See related
    EnsemblRapid:ENSRNOG00000000463 AllianceGenome:RGD:2373
    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 heparin binding activity. Predicted to be an extracellular matrix structural constituent conferring tensile strength. Involved in osteoblast differentiation. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Human ortholog(s) of this gene implicated in cleft palate; nonsyndromic deafness (multiple); and osteochondrodysplasia (multiple). Orthologous to human COL11A2 (collagen type XI alpha 2 chain). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Muscle (RPKM 69.6), Brain (RPKM 58.8) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col11a2 in Genome Data Viewer
    Location:
    20p12
    Exon count:
    67
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (4788829..4818492, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (4786932..4816598, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (3829324..3859022)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene RT1 class II, locus Ha Neighboring gene RT1 class II, locus Hb, pseudogene 1 Neighboring gene retinoid X receptor beta Neighboring gene solute carrier family 39 member 7 Neighboring gene hydroxysteroid (17-beta) dehydrogenase 8

    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
    • 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. Identification of an enhancer sequence within the first intron required for cartilage-specific transcription of the alpha2(XI) collagen gene. Liu Y, et al. J Biol Chem, 2000 Apr 28. PMID 10777565
    2. Mutation of COL11A2 causes autosomal recessive non-syndromic hearing loss at the DFNB53 locus. Chen W, et al. J Med Genet, 2005 Oct. PMID 16033917, Free PMC Article
    3. Targeted disruption of Col11a2 produces a mild cartilage phenotype in transgenic mice: comparison with the human disorder otospondylomegaepiphyseal dysplasia (OSMED). Li SW, et al. Dev Dyn, 2001 Oct. PMID 11668593
    4. Autosomal recessive disorder otospondylomegaepiphyseal dysplasia is associated with loss-of-function mutations in the COL11A2 gene. Melkoniemi M, et al. Am J Hum Genet, 2000 Feb. PMID 10677296, Free PMC Article
    5. Oto- spondylo-megaepiphyseal dysplasia (OSMED): clinical description of three patients homozygous for a missense mutation in the COL11A2 gene. van Steensel MA, et al. Am J Med Genet, 1997 Jun 13. PMID 9188673

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cartilage development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cartilage development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within chondrocyte differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in collagen fibril organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in osteoblast differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in roof of mouth development ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of sound IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in skeletal system development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within skeletal system morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in soft palate development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within tissue homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    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(XI) chain
    Names
    collagen alpha-2(XI) chain-like
    collagen, type XI, alpha 2
    procollagen, type XI, alpha 2
    type XI collagen alpha2 chain

    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_001401302.1 → NP_001388231.1  collagen alpha-2(XI) chain isoform 1 precursor

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A0A0G2K069
      Related
      ENSRNOP00000071327.2, ENSRNOT00000084117.3

    2. NM_212528.2 → NP_997693.1  collagen alpha-2(XI) chain isoform 2 precursor

      See identical proteins and their annotated locations for NP_997693.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000020
      UniProtKB/TrEMBL
      A6JJF6, Q6MGB2
      Conserved Domains (3) summary
      pfam01391
      Location:1187 → 1245
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:1421 → 1616
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:32 → 213
      TSPN; Thrombospondin N-terminal -like domains

    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_086038.1 Reference GRCr8

      Range
      4788829..4818492 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006255929.5 → XP_006255991.1  collagen alpha-2(XI) chain isoform X9

      UniProtKB/TrEMBL
      A6JJF6, F6T0B3
      Conserved Domains (3) summary
      pfam01391
      Location:1181 → 1240
      Collagen; Collagen triple helix repeat (20 copies)
      smart00038
      Location:1433 → 1628
      COLFI; Fibrillar collagens C-terminal domain
      smart00210
      Location:32 → 213
      TSPN; Thrombospondin N-terminal -like domains

    2. XM_039098500.2 → XP_038954428.2  collagen alpha-2(XI) chain isoform X5

    3. XM_039098499.2 → XP_038954427.2  collagen alpha-2(XI) chain isoform X2

    4. XM_017601585.3 → XP_017457074.1  collagen alpha-2(XI) chain isoform X8

      UniProtKB/TrEMBL
      A6JJF6
      Related
      ENSRNOP00000073041.2, ENSRNOT00000085547.3

    5. XM_017601584.3 → XP_017457073.1  collagen alpha-2(XI) chain isoform X7

      UniProtKB/TrEMBL
      A0A8I6A1U6

    6. XM_017601583.3 → XP_017457072.1  collagen alpha-2(XI) chain isoform X6

      UniProtKB/TrEMBL
      A0A8I5ZR92

    7. XM_017601581.3 → XP_017457070.1  collagen alpha-2(XI) chain isoform X3

      UniProtKB/TrEMBL
      A0A8I5ZM36
      Related
      ENSRNOP00000111025.1, ENSRNOT00000171964.1

    8. XM_017601582.3 → XP_017457071.1  collagen alpha-2(XI) chain isoform X4

      UniProtKB/TrEMBL
      A0A8I5ZR92

    9. XM_017601580.3 → XP_017457069.1  collagen alpha-2(XI) chain isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZM36

    10. XM_063279020.1 → XP_063135090.1  collagen alpha-2(XI) chain isoform X10

    RNA

    1. XR_005497184.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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