Col4a4 collagen, type IV, alpha 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Col4a4provided by MGI
Official Full Name: collagen, type IV, alpha 4provided by MGI
Primary source: MGI:MGI:104687
See related: Ensembl:ENSMUSG00000067158 AllianceGenome:MGI:104687
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: [a]4(IV); E130010M05Rik
Summary: An extracellular matrix structural constituent. Acts upstream of or within glomerular basement membrane development. Located in basement membrane. Part of collagen type IV trimer. Is expressed in glomerular tuft and testis. Used to study autosomal recessive Alport syndrome. Human ortholog(s) of this gene implicated in autosomal recessive Alport syndrome; benign familial hematuria; and end stage renal disease. Orthologous to human COL4A4 (collagen type IV alpha 4 chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in kidney adult (RPKM 12.0), lung adult (RPKM 10.4) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 C5; 1 42.2 cM

Exon count:: 50

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (82426140..82564570, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (82448419..82587034, complement)

Chromosome 1 - NC_000067.7 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?

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.
the NC1 domain of {alpha}3 chain is critical for {alpha}3{alpha}4{alpha}5 type IV collagen network assembly
Title: Identification of the NC1 domain of {alpha}3 chain as critical for {alpha}3{alpha}4{alpha}5 type IV collagen network assembly.
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.
Collagen alpha3(IV) nor alpha4(IV) were detected in the lens capsule 2 weeks postnatal.
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.

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Variation

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Alleles

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

Spontaneous (1) 1 citation
Gene trapped (1)
Chemically induced (ENU) (2) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

COL4A4 (e-PCR)
- UniSTS:262918

D1Mit44 (e-PCR), detects polymorphism
- UniSTS:128808

D1S3696 (e-PCR)
- UniSTS:474274

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent	IPI Inferred from Physical Interaction more info	PubMed
enables extracellular matrix structural constituent	ISO Inferred from Sequence Orthology more info
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
enables molecular adaptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in glomerular basement membrane development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within glomerular basement membrane development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in glomerular basement membrane development	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in basement membrane	ISO Inferred from Sequence Orthology more info
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
part_of collagen type IV trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type IV trimer	IDA Inferred from Direct Assay more info	PubMed
part_of collagen type IV trimer	ISO Inferred from Sequence Orthology more info
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-4(IV) chain

Names: procollagen, type IV, alpha 4

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_007735.2 → NP_031761.1 collagen alpha-4(IV) chain precursor

See identical proteins and their annotated locations for NP_031761.1

Status: VALIDATED

Source sequence(s)

AC160543, AF169388, AK164732

Consensus CDS

CCDS35630.1

UniProtKB/Swiss-Prot

Q149M2, Q64457, Q9QZR9

Related

ENSMUSP00000084282.6, ENSMUST00000087050.7

Conserved Domains (2) summary

pfam01391
Location:54 → 111

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1458 → 1562

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_000067.7 Reference GRCm39 C57BL/6J

Range

82426140..82564570 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011238652.1 → XP_011236954.1 collagen alpha-4(IV) chain isoform X1

Conserved Domains (2) summary

pfam01391
Location:792 → 851

Collagen; Collagen triple helix repeat (20 copies)

pfam01413
Location:1361 → 1465

C4; C-terminal tandem repeated domain in type 4 procollagen
XM_011238653.4 → XP_011236955.1 collagen alpha-4(IV) chain isoform X2

Conserved Domains (1) summary

pfam01391
Location:54 → 111

Collagen; Collagen triple helix repeat (20 copies)