Col11a1 MGI Mouse Gene Detail - MGI:88446 - collagen, type XI, alpha 1

Symbol

Col11a1
Name

collagen, type XI, alpha 1
Synonyms

C530001D20Rik

Feature Type

protein coding gene
IDs

MGI:88446
NCBI Gene: 12814
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr3:113824189-114014367 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 49.35 cM
Mapping Data

5 experiments

SNPs within 2kb

5748 from dbSNP Build 142
Strain Annotations

18
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_88446	protein coding gene	Chr3:113823933-114014405 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027801	protein coding gene	Chr3:115813864-116014272 (+)
A/J	MGP_AJ_G0027759	protein coding gene	Chr3:112054055-112247020 (+)
AKR/J	MGP_AKRJ_G0027725	protein coding gene	Chr3:114855174-115055050 (+)
BALB/cJ	MGP_BALBcJ_G0027771	protein coding gene	Chr3:111902922-112097402 (+)
C3H/HeJ	MGP_C3HHeJ_G0027502	protein coding gene	Chr3:115240529-115443984 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028217	protein coding gene	Chr3:120084719-120303809 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025556	protein coding gene	Chr3:107860119-108047252 (+)
CAST/EiJ	MGP_CASTEiJ_G0026958	protein coding gene	Chr3:114492010-114706504 (+)
CBA/J	MGP_CBAJ_G0027477	protein coding gene	Chr3:124197046-124416940 (+)
DBA/2J	MGP_DBA2J_G0027618	protein coding gene	Chr3:111310093-111503757 (+)
FVB/NJ	MGP_FVBNJ_G0027586	protein coding gene	Chr3:108999703-109188420 (+)
LP/J	MGP_LPJ_G0027728	protein coding gene	Chr3:117371281-117569597 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027616	protein coding gene	Chr3:131226639-131519371 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028273	protein coding gene	Chr3:114445335-114644106 (+)
PWK/PhJ	MGP_PWKPhJ_G0026684	protein coding gene	Chr3:110930208-111127743 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026506	protein coding gene	Chr3:112456273-112752885 (+)
WSB/EiJ	MGP_WSBEiJ_G0027038	protein coding gene	Chr3:115087579-115298026 (+)

Human Ortholog

COL11A1, collagen type XI alpha 1 chain

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

COL11A1, collagen type XI alpha 1 chain
Synonyms

CO11A1, COLL6, DFNA37, STL2
Links

HGNC:2186

NCBI Gene ID: 1301

neXtProt AC: NX_P12107

UniProt: P12107
Chr Location

1p21.1; chr1:102876467-103108872 (-) GRCh38

MGI Vertebrate Homology

Col11a1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: COL11A1
Gene Tree

Col11a1

Diseases

2 with Col11a1 mouse models; 4 with human COL11A1 associations

Human Disease

Mouse Models

osteoarthritis

IDs

View 1 model

Stickler syndrome

IDs

View 1 model

autosomal dominant nonsyndromic deafness

IDs

fibrochondrogenesis 1

IDs

Marshall syndrome

IDs

Stickler syndrome 2

IDs

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

Mutations/Alleles

1 with disease annotations

References

3 with disease annotations

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Phenotype Summary

41 phenotypes from 2 alleles in 2 genetic backgrounds
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

8
Chemically induced (other)

1
Endonuclease-mediated

4
Radiation induced

1
Spontaneous

1
Targeted

1
Genomic Mutations

2 involving Col11a1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

90 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous mutation of this gene results in perinatal lethality by asphyxia. Mutants animals display weak tracheal cartilage, short snout, short mandible, cleft palate, short limbs, and externally rotated distal portion of the hindlimbs.

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All GO Annotations

40
GO References

19

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

1072
Tissues

124
cDNA Data

108
Literature Summary

30

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

ZFIN col11a1a, col11a1b

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All Sequences

72
RefSeq

11
UniProt

10
CCDS

CCDS17778.1

Ensembl

ENSMUSG00000027966 (Evidence)
NCBI Gene

12814

			Length	Strain/Species	Flank
genomic	ENSMUSG00000027966	Ensembl Gene Model \| MGI Sequence Detail	190179	C57BL/6J	± kb
transcript	ENSMUST00000092155	Ensembl \| MGI Sequence Detail	7667	Not Applicable
polypeptide	ENSMUSP00000089793	Ensembl \| MGI Sequence Detail	1804	Not Applicable

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UniProt

10 Sequences
Protein Ontology

PR:000005694 collagen alpha-1(XI) 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

IPR050632 Nematode Cuticular Collagen

IPR048287 Thrombospondin-like, N-terminal domain
GlyGen

Q61245 1 site, 1 N-linked glycan (1 site)

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All nucleic 121

Genomic 2

cDNA 108

Primer pair 8

Other 3

Microarray probesets 4

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MGD-MRK-1972, MGD-MRK-2053, MGI:1924905

Summaries

All 91

Developmental Gene Expression 30

Diseases 3

Gene Ontology 19

Phenotypes 28
Earliest

J:5198 Seegmiller R, et al., A new chondrodystrophic mutant in mice. Electron microscopy of normal and abnormal chondrogenesis. J Cell Biol. 1971 Mar;48(3):580-93
Latest

J:351385 Kaneko N, et al., ADAMTS2 promotes radial migration by activating TGF-beta signaling in the developing neocortex. EMBO Rep. 2024 Jul;25(7):3090-3115

TSS for Col11a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr1026	Chr3:113824122-113824129 (+)	-63 bp
Tssr31311	Chr3:113824133-113824142 (+)	-51 bp
Tssr31312	Chr3:113824181-113824220 (+)	12 bp
Tssr31313	Chr3:113824233-113824287 (+)	71 bp
Tssr31314	Chr3:113824428-113824482 (+)	266 bp
Tssr31315	Chr3:113824485-113824514 (+)	311 bp
Tssr31316	Chr3:113824515-113824529 (+)	333 bp
Tssr31317	Chr3:113888207-113888229 (+)	64,029 bp
Tssr31318	Chr3:113911661-113911662 (+)	87,473 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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