Col25a1 MGI Mouse Gene Detail - MGI:1924268 - collagen, type XXV, alpha 1

Symbol

Col25a1
Name

collagen, type XXV, alpha 1
Synonyms

2700062B08Rik

Feature Type

protein coding gene
IDs

MGI:1924268
NCBI Gene: 77018
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr3:129973992-130393533 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 59.99 cM, cytoband H1
Mapping Data

2 experiments

SNPs within 2kb

12397 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924268	protein coding gene	Chr3:129925150-130393533 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027880	protein coding gene	Chr3:132853330-133335576 (+)
A/J	MGP_AJ_G0027838	protein coding gene	Chr3:128203950-128673160 (+)
AKR/J	MGP_AKRJ_G0027803	protein coding gene	Chr3:131529564-132007672 (+)
BALB/cJ	MGP_BALBcJ_G0027851	protein coding gene	Chr3:128055484-128520742 (+)
C3H/HeJ	MGP_C3HHeJ_G0027580	protein coding gene	Chr3:131929837-132407595 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028295	protein coding gene	Chr3:137577311-138073324 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025633	protein coding gene	Chr3:123733727-124196228 (+)
CAST/EiJ	MGP_CASTEiJ_G0027037	protein coding gene	Chr3:131624418-132122621 (+)
CBA/J	MGP_CBAJ_G0027556	protein coding gene	Chr3:142205219-142712056 (+)
DBA/2J	MGP_DBA2J_G0027697	protein coding gene	Chr3:127398672-127870938 (+)
FVB/NJ	MGP_FVBNJ_G0027664	protein coding gene	Chr3:124990176-125450693 (+)
LP/J	MGP_LPJ_G0027806	protein coding gene	Chr3:134347828-134824192 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027695	protein coding gene	Chr3:150166974-150659592 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028352	protein coding gene	Chr3:131193218-131678290 (+)
PWK/PhJ	MGP_PWKPhJ_G0026761	protein coding gene	Chr3:127137086-127605878 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026586	protein coding gene	Chr3:129265905-129736895 (+)
WSB/EiJ	MGP_WSBEiJ_G0027116	protein coding gene	Chr3:131922650-132409946 (+)

Human Ortholog

COL25A1, collagen type XXV alpha 1 chain

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL25A1, collagen type XXV alpha 1 chain
Synonyms

AMY, CFEOM5, CLAC, CLAC-P, CLACP
Links

HGNC:18603

NCBI Gene ID: 84570

neXtProt AC: NX_Q9BXS0

UniProt: Q9BXS0
Chr Location

4q25; chr4:108808725-109302752 (-) GRCh38

MGI Vertebrate Homology

Col25a1 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: COL25A1
Gene Tree

Col25a1

Diseases

1 with human COL25A1 associations

				Human Disease	Mouse Models
				congenital fibrosis of the extraocular muscles 5 IDs congenital fibrosis of the extraocular muscles 5 DOID:0081020 OMIM:616219

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

References

1 with disease annotations

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Phenotype Summary

13 phenotypes from 1 allele in 2 genetic backgrounds
2 phenotypes from multigenic genotypes
6 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

5
Chemically induced (other)

1
Endonuclease-mediated

2
Radiation induced

1
Targeted

1
Genomic Mutations

2 involving Col25a1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

46 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit neonatal lethality, cyanosis and abnormal body curvature with apoptosis of phrenic nerve motor neurons and failure of diaphragm innervation.

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All GO Annotations

14
GO References

7

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

732
Tissues

12
cDNA Data

9
Literature Summary

7

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase col25a1.2

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All Sequences

111
RefSeq

64
UniProt

6
CCDS

CCDS38636.1, CCDS38637.1

Ensembl

ENSMUSG00000058897 (Evidence)
NCBI Gene

77018

			Length	Strain/Species	Flank
genomic	77018	NCBI Gene Model \| MGI Sequence Detail	419542	C57BL/6J	± kb
transcript	NM_029838	RefSeq \| MGI Sequence Detail	7421	C57BL/6
polypeptide	Q99MQ5	UniProt \| EBI \| MGI Sequence Detail	666	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000005709 collagen alpha-1(XXV) chain

(term hierarchy)
InterPro Domains

IPR050938 Collagen and Collagen-like Structural Proteins

IPR008160 Collagen triple helix repeat

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All nucleic 13

cDNA 9

Primer pair 1

Other 3

Microarray probesets 4

Summaries

All 36

Developmental Gene Expression 7

Diseases 1

Gene Ontology 7

Phenotypes 6
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:331098 Xu J, et al., Three-dimensional mapping reveals heterochronic development of the neuromuscular system in postnatal mouse skeletal muscles. Commun Biol. 2022 Nov 8;5(1):1200

TSS for Col25a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr31667	Chr3:129974484-129974503 (+)	502 bp
Tssr31668	Chr3:129974531-129974548 (+)	548 bp
Tssr31669	Chr3:129978870-129978874 (+)	4,880 bp
Tssr31670	Chr3:129994994-129994999 (+)	21,005 bp
Tssr31671	Chr3:130040685-130040688 (+)	66,695 bp
Tssr1047	Chr3:130214277-130214278 (+)	240,286 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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