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Col2a1 Gene Detail
Summary
  • Symbol
    Col2a1
  • Name
    collagen, type II, alpha 1
  • Synonyms
    Col2, Col2a, Col2a-1, Del1, Lpk, M100413, M100856, Rgsc413, Rgsc856
  • Feature Type
    protein coding gene
  • IDs
    MGI:88452
    NCBI Gene: 12824
  • Alliance
    gene page
  • Transcription Start Sites
    26 TSS
Location &
Maps
more
  • Sequence Map
    Chr15:97873483-97902525 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 15, 53.97 cM
  • Mapping Data
    11 experiments
Strain
Comparison
more
  • SNPs within 2kb
    736 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    3
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_88452
 protein coding gene Chr15:97873483-97902576 (-)
129S1/SvImJ MGP_129S1SvImJ_G0022283
 protein coding gene Chr15:99661846-99692566 (-)
A/J MGP_AJ_G0022242
 protein coding gene Chr15:95717121-95746211 (-)
AKR/J MGP_AKRJ_G0022217
 protein coding gene Chr15:98609453-98638520 (-)
BALB/cJ MGP_BALBcJ_G0022248
 protein coding gene Chr15:95942505-95971568 (-)
C3H/HeJ MGP_C3HHeJ_G0022018
 protein coding gene Chr15:98679176-98708299 (-)
C57BL/6NJ MGP_C57BL6NJ_G0022693
 protein coding gene Chr15:103346233-103375456 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0020219
 protein coding gene Chr15:91662929-91692380 (-)
CAST/EiJ MGP_CASTEiJ_G0021540
 protein coding gene Chr15:99558313-99589589 (-)
CBA/J MGP_CBAJ_G0021985
 protein coding gene Chr15:106801715-106837710 (-)
DBA/2J MGP_DBA2J_G0022112
 protein coding gene Chr15:95169139-95198847 (-)
FVB/NJ MGP_FVBNJ_G0022091
 protein coding gene Chr15:94157641-94186920 (-)
LP/J MGP_LPJ_G0022183
 protein coding gene Chr15:99774976-99805456 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0022111
 protein coding gene Chr15:110917053-110947483 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0022708
 protein coding gene Chr15:98761286-98790510 (-)
PWK/PhJ MGP_PWKPhJ_G0021281
 protein coding gene Chr15:95272418-95305021 (-)
SPRET/EiJ MGP_SPRETEiJ_G0021115
 protein coding gene Chr15:98538242-98568394 (-)
WSB/EiJ MGP_WSBEiJ_G0021589
 protein coding gene Chr15:99275311-99305961 (-)



Homology
more
  • Human Ortholog
    COL2A1, collagen type II alpha 1 chain
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    COL2A1, collagen type II alpha 1 chain
  • Synonyms
    ANFH, AOM, COL11A3, SEDC, STL1
  • Links
    NCBI Gene ID: 1280
    neXtProt AC: NX_P02458
    UniProt: P02458

  • Chr Location
    12q13.11; chr12:47972967-48006212 (-)  GRCh38
Human Diseases
more
  • Diseases
    4 with Col2a1 mouse models; 21 with human COL2A1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
IDs
 View 7 models
      
IDs
 View 1 model
IDs
 View 2 models
      
IDs
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Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    9 with disease annotations
  • References
    10 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    163 phenotypes from 15 alleles in 17 genetic backgrounds
    27 phenotypes from multigenic genotypes
    9 images
    86 phenotype references
Phenotype Overview

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.
Mutations in this locus affect cartilage development. Homozygotes die perinatally with anomalies such as shortened limbs without epiphiseal growth plates, cleft palate and persistence of notochord. Heterozygotes are dwarfed with reduced cartilage matrix.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    70
  • GO References
    44
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.
Expression
less
Expression Overview

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
    2884
  • Tissues
    830
  • cDNA Data
    265
  • Literature Summary
    712
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 12824 NCBI Gene Model | MGI Sequence Detail 29043 C57BL/6J ±  kb
    transcript NR_177066 RefSeq | MGI Sequence Detail 5805 ZRU/MplStud  
    polypeptide P28481 UniProt | EBI | MGI Sequence Detail 1487 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 401
      Genomic 10
      cDNA 285
      Primer pair 39
      Other 67

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-2061, MGD-MRK-2062, MGD-MRK-2063, MGD-MRK-8871, MGI:3800690, MGI:3808757, MGI:3847802
    References
    more
    • Summaries
      All 879
      Developmental Gene Expression 712
      Diseases 10
      Gene Ontology 44
      Phenotypes 86
    • Earliest
      J:6582 Brown KS, et al., Disproportionate micromelia (Dmm): an incomplete dominant mouse dwarfism with abnormal cartilage matrix. J Embryol Exp Morphol. 1981 Apr;62(1):165-82
    • Latest
      J:353660 Saeki N, et al., Deletion of Trps1 regulatory elements recapitulates postnatal hip joint abnormalities and growth retardation of Trichorhinophalangeal syndrome in mice. Hum Mol Genet. 2024 Sep 3;33(18):1618-1629
    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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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/05/2024
    MGI 6.24     		The Jackson Laboratory