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COL2A1 collagen type II alpha 1 chain [ Bos taurus (cattle) ]

Gene ID: 407142, updated on 25-May-2017
Gene symbol
COL2A1
Gene description
collagen type II alpha 1 chain
See related
Ensembl:ENSBTAG00000013155
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Bos taurus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Laurasiatheria; Cetartiodactyla; Ruminantia; Pecora; Bovidae; Bovinae; Bos
Also known as
CB11
Orthologs
Location:
chromosome: 5
Exon count:
54
Annotation release Status Assembly Chr Location
105 current Bos_taurus_UMD_3.1.1 (GCF_000003055.6) 5 AC_000162.1 (32450453..32481246)

Chromosome 5 - AC_000162.1Genomic Context describing neighboring genes Neighboring gene phosphofructokinase, muscle Neighboring gene SUMO1/sentrin specific peptidase 1 Neighboring gene transmembrane protein 106C Neighboring gene 60S ribosomal protein L22-like 1 Neighboring gene vitamin D receptor

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • Assembly of collagen fibrils and other multimeric structures, organism-specific biosystem (from REACTOME)
    Assembly of collagen fibrils and other multimeric structures, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • ECM-receptor interaction, organism-specific biosystem (from KEGG)
    ECM-receptor interaction, organism-specific biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • ECM-receptor interaction, conserved biosystem (from KEGG)
    ECM-receptor interaction, conserved biosystemThe extracellular matrix (ECM) consists of a complex mixture of structural and functional macromolecules and serves an important role in tissue and organ morphogenesis and in the maintenance of cell ...
  • Endochondral Ossification, organism-specific biosystem (from WikiPathways)
    Endochondral Ossification, organism-specific biosystemEndochondral ossification is the process by which the embryonic cartilaginous model of most bones contributes to longitudinal growth and is gradually replaced by bone. During endochondral ossificatio...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemcomputationally inferred pathway (not manually curated)
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Neural Crest Differentiation, organism-specific biosystem (from WikiPathways)
    Neural Crest Differentiation, organism-specific biosystemGene regulatory network model of cranial neural crest cell (CNCC) development, adaped from PMID: 19575671. Most interactions in the model are proposed to regulate transcription of core factors involv...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Protein digestion and absorption, organism-specific biosystem (from KEGG)
    Protein digestion and absorption, organism-specific biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Protein digestion and absorption, conserved biosystem (from KEGG)
    Protein digestion and absorption, conserved biosystemProtein is a dietary component essential for nutritional homeostasis in humans. Normally, ingested protein undergoes a complex series of degradative processes following the action of gastric, pancrea...
  • Spinal Cord Injury, organism-specific biosystem (from WikiPathways)
    Spinal Cord Injury, organism-specific biosystemThis pathway provides an overview of cell types, therapeutic targets, drugs, new proposed targets and pathways implicated in spinal cord injury. Spinal cord injury is a complex multistep process that...

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
MHC class II protein binding IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix structural constituent IEA
Inferred from Electronic Annotation
more info
 
identical protein binding IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cartilage condensation IEA
Inferred from Electronic Annotation
more info
 
cartilage development involved in endochondral bone morphogenesis IEA
Inferred from Electronic Annotation
more info
 
cellular response to BMP stimulus IEA
Inferred from Electronic Annotation
more info
 
central nervous system development IEA
Inferred from Electronic Annotation
more info
 
chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
collagen fibril organization IEA
Inferred from Electronic Annotation
more info
 
embryonic skeletal joint morphogenesis IEA
Inferred from Electronic Annotation
more info
 
endochondral ossification IEA
Inferred from Electronic Annotation
more info
 
extracellular matrix organization TAS
Traceable Author Statement
more info
 
heart morphogenesis IEA
Inferred from Electronic Annotation
more info
 
inner ear morphogenesis IEA
Inferred from Electronic Annotation
more info
 
limb bud formation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand IEA
Inferred from Electronic Annotation
more info
 
notochord development IEA
Inferred from Electronic Annotation
more info
 
otic vesicle development IEA
Inferred from Electronic Annotation
more info
 
palate development IEA
Inferred from Electronic Annotation
more info
 
proteoglycan metabolic process IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression IEA
Inferred from Electronic Annotation
more info
 
sensory perception of sound IEA
Inferred from Electronic Annotation
more info
 
tissue homeostasis IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
more info
 
collagen type II trimer IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
collagen alpha-1(II) chain
Names
alpha-1 type II collagen
collagen, type II, alpha 1
pro-alpha 1(II)

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_001001135.3NP_001001135.2  collagen alpha-1(II) chain isoform 1 preproprotein

    See identical proteins and their annotated locations for NP_001001135.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
    Source sequence(s)
    DAAA02012985, DAAA02012986
    UniProtKB/Swiss-Prot
    P02459
    Related
    ENSBTAP00000017505.5, ENSBTAT00000017505.5
    Conserved Domains (3) summary
    pfam01391
    Location:801860
    Collagen; Collagen triple helix repeat (20 copies)
    pfam00093
    Location:3489
    VWC; von Willebrand factor type C domain
    pfam01410
    Location:12541486
    COLFI; Fibrillar collagen C-terminal domain
  2. NM_001113224.2NP_001106695.1  collagen alpha-1(II) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_001106695.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in a shorter protein. The resulting protein (isoform 2) lacks the von Willebrand factor type C (VWC) domain, compared to isoform 1. This isoform (2) may undergo proteolytic processing similar to isoform 1.
    Source sequence(s)
    DAAA02012985, DAAA02012986
    UniProtKB/TrEMBL
    F1MSR8
    Related
    ENSBTAP00000017509.5, ENSBTAT00000017509.5
    Conserved Domains (2) summary
    pfam01391
    Location:732791
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01410
    Location:11851417
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Bos taurus Annotation Release 105 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference Bos_taurus_UMD_3.1.1 Primary Assembly

Genomic

  1. AC_000162.1 Reference Bos_taurus_UMD_3.1.1 Primary Assembly

    Range
    32450453..32481246
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate Btau_5.0.1

Genomic

  1. NC_007303.6 Alternate Btau_5.0.1

    Range
    32520273..32551066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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