Col3a1 MGI Mouse Gene Detail - MGI:88453 - collagen, type III, alpha 1

Symbol

Col3a1
Name

collagen, type III, alpha 1
Synonyms

Col3a-1, Tsk2, Tsk-2

Feature Type

protein coding gene
IDs

MGI:88453
NCBI Gene: 12825
Alliance

gene page
Transcription Start Sites

25 TSS

Sequence Map

Chr1:45350698-45388866 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 23.67 cM
Mapping Data

22 experiments

SNPs within 2kb

259 from dbSNP Build 142
Strain Annotations

18
RFLP

4

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88453	protein coding gene	Chr1:45350698-45388866 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0015992	protein coding gene	Chr1:44333129-44385724 (+)
A/J	MGP_AJ_G0015976	protein coding gene	Chr1:42989212-43028390 (+)
AKR/J	MGP_AKRJ_G0015931	protein coding gene	Chr1:43616218-43654556 (+)
BALB/cJ	MGP_BALBcJ_G0015930	protein coding gene	Chr1:42615031-42654925 (+)
C3H/HeJ	MGP_C3HHeJ_G0015763	protein coding gene	Chr1:44003501-44047978 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0016383	protein coding gene	Chr1:46187689-46232092 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014105	protein coding gene	Chr1:39696683-39734592 (+)
CAST/EiJ	MGP_CASTEiJ_G0015344	protein coding gene	Chr1:43908867-43949888 (+)
CBA/J	MGP_CBAJ_G0015735	protein coding gene	Chr1:47507405-47545210 (+)
DBA/2J	MGP_DBA2J_G0015836	protein coding gene	Chr1:42283954-42325802 (+)
FVB/NJ	MGP_FVBNJ_G0015838	protein coding gene	Chr1:41737556-41776245 (+)
LP/J	MGP_LPJ_G0015906	protein coding gene	Chr1:44695917-44738653 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0015858	protein coding gene	Chr1:49605000-49649957 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016430	protein coding gene	Chr1:43800838-43841544 (+)
PWK/PhJ	MGP_PWKPhJ_G0015127	protein coding gene	Chr1:42076556-42116865 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0014909	protein coding gene	Chr1:43823651-43867767 (+)
WSB/EiJ	MGP_WSBEiJ_G0015406	protein coding gene	Chr1:43782459-43830108 (+)

Human Ortholog

COL3A1, collagen type III alpha 1 chain

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL3A1, collagen type III alpha 1 chain
Synonyms

EDS4A, EDSVASC, PMGEDSV
Links

HGNC:2201

NCBI Gene ID: 1281

neXtProt AC: NX_P02461

UniProt: P02461
Chr Location

2q32.2; chr2:188974373-189012746 (+) GRCh38

MGI Vertebrate Homology

Col3a1 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: COL3A1
Gene Tree

Col3a1

Diseases

2 with Col3a1 mouse models; 4 with human COL3A1 associations

Human Disease

Mouse Models

vascular type Ehlers-Danlos syndrome

IDs

View 2 models

systemic scleroderma

IDs

View 1 model

Ehlers-Danlos syndrome

IDs

Ehlers-Danlos syndrome hypermobility type

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

3 with disease annotations

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Phenotype Summary

32 phenotypes from 4 alleles in 6 genetic backgrounds
3 images
28 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

13
Chemically induced (ENU)

2
Chemically induced (other)

1
Endonuclease-mediated

5
Spontaneous

1
Targeted

4
Genomic Mutations

1 involving Col3a1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

85 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Most homozygous mutants die within 48 hours after birth. Surviving mutants have reduced body size, skin lesions, enlarged intestines, and die by 6 months of age from ruptured blood vessels. Occasionally intestinal rupture also results in early death. Heterozygotes exhibit tight skin.

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All GO Annotations

80
GO References

29

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	non-membrane-bounded 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

1219
Tissues

245
cDNA Data

1140
Literature Summary

120

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase col3a1

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All Sequences

77
RefSeq

2
UniProt

14
CCDS

CCDS35554.1

Ensembl

ENSMUSG00000026043 (Evidence)
NCBI Gene

12825

			Length	Strain/Species	Flank
genomic	12825	NCBI Gene Model \| MGI Sequence Detail	38169	C57BL/6J	± kb
transcript	NM_009930	RefSeq \| MGI Sequence Detail	5564	ZRU/MplStud
polypeptide	P08121	UniProt \| EBI \| MGI Sequence Detail	1464	Not Applicable

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UniProt

14 Sequences
Protein Ontology

PR:000003328 collagen alpha-1(III) chain

(term hierarchy)
InterPro Domains

IPR008160 Collagen triple helix repeat

IPR000885 Fibrillar collagen, C-terminal

IPR001007 VWFC domain

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All nucleic 1156

Genomic 6

cDNA 1141

Primer pair 8

Other 1

Microarray probesets 3

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MGD-MRK-15277, MGD-MRK-15278, MGD-MRK-2064, MGD-MRK-2065, MGI:2138608, MGI:98851

Summaries

All 218

Developmental Gene Expression 120

Diseases 3

Gene Ontology 29

Phenotypes 28
Earliest

J:20241 Liau G, et al., Coordinate regulation of the levels of type III and type I collagen mRNA in most but not all mouse fibroblasts. J Biol Chem. 1985 Jan 10;260(1):531-6
Latest

J:343286 Queen R, et al., Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves. PLoS Genet. 2023 Nov;19(11):e1010777

TSS for Col3a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr6578	Chr1:45360749-45360801 (+)	10,077 bp
Tssr6579	Chr1:45369711-45369731 (+)	19,023 bp
Tssr6580	Chr1:45371290-45371302 (+)	20,598 bp
Tssr6581	Chr1:45371319-45371344 (+)	20,634 bp
Tssr6582	Chr1:45372120-45372156 (+)	21,440 bp
Tssr6583	Chr1:45372764-45372778 (+)	22,073 bp
Tssr6584	Chr1:45376454-45376474 (+)	25,766 bp
Tssr6585	Chr1:45376577-45376599 (+)	25,890 bp
Tssr6586	Chr1:45377866-45377900 (+)	27,185 bp
Tssr6587	Chr1:45385001-45385015 (+)	34,310 bp
Tssr6588	Chr1:45385016-45385088 (+)	34,354 bp
Tssr6589	Chr1:45385103-45385145 (+)	34,426 bp
Tssr6590	Chr1:45385197-45385218 (+)	34,510 bp
Tssr6591	Chr1:45386348-45386387 (+)	35,670 bp
Tssr6592	Chr1:45386792-45386854 (+)	36,125 bp
Tssr6593	Chr1:45386862-45386924 (+)	36,195 bp
Tssr6594	Chr1:45386929-45386947 (+)	36,240 bp
Tssr6595	Chr1:45387767-45387784 (+)	37,078 bp
Tssr6596	Chr1:45387790-45387825 (+)	37,110 bp
Tssr6597	Chr1:45387875-45387916 (+)	37,198 bp
Tssr6598	Chr1:45387944-45387989 (+)	37,269 bp
Tssr6599	Chr1:45388051-45388096 (+)	37,376 bp
Tssr6600	Chr1:45388110-45388121 (+)	37,418 bp
Tssr6601	Chr1:45388124-45388156 (+)	37,442 bp
Tssr72	Chr1:45388759-45388762 (+)	38,063 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)
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