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

Gene ID: 294279, updated on 13-Apr-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
Ensembl: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 be an extracellular matrix structural constituent. Involved in osteoblast differentiation. Predicted to be part of collagen trimer. Predicted to be active in 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, Apr 2022]
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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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
  
enables heparin binding 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, ENSRNOT00000084117.2

  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
    Related
    ENSRNOP00000073041.1, ENSRNOT00000085547.2
    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
    Related
    ENSRNOP00000048846.4
    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

  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

  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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