Col5a1 MGI Mouse Gene Detail - MGI:88457 - collagen, type V, alpha 1

Symbol

Col5a1
Name

collagen, type V, alpha 1

Feature Type

protein coding gene
IDs

MGI:88457
NCBI Gene: 12831
Alliance

gene page
Transcription Start Sites

14 TSS

Sequence Map

Chr2:27776437-27929526 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 19.38 cM, cytoband A2-B
Mapping Data

13 experiments

SNPs within 2kb

4839 from dbSNP Build 142
Strain Annotations

18
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88457	protein coding gene	Chr2:27776393-27929526 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0025517	protein coding gene	Chr2:25889486-26049391 (+)
A/J	MGP_AJ_G0025494	protein coding gene	Chr2:24934317-25088036 (+)
AKR/J	MGP_AKRJ_G0025464	protein coding gene	Chr2:25763267-25918294 (+)
BALB/cJ	MGP_BALBcJ_G0025490	protein coding gene	Chr2:25051203-25206766 (+)
C3H/HeJ	MGP_C3HHeJ_G0025251	protein coding gene	Chr2:25671115-25827264 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025934	protein coding gene	Chr2:26784873-26949071 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023345	protein coding gene	Chr2:23736295-23890003 (+)
CAST/EiJ	MGP_CASTEiJ_G0024714	protein coding gene	Chr2:25568599-25729162 (+)
CBA/J	MGP_CBAJ_G0025229	protein coding gene	Chr2:27699222-27870670 (+)
DBA/2J	MGP_DBA2J_G0025362	protein coding gene	Chr2:24746605-24899684 (+)
FVB/NJ	MGP_FVBNJ_G0025324	protein coding gene	Chr2:24511582-24672839 (+)
LP/J	MGP_LPJ_G0025448	protein coding gene	Chr2:25849331-26009252 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025355	protein coding gene	Chr2:27710628-27876004 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025993	protein coding gene	Chr2:25665157-25823379 (+)
PWK/PhJ	MGP_PWKPhJ_G0024462	protein coding gene	Chr2:24537698-24692880 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0024262	protein coding gene	Chr2:25824666-25984369 (+)
WSB/EiJ	MGP_WSBEiJ_G0024783	protein coding gene	Chr2:25805504-25960797 (+)

Human Ortholog

COL5A1, collagen type V alpha 1 chain

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL5A1, collagen type V alpha 1 chain
Synonyms

EDSC, EDSCL1, FMDMF
Links

HGNC:2209

NCBI Gene ID: 1289

neXtProt AC: NX_P20908

UniProt: P20908
Chr Location

9q34.3; chr9:134641803-134844843 (+) GRCh38

MGI Vertebrate Homology

Col5a1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: COL5A1
Gene Tree

Col5a1

Diseases

1 with Col5a1 mouse models; 2 with human COL5A1 associations

Human Disease

Mouse Models

Ehlers-Danlos syndrome classic type 1

IDs

View 3 models

Ehlers-Danlos syndrome

IDs

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

Mutations/Alleles

2 with disease annotations

References

3 with disease annotations

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Phenotype Summary

19 phenotypes from 3 alleles in 5 genetic backgrounds
8 images
18 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

7
Endonuclease-mediated

2
Gene trapped

1
Targeted

4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

66 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutation of this gene results in lethality around E10-11 due to cardiovascular insufficiency and lack of collagen fibril formation. Heterozygotes exhibit poorly organized and less dense fibers in the dermis and reduced skin tensile strength and are a model for Ehlers-Danlos Syndrome.

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All GO Annotations

51
GO References

16

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

886
Tissues

116
cDNA Data

178
Literature Summary

44

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA COL5A1

Xenbase col5a1

ZFIN col5a1

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All Sequences

47
RefSeq

4
UniProt

4
CCDS

CCDS15831.1

Ensembl

ENSMUSG00000026837 (Evidence)
NCBI Gene

12831

			Length	Strain/Species	Flank
genomic	ENSMUSG00000026837	Ensembl Gene Model \| MGI Sequence Detail	153090	C57BL/6J	± kb
transcript	ENSMUST00000028280	Ensembl \| MGI Sequence Detail	8406	Not Applicable
polypeptide	ENSMUSP00000028280	Ensembl \| MGI Sequence Detail	1838	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000003345 collagen alpha-1(V) chain

(term hierarchy)
InterPro Domains

IPR050149 Collagen superfamily

IPR008160 Collagen triple helix repeat

IPR013320 Concanavalin A-like lectin/glucanase domain superfamily

IPR000885 Fibrillar collagen, C-terminal

IPR001791 Laminin G domain

IPR048287 Thrombospondin-like, N-terminal domain
GlyGen

O88207 3 sites, 2 N-linked glycans (3 sites)

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All nucleic 193

cDNA 179

Primer pair 10

Other 4

Microarray probesets 5

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MGD-MRK-2071, MGI:2138923

Summaries

All 107

Developmental Gene Expression 44

Diseases 3

Gene Ontology 16

Phenotypes 18
Earliest

J:12787 Mattei MG, et al., Mouse alpha 1 type V collagen gene maps to the [A2-B] region of chromosome 2. Genomics. 1993 Jun;16(3):786-8
Latest

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

TSS for Col5a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr16881	Chr2:27776017-27776059 (+)	-399 bp
Tssr16882	Chr2:27776396-27776407 (+)	-35 bp
Tssr16883	Chr2:27776428-27776452 (+)	3 bp
Tssr16884	Chr2:27776456-27776473 (+)	28 bp
Tssr16885	Chr2:27776491-27776505 (+)	61 bp
Tssr16886	Chr2:27785303-27785314 (+)	8,872 bp
Tssr16887	Chr2:27801901-27801904 (+)	25,466 bp
Tssr446	Chr2:27840646-27840663 (+)	64,218 bp
Tssr16888	Chr2:27841295-27841323 (+)	64,872 bp
Tssr16889	Chr2:27841377-27841391 (+)	64,947 bp
Tssr16890	Chr2:27891967-27892001 (+)	115,547 bp
Tssr16891	Chr2:27922067-27922085 (+)	145,639 bp
Tssr16892	Chr2:27922099-27922110 (+)	145,668 bp
Tssr16893	Chr2:27922782-27922805 (+)	146,357 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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