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

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: human all
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Genomic context

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_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Development of an exon skipping therapy for X-linked Alport syndrome with truncating variants in COL4A5.
Title: Development of an exon skipping therapy for X-linked Alport syndrome with truncating variants in COL4A5.
although alpha5 and alpha6 (IV) chains are induced in the glomerular basement membrane in autosomal recessive Alport syndrome, their induction does not seem to play a major compensatory role
Title: COL4A6 is dispensable for autosomal recessive Alport syndrome.
Findings indicate a role for collagen alpha-5(IV) chain (Col4a5) in the regulation of macrophage responses to mycobacterial infection and identify Col4a5 as a potential target for the host-directed anti-mycobacterial therapy.
Title: A potential target gene for the host-directed therapy of mycobacterial infection in murine macrophages.
alpha5(IV), but not alpha1(IV), promotes lung cancer cell proliferation and tumor angiogenesis through non-integrin collagen receptor DDR1-mediated ERK activation.
Title: Minor Type IV Collagen α5 Chain Promotes Cancer Progression through Discoidin Domain Receptor-1.
Report novel mouse model of Alport syndrome with accumulation abnormal collagen alpha3alpha4alpha5(IV) trimers in the glomerular basement membrane.
Title: A mouse Col4a4 mutation causing Alport glomerulosclerosis with abnormal collagen α3α4α5(IV) trimers.
In kidney, when expressed onto Col4a3(-/-) background, human alpha3(IV) chain restored expression of and co-assembled with mouse alpha4 and alpha5(IV) chains at sites where human alpha3(IV) was expressed. All three chains required for network assembly.
Title: A human-mouse chimera of the alpha3alpha4alpha5(IV) collagen protomer rescues the renal phenotype in Col4a3-/- Alport mice.
In murine embryos, collagen IV subunits alpha1(IV), alpha2(IV), alpha5(IV) and alpha6(IV) were detected in the basement membrane surrounding the lens vesicle, and they persisted in the capsule until adulthood.
Title: Collagen IV in the developing lens capsule.
Alpha3(IV), alpha4(IV), and alpha5(IV) chains form a complex, which is a heterotrimer, and a defect in complex formation might be one of the molecular mechanisms underlying the pathogenesis of Alport syndrome.
Title: Characterization of assembly of recombinant type IV collagen alpha3, alpha4, and alpha5 chains in transfected cell strains.
the proximal bifunctional promoter regulates the expression of the alpha5(IV) and alpha6(IV) genes in a cell-specific manner and demonstrates promoter plasticity in growth factor regulation of type IV collagen genes in different tissues of the body.
Title: Bifunctional promoter of type IV collagen COL4A5 and COL4A6 genes regulates the expression of alpha5 and alpha6 chains in a distinct cell-specific fashion.

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Variation

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Alleles

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

Targeted (4) 1 citation
Endonuclease-mediated (4) 1 citation

General gene information

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Markers

px-44h5 (e-PCR)
- UniSTS:257828

px-11_b12 (e-PCR)
- UniSTS:257254

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within collagen-activated tyrosine kinase receptor signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in extracellular matrix organization	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuromuscular junction development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in basement membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IV trimer	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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)

NM_001163155.1 → NP_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:1074 → 1132

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1579 → 1688

C4; C-terminal tandem repeated domain in type 4 procollagen
NM_001411947.1 → NP_001398876.1 collagen alpha-5(IV) chain isoform 2 precursor

Status: VALIDATED

Source sequence(s)

AL671856, AL713983, BX571779
NM_007736.4 → NP_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:1074 → 1132

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1579 → 1688

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

NC_000086.8 Reference GRCm39 C57BL/6J

Range

140258367..140472232

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (2) summary

pfam01391
Location:1074 → 1132

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1465 → 1571

C4; C-terminal tandem repeated domain in type 4 procollagen
XM_017318372.3 → XP_017173861.1 collagen alpha-5(IV) chain isoform X3

Conserved Domains (2) summary

pfam01391
Location:1059 → 1117

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1453 → 1559

C4; C-terminal tandem repeated domain in type 4 procollagen