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Col5a1 collagen, type V, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 12831, updated on 7-Sep-2021

Summary

Official Symbol
Col5a1provided by MGI
Official Full Name
collagen, type V, alpha 1provided by MGI
Primary source
MGI:MGI:88457
See related
Ensembl:ENSMUSG00000026837
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
AI413331
Expression
Broad expression in limb E14.5 (RPKM 82.9), bladder adult (RPKM 28.4) and 15 other tissues See more
Orthologs
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Genomic context

See Col5a1 in Genome Data Viewer
Location:
2 A3; 2 19.38 cM
Exon count:
67
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (27776393..27929522)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (27886381..28039510)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (27741945..27895030)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene retinoid X receptor alpha Neighboring gene predicted gene, 39777 Neighboring gene predicted gene 13372 Neighboring gene RIKEN cDNA F730016J06 gene Neighboring gene ficolin B

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables extracellular matrix structural constituent IDA
Inferred from Direct Assay
more info
PubMed 
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
enables heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables heparin binding ISO
Inferred from Sequence Orthology
more info
 
enables platelet-derived growth factor binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables proteoglycan binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within blood vessel development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell adhesion ISO
Inferred from Sequence Orthology
more info
 
involved_in cell migration ISO
Inferred from Sequence Orthology
more info
 
involved_in collagen biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
acts_upstream_of_or_within collagen fibril organization IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in collagen fibril organization ISO
Inferred from Sequence Orthology
more info
 
involved_in extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in eye morphogenesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within heart morphogenesis IGI
Inferred from Genetic Interaction
more info
PubMed 
involved_in integrin biosynthetic process ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of endodermal cell differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of cellular component organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within skin development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in skin development ISO
Inferred from Sequence Orthology
more info
 
involved_in supramolecular fiber organization ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within tendon development IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within tendon development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in wound healing, spreading of epidermal cells ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in basement membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
part_of collagen trimer IMP
Inferred from Mutant Phenotype
more info
PubMed 
part_of collagen type V trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
part_of collagen type V trimer ISO
Inferred from Sequence Orthology
more info
 
located_in collagen-containing extracellular matrix HDA PubMed 
located_in collagen-containing extracellular matrix ISO
Inferred from Sequence Orthology
more info
 
is_active_in extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in extracellular matrix IDA
Inferred from Direct Assay
more info
PubMed 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in extracellular space HDA PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(V) chain
Names
alpha1(V) collagen
pro-alpha1(V) collagen
procollagen type V 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_015734.2NP_056549.2  collagen alpha-1(V) chain precursor

    See identical proteins and their annotated locations for NP_056549.2

    Status: VALIDATED

    Source sequence(s)
    AB009993, AK148055, AL731778, BP759660, BQ768928, BQ885116, BY713878
    Consensus CDS
    CCDS15831.1
    UniProtKB/Swiss-Prot
    O88207
    UniProtKB/TrEMBL
    B1AWB9
    Related
    ENSMUSP00000028280.8, ENSMUST00000028280.14
    Conserved Domains (3) summary
    pfam01391
    Location:871930
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:39230
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:16101836
    COLFI; Fibrillar collagen C-terminal domain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    27776393..27929522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006497644.5XP_006497707.1  collagen alpha-1(V) chain isoform X1

    Conserved Domains (3) summary
    pfam01391
    Location:871930
    Collagen; Collagen triple helix repeat (20 copies)
    smart00210
    Location:39230
    TSPN; Thrombospondin N-terminal -like domains
    pfam01410
    Location:16071836
    COLFI; Fibrillar collagen C-terminal domain
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