Col12a1 MGI Mouse Gene Detail - MGI:88448 - collagen, type XII, alpha 1

Symbol

Col12a1
Name

collagen, type XII, alpha 1

Feature Type

protein coding gene
IDs

MGI:88448
NCBI Gene: 12816
Alliance

gene page
Transcription Start Sites

14 TSS

Sequence Map

Chr9:79506273-79626113 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 43.82 cM
Mapping Data

4 experiments

SNPs within 2kb

3032 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88448	protein coding gene	Chr9:79506269-79628423 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0035074	protein coding gene	Chr9:80125054-80251024 (-)
A/J	MGP_AJ_G0035055	protein coding gene	Chr9:77392903-77513674 (-)
AKR/J	MGP_AKRJ_G0034983	protein coding gene	Chr9:79192050-79314738 (-)
BALB/cJ	MGP_BALBcJ_G0035043	protein coding gene	Chr9:77013468-77134494 (-)
C3H/HeJ	MGP_C3HHeJ_G0034755	protein coding gene	Chr9:79713336-79837665 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0035566	protein coding gene	Chr9:82312170-82438687 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032473	protein coding gene	Chr9:76534325-76654312 (-)
CAST/EiJ	MGP_CASTEiJ_G0034073	protein coding gene	Chr9:80041307-80166409 (-)
CBA/J	MGP_CBAJ_G0034728	protein coding gene	Chr9:85230271-85369591 (-)
DBA/2J	MGP_DBA2J_G0034886	protein coding gene	Chr9:77000764-77120134 (-)
FVB/NJ	MGP_FVBNJ_G0034829	protein coding gene	Chr9:76215147-76338356 (-)
LP/J	MGP_LPJ_G0034967	protein coding gene	Chr9:80381360-80505862 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0034871	protein coding gene	Chr9:86468849-86615001 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035587	protein coding gene	Chr9:79387041-79515202 (-)
PWK/PhJ	MGP_PWKPhJ_G0033777	protein coding gene	Chr9:77197712-77319007 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0033613	protein coding gene	Chr9:79532688-79667162 (-)
WSB/EiJ	MGP_WSBEiJ_G0034190	protein coding gene	Chr9:79344073-79471684 (-)

Human Ortholog

COL12A1, collagen type XII alpha 1 chain

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL12A1, collagen type XII alpha 1 chain
Synonyms

BA209D8.1, BTHLM2, COL12A1L, DJ234P15.1, EDSMYP, UCMD2
Links

HGNC:2188

NCBI Gene ID: 1303

neXtProt AC: NX_Q99715

UniProt: Q99715
Chr Location

6q13-q14.1; chr6:75084326-75206267 (-) GRCh38

MGI Vertebrate Homology

Col12a1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: COL12A1
Gene Tree

Col12a1

Diseases

2 with human COL12A1 associations

				Human Disease	Mouse Models
				Bethlem myopathy IDs Bethlem myopathy DOID:0050663 MESH:C535436 OMIM:158810
				Ullrich congenital muscular dystrophy 2 IDs Ullrich congenital muscular dystrophy 2 DOID:0060948 OMIM:616470 ORDO:75840

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

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Phenotype Summary

29 phenotypes from 1 allele in 2 genetic backgrounds
6 images
23 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

12
Chemically induced (other)

1
Endonuclease-mediated

3
Radiation induced

1
Targeted

7
Genomic Mutations

2 involving Col12a1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

177 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit partial perinatal lethality, decreased body weight, shorter and slender long bones, altered vertebrae structure, kyphosis, decreased bone strength, and abnormalities in osteoblast differentiation and bone matrix formation.

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All GO Annotations

8
GO References

8

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

809
Tissues

70
cDNA Data

28
Literature Summary

24

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase col12a1

ZFIN col12a1a, col12a1b

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All Sequences

61
RefSeq

6
UniProt

4
CCDS

CCDS72284.1

Ensembl

ENSMUSG00000032332 (Evidence)
NCBI Gene

12816

			Length	Strain/Species	Flank
genomic	ENSMUSG00000032332	Ensembl Gene Model \| MGI Sequence Detail	119841	C57BL/6J	± kb
transcript	ENSMUST00000071750	Ensembl \| MGI Sequence Detail	11511	Not Applicable
polypeptide	ENSMUSP00000071662	Ensembl \| MGI Sequence Detail	3065	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000005696 collagen alpha-1(XII) chain

(term hierarchy)
InterPro Domains

IPR050149 Collagen superfamily

IPR008160 Collagen triple helix repeat

IPR013320 Concanavalin A-like lectin/glucanase domain superfamily

IPR050525 Extracellular Matrix Assembly and Organization

IPR003961 Fibronectin type III

IPR036116 Fibronectin type III superfamily

IPR013783 Immunoglobulin-like fold

IPR048287 Thrombospondin-like, N-terminal domain

IPR036465 von Willebrand factor A-like domain superfamily

IPR002035 von Willebrand factor, type A
GlyGen

Q60847 9 sites, 3 N-linked glycans (3 sites)

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All nucleic 48

Genomic 6

cDNA 34

Primer pair 4

Other 4

Microarray probesets 6

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MGD-MRK-2055, MGI:2143350

Summaries

All 79

Developmental Gene Expression 24

Gene Ontology 8

Phenotypes 23
Earliest

J:12013 Russell LB, Definition of functional units in a small chromosomal segment of the mouse and its use in interpreting the nature of radiation-induced mutations. Mutat Res. 1971 Jan;11(1):107-23
Latest

J:354501 Zhu M, et al., Ablation of collagen XII disturbs joint extracellular matrix organization and causes patellar subluxation. iScience. 2023 Jul 21;26(7):107225

TSS for Col12a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr90676	Chr9:79626117-79626124 (-)	-8 bp
Tssr90675	Chr9:79626085-79626100 (-)	20 bp
Tssr90674	Chr9:79626073-79626083 (-)	35 bp
Tssr90673	Chr9:79626047-79626059 (-)	60 bp
Tssr90672	Chr9:79626038-79626045 (-)	71 bp
Tssr90671	Chr9:79626023-79626034 (-)	84 bp
Tssr90670	Chr9:79625913-79625930 (-)	191 bp
Tssr90669	Chr9:79625894-79625902 (-)	215 bp
Tssr90668	Chr9:79625869-79625874 (-)	241 bp
Tssr90667	Chr9:79625851-79625854 (-)	260 bp
Tssr90666	Chr9:79606011-79606012 (-)	20,101 bp
Tssr90665	Chr9:79598619-79598623 (-)	27,492 bp
Tssr90664	Chr9:79547054-79547060 (-)	79,056 bp
Tssr90663	Chr9:79506436-79506439 (-)	119,675 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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