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    Col11a1 collagen type XI alpha 1 chain [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25654, updated on 30-Mar-2024

    Summary

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    Official Symbol
    Col11a1provided by RGD
    Official Full Name
    collagen type XI alpha 1 chainprovided by RGD
    Primary source
    RGD:2372
    See related
    Ensembl:ENSRNOG00000023148 AllianceGenome:RGD:2372
    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
    Enables heparan sulfate binding activity and heparin binding activity. Involved in ossification. Located in collagen-containing extracellular matrix. Human ortholog(s) of this gene implicated in Marshall syndrome; Stickler syndrome 2; autosomal dominant nonsyndromic deafness; and fibrochondrogenesis 1. Orthologous to human COL11A1 (collagen type XI alpha 1 chain). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Muscle (RPKM 88.0), Spleen (RPKM 40.5) and 8 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Col11a1 in Genome Data Viewer
    Location:
    2q42
    Exon count:
    69
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (204509136..204702264)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (201820715..202013853)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (216863423..217056523)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene ribosomal protein L5, pseudogene 7 Neighboring gene 39S ribosomal protein L30, mitochondrial-like Neighboring gene transfer RNA leucine (anticodon AAG) 14 Neighboring gene small nucleolar RNA SNORA18 Neighboring gene uncharacterized LOC134485952

    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. Isoform-specific heparan sulfate binding within the amino-terminal noncollagenous domain of collagen alpha1(XI). Warner LR, et al. J Biol Chem, 2006 Dec 22. PMID 17062562, Free PMC Article
    2. BMP-1-mediated proteolytic processing of alternatively spliced isoforms of collagen type XI. Medeck RJ, et al. Biochem J, 2003 Dec 1. PMID 12962540, Free PMC Article
    3. Marshall syndrome associated with a splicing defect at the COL11A1 locus. Griffith AJ, et al. Am J Hum Genet, 1998 Apr. PMID 9529347, Free PMC Article
    4. Alternative exon splicing within the amino-terminal nontriple-helical domain of the rat pro-alpha 1(XI) collagen chain generates multiple forms of the mRNA transcript which exhibit tissue-dependent variation. Oxford JT, et al. J Biol Chem, 1995 Apr 21. PMID 7721875
    5. Cis-acting elements regulate alternative splicing of exons 6A, 6B and 8 of the alpha1(XI) collagen gene and contribute to the regional diversification of collagen XI matrices. Chen Y, et al. Matrix Biol, 2001 Dec. PMID 11731275

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. giantin plays a pivotal role in coordinated production of aggrecan, link protein and type XI collagen in chondrocytes.
      Title: Giantin is required for coordinated production of aggrecan, link protein and type XI collagen during chondrogenesis.
    2. two additional binding sites located within the noncollagenous amino-terminal domain may play a role in the function of collagen type XI
      Title: Isoform-specific heparan sulfate binding within the amino-terminal noncollagenous domain of collagen alpha1(XI).
    3. Bone morphogenetic protein 1 generates alternatively spliced isoforms of the collagen type XI a1 chain.
      Title: BMP-1-mediated proteolytic processing of alternatively spliced isoforms of collagen type XI.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    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 
    enables extracellular matrix structural constituent conferring tensile strength IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables heparan sulfate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables heparin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables heparin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cartilage condensation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within cartilage development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within chondrocyte development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within collagen fibril organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in collagen fibril organization TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in detection of mechanical stimulus involved in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within embryonic skeletal system morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in endodermal cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within heart morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within inner ear morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in ossification IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within proteoglycan metabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in sensory perception of sound ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within skeletal system morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within tendon development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in visual perception ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of collagen type XI trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen type XI trimer ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular matrix ISO
    Inferred from Sequence Orthology
    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-1(XI) chain
    Names
    collagen type a1(XI)6A-7-8
    collagen type a1(XI)6B-7
    collagen, type XI, alpha 1
    procollagen type XI 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_013117.1 → NP_037249.1  collagen alpha-1(XI) chain precursor

      See identical proteins and their annotated locations for NP_037249.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000002
      UniProtKB/Swiss-Prot
      F1LSI4, P20909, Q62750, Q63391, Q63392, Q63393, Q8VBY8, Q920Z7, Q920Z8, Q920Z9, Q921A0, Q921A1
      UniProtKB/TrEMBL
      A6HV70
      Related
      ENSRNOP00000061595.1, ENSRNOT00000068413.4
      Conserved Domains (3) summary
      pfam01391
      Location:839 → 898
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:37 → 228
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1576 → 1802
      COLFI; Fibrillar collagen C-terminal domain

    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_086020.1 Reference GRCr8

      Range
      204509136..204702264
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006233210.5 → XP_006233272.1  collagen alpha-1(XI) chain isoform X2

      UniProtKB/TrEMBL
      A6HV70
      Conserved Domains (3) summary
      pfam01391
      Location:851 → 910
      Collagen; Collagen triple helix repeat (20 copies)
      smart00210
      Location:37 → 228
      TSPN; Thrombospondin N-terminal -like domains
      pfam01410
      Location:1588 → 1814
      COLFI; Fibrillar collagen C-terminal domain

    2. XM_063281374.1 → XP_063137444.1  collagen alpha-1(XI) chain isoform X1

    RNA

    1. XR_010063586.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P20909.2 GenPept UniProtKB/Swiss-Prot:P20909

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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