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Col4a5 collagen, type IV, alpha 5 [ Mus musculus (house mouse) ]

Gene ID: 12830, updated on 5-Mar-2024

Summary

Official Symbol
Col4a5provided by MGI
Official Full Name
collagen, type IV, alpha 5provided by MGI
Primary source
MGI:MGI:88456
See related
Ensembl:ENSMUSG00000031274 AllianceGenome:MGI:88456
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
Summary
Predicted to be an extracellular matrix structural constituent. Acts upstream of or within collagen-activated tyrosine kinase receptor signaling pathway and neuromuscular junction development. Located in basement membrane and neuromuscular junction. Part of collagen type IV trimer. Is expressed in several structures, including alimentary system; brain; extraembryonic component; genitourinary system; and spinal cord. Used to study X-linked Alport syndrome. Human ortholog(s) of this gene implicated in Alport syndrome and X-linked Alport syndrome. Orthologous to human COL4A5 (collagen type IV alpha 5 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in bladder adult (RPKM 17.4), lung adult (RPKM 8.1) and 15 other tissues See more
Orthologs
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Genomic context

See Col4a5 in Genome Data Viewer
Location:
X F2; X 62.16 cM
Exon count:
53
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (140258367..140472232)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (141475370..141689236)

Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene collagen, type IV, alpha 6 Neighboring gene predicted gene, 39539 Neighboring gene STARR-seq mESC enhancer starr_48012 Neighboring gene prohibitin pseudogene Neighboring gene STARR-seq mESC enhancer starr_48013 Neighboring gene predicted gene 15295 Neighboring gene STARR-seq mESC enhancer starr_48014 Neighboring gene insulin receptor substrate 4 Neighboring gene STARR-seq mESC enhancer starr_48015 Neighboring gene high-mobility group nucleosomal binding domain 2-like 6

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

General protein information

Preferred Names
collagen alpha-5(IV) chain
Names
collagen type IV alpha5 chain
procollagen type IV alpha 5

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_001163155.1NP_001156627.1  collagen alpha-5(IV) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_001156627.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Both variants encode the same protein.
    Source sequence(s)
    AK133179, AL713983, BX571779, CN668672
    Consensus CDS
    CCDS41154.1
    UniProtKB/TrEMBL
    Q63ZW6
    Related
    ENSMUSP00000108553.2, ENSMUST00000112931.8
    Conserved Domains (2) summary
    pfam01391
    Location:10741132
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15791688
    C4; C-terminal tandem repeated domain in type 4 procollagen
  2. NM_001411947.1NP_001398876.1  collagen alpha-5(IV) chain isoform 2 precursor

    Status: VALIDATED

    Source sequence(s)
    AL671856, AL713983, BX571779
  3. NM_007736.4NP_031762.2  collagen alpha-5(IV) chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_031762.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants encode the same protein.
    Source sequence(s)
    AK133179, BX571779
    Consensus CDS
    CCDS41154.1
    UniProtKB/TrEMBL
    Q63ZW6
    Related
    ENSMUSP00000108552.2, ENSMUST00000112930.8
    Conserved Domains (2) summary
    pfam01391
    Location:10741132
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:15791688
    C4; C-terminal tandem repeated domain in type 4 procollagen

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000086.8 Reference GRCm39 C57BL/6J

    Range
    140258367..140472232
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006528696.4XP_006528759.1  collagen alpha-5(IV) chain isoform X1

    Conserved Domains (2) summary
    pfam01391
    Location:10741132
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14651571
    C4; C-terminal tandem repeated domain in type 4 procollagen
  2. XM_017318372.3XP_017173861.1  collagen alpha-5(IV) chain isoform X3

    Conserved Domains (2) summary
    pfam01391
    Location:10591117
    Collagen; Collagen triple helix repeat (20 copies)
    pfam01413
    Location:14531559
    C4; C-terminal tandem repeated domain in type 4 procollagen