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

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

Summary

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
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Genomic context

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

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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_013117.1NP_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:839898
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15761802
    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_006233210.5XP_006233272.1  collagen alpha-1(XI) chain isoform X2

    UniProtKB/TrEMBL
    A6HV70
    Conserved Domains (3) summary
    pfam01391
    Location:851910
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:37228
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:15881814
    COLFI; Fibrillar collagen C-terminal domain
  2. XM_063281374.1XP_063137444.1  collagen alpha-1(XI) chain isoform X1

RNA

  1. XR_010063586.1 RNA Sequence