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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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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

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