Col4a4 MGI Mouse Gene Detail - MGI:104687 - collagen, type IV, alpha 4

Symbol

Col4a4
Name

collagen, type IV, alpha 4
Synonyms

[a]4(IV), E130010M05Rik

Feature Type

protein coding gene
IDs

MGI:104687
NCBI Gene: 12829
Alliance

gene page
Transcription Start Sites

11 TSS

Sequence Map

Chr1:82426144-82564570 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 42.20 cM
Mapping Data

3 experiments

SNPs within 2kb

3936 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104687	protein coding gene	Chr1:82426140-82564570 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0016216	protein coding gene	Chr1:83363851-83499024 (-)
A/J	MGP_AJ_G0016199	protein coding gene	Chr1:80393295-80534418 (-)
AKR/J	MGP_AKRJ_G0016156	protein coding gene	Chr1:82580036-82720969 (-)
BALB/cJ	MGP_BALBcJ_G0016154	protein coding gene	Chr1:80473789-80604062 (-)
C3H/HeJ	MGP_C3HHeJ_G0015984	protein coding gene	Chr1:82966464-83114992 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0016607	protein coding gene	Chr1:86566252-86718695 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014327	protein coding gene	Chr1:75638461-75764860 (-)
CAST/EiJ	MGP_CASTEiJ_G0015570	protein coding gene	Chr1:82387039-82522462 (-)
CBA/J	MGP_CBAJ_G0015958	protein coding gene	Chr1:89335541-89493093 (-)
DBA/2J	MGP_DBA2J_G0016059	protein coding gene	Chr1:79694652-79827395 (-)
FVB/NJ	MGP_FVBNJ_G0016062	protein coding gene	Chr1:78798243-78923331 (-)
LP/J	MGP_LPJ_G0016132	protein coding gene	Chr1:84486871-84620736 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016082	protein coding gene	Chr1:92746012-92900179 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016654	protein coding gene	Chr1:82764804-82898263 (-)
PWK/PhJ	MGP_PWKPhJ_G0015355	protein coding gene	Chr1:79131632-79261552 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0015133	protein coding gene	Chr1:81969091-82096253 (-)
WSB/EiJ	MGP_WSBEiJ_G0015630	protein coding gene	Chr1:82542271-82691630 (-)

Human Ortholog

COL4A4, collagen type IV alpha 4 chain

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL4A4, collagen type IV alpha 4 chain
Synonyms

ATS2, BFH, BFH1, CA44
Links

HGNC:2206

NCBI Gene ID: 1286

neXtProt AC: NX_P53420

UniProt: P53420
Chr Location

2q36.3; chr2:226967360-227164488 (-) GRCh38

MGI Vertebrate Homology

Col4a4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: COL4A4
Gene Tree

Col4a4

Diseases

1 with Col4a4 mouse models; 3 with human COL4A4 associations

Human Disease

Mouse Models

autosomal recessive Alport syndrome

IDs

View 5 models

benign familial hematuria

IDs

end stage renal disease

IDs

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

3 with disease annotations

References

4 with disease annotations

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Phenotype Summary

46 phenotypes from 4 alleles in 7 genetic backgrounds
14 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

9
Chemically induced (ENU)

2
Chemically induced (other)

1
Endonuclease-mediated

3
Gene trapped

1
Radiation induced

1
Spontaneous

1
Genomic Mutations

2 involving Col4a4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

105 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for an ENU-induced mutation develop an early nephritic syndrome associated with uremia, proteinuria, hematuria, leukocyturia, and focal segmental glomerulosclerosis, and die prematurely of kidney failure. Some homozygotes exhibit moderatesensorineural hearing loss.

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All GO Annotations

18
GO References

11

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

722
Tissues

8
cDNA Data

9
Literature Summary

24

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

ZFIN col4a4

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All Sequences

43
RefSeq

6
UniProt

3
CCDS

CCDS35630.1

Ensembl

ENSMUSG00000067158 (Evidence)
NCBI Gene

12829

			Length	Strain/Species	Flank
genomic	ENSMUSG00000067158	Ensembl Gene Model \| MGI Sequence Detail	138427	C57BL/6J	± kb
transcript	ENSMUST00000087050	Ensembl \| MGI Sequence Detail	10108	Not Applicable
polypeptide	ENSMUSP00000084282	Ensembl \| MGI Sequence Detail	1682	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000003337 collagen alpha-4(IV) chain

(term hierarchy)
InterPro Domains

IPR001442 Collagen IV, non-collagenous

IPR036954 Collagen IV, non-collagenous domain superfamily

IPR050149 Collagen superfamily

IPR008160 Collagen triple helix repeat

IPR016187 C-type lectin fold
GlyGen

Q9QZR9 3 sites

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All nucleic 12

Genomic 1

cDNA 9

Primer pair 1

Other 1

Microarray probesets 5

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MGD-MRK-27050, MGI:2442835

Summaries

All 79

Developmental Gene Expression 24

Diseases 4

Gene Ontology 11

Phenotypes 14
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Col4a4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr12521	Chr1:82564778-82564800 (-)	-219 bp
Tssr12520	Chr1:82564755-82564776 (-)	-196 bp
Tssr12519	Chr1:82564577-82564584 (-)	-11 bp
Tssr12518	Chr1:82564502-82564563 (-)	37 bp
Tssr12517	Chr1:82564481-82564500 (-)	79 bp
Tssr12516	Chr1:82564468-82564479 (-)	96 bp
Tssr12515	Chr1:82484249-82484275 (-)	80,308 bp
Tssr12514	Chr1:82460455-82460457 (-)	104,114 bp
Tssr12513	Chr1:82455885-82455897 (-)	108,679 bp
Tssr12512	Chr1:82455812-82455817 (-)	108,755 bp
Tssr132	Chr1:82430333-82430337 (-)	134,235 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/19/2024 MGI 6.24