Format

Send to:

Choose Destination

Col11a2 collagen, type XI, alpha 2 [ Mus musculus (house mouse) ]

Gene ID: 12815, updated on 3-Jun-2018
Official Symbol
Col11a2provided by MGI
Official Full Name
collagen, type XI, alpha 2provided by MGI
Primary source
MGI:MGI:88447
See related
Ensembl:ENSMUSG00000024330 Vega:OTTMUSG00000022512
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
This gene encodes the alpha-2 subunit of type XI collagen, one of the low abundance fibrillar collagens found in cartilage. The encoded protein, in association with other collagen subunits, forms a heterotrimeric type XI procollagen that may undergo proteolytic processing similar to the alpha-1 subunit. Mice lacking the encoded protein exhibit a mild phenotype similar to nonocular Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED) as well as a nonsyndromic form of deafness called DFNA13. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Expression
Biased expression in limb E14.5 (RPKM 60.6) and CNS E14 (RPKM 9.3) See more
Orthologs
See Col11a2 in Genome Data Viewer
Location:
17 B1; 17 17.98 cM
Exon count:
68
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 17 NC_000083.6 (34038506..34066684)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 17 NC_000083.5 (34176382..34203187)

Chromosome 17 - NC_000083.6Genomic Context describing neighboring genes Neighboring gene solute carrier family 39 (zinc transporter), member 7 Neighboring gene retinoid X receptor beta Neighboring gene histocompatibility 2, P region beta locus Neighboring gene cDNA sequence BC051537 Neighboring gene histocompatibility 2, P region alpha locus

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent IC
Inferred by Curator
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cartilage development IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cartilage development ISO
Inferred from Sequence Orthology
more info
 
chondrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen fibril organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
collagen fibril organization ISO
Inferred from Sequence Orthology
more info
 
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
roof of mouth development ISO
Inferred from Sequence Orthology
more info
 
sensory perception of sound IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sensory perception of sound IMP
Inferred from Mutant Phenotype
more info
PubMed 
sensory perception of sound ISO
Inferred from Sequence Orthology
more info
 
skeletal system development ISO
Inferred from Sequence Orthology
more info
 
skeletal system morphogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
soft palate development ISO
Inferred from Sequence Orthology
more info
 
tissue homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 
extracellular region IEA
Inferred from Electronic Annotation
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Preferred Names
collagen alpha-2(XI) chain
Names
procollagen, type XI, alpha 2

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001317722.1NP_001304651.1  collagen alpha-2(XI) chain isoform 1 precursor

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    CR974462
    UniProtKB/Swiss-Prot
    Q64739
    Conserved Domains (3) summary
    pfam01391
    Location:12701328
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15191714
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  2. NM_009926.2NP_034056.1  collagen alpha-2(XI) chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_034056.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains one alternate in-frame exon and lacks two exons in the 5' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    CR974462
    Consensus CDS
    CCDS28640.1
    UniProtKB/Swiss-Prot
    Q64739
    UniProtKB/TrEMBL
    I7HJS8
    Related
    ENSMUSP00000084772.4, OTTMUSP00000025657, ENSMUST00000087497.10, OTTMUST00000053896
    Conserved Domains (3) summary
    pfam01391
    Location:12051263
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14541649
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000083.6 Reference GRCm38.p4 C57BL/6J

    Range
    34038506..34066684
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006523559.3XP_006523622.1  collagen alpha-2(XI) chain isoform X1

    See identical proteins and their annotated locations for XP_006523622.1

    Conserved Domains (3) summary
    pfam01391
    Location:13751433
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:16241819
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  2. XM_006523562.3XP_006523625.1  collagen alpha-2(XI) chain isoform X4

    See identical proteins and their annotated locations for XP_006523625.1

    Conserved Domains (3) summary
    pfam01391
    Location:13151373
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15641759
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  3. XM_006523560.3XP_006523623.1  collagen alpha-2(XI) chain isoform X2

    See identical proteins and their annotated locations for XP_006523623.1

    Conserved Domains (3) summary
    pfam01391
    Location:13541412
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:16031798
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  4. XM_006523563.3XP_006523626.1  collagen alpha-2(XI) chain isoform X5

    See identical proteins and their annotated locations for XP_006523626.1

    Conserved Domains (3) summary
    pfam01391
    Location:12941352
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15431738
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  5. XM_006523564.3XP_006523627.1  collagen alpha-2(XI) chain isoform X6

    See identical proteins and their annotated locations for XP_006523627.1

    UniProtKB/Swiss-Prot
    Q64739
    Conserved Domains (3) summary
    pfam01391
    Location:12911349
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15401735
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  6. XM_006523568.3XP_006523631.1  collagen alpha-2(XI) chain isoform X9

    See identical proteins and their annotated locations for XP_006523631.1

    Conserved Domains (3) summary
    pfam01391
    Location:12311289
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14801675
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  7. XM_006523569.3XP_006523632.1  collagen alpha-2(XI) chain isoform X10

    See identical proteins and their annotated locations for XP_006523632.1

    UniProtKB/Swiss-Prot
    Q64739
    Related
    ENSMUSP00000109890.1, ENSMUST00000114252.7
    Conserved Domains (3) summary
    pfam01391
    Location:12101268
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14591654
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  8. XM_006523561.3XP_006523624.1  collagen alpha-2(XI) chain isoform X3

    See identical proteins and their annotated locations for XP_006523624.1

    Conserved Domains (4) summary
    pfam01391
    Location:13491407
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15981793
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
    pfam15392
    Location:252397
    Joubert; Joubert syndrome-associated
  9. XM_006523566.3XP_006523629.1  collagen alpha-2(XI) chain isoform X7

    See identical proteins and their annotated locations for XP_006523629.1

    UniProtKB/Swiss-Prot
    Q64739
    Conserved Domains (3) summary
    pfam01391
    Location:12651323
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:15141709
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  10. XM_006523567.3XP_006523630.1  collagen alpha-2(XI) chain isoform X8

    See identical proteins and their annotated locations for XP_006523630.1

    UniProtKB/Swiss-Prot
    Q64739
    Related
    ENSMUSP00000109893.1, ENSMUST00000114255.7
    Conserved Domains (3) summary
    pfam01391
    Location:12441302
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14931688
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  11. XM_006523570.3XP_006523633.1  collagen alpha-2(XI) chain isoform X11

    See identical proteins and their annotated locations for XP_006523633.1

    UniProtKB/Swiss-Prot
    Q64739
    Conserved Domains (3) summary
    pfam01391
    Location:11841242
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:14331628
    COLFI; Fibrillar collagens C-terminal domain
    smart00210
    Location:32213
    TSPN; Thrombospondin N-terminal -like domains
  12. XM_006523571.1XP_006523634.1  collagen alpha-2(XI) chain isoform X12

    See identical proteins and their annotated locations for XP_006523634.1

    Conserved Domains (2) summary
    pfam01391
    Location:897955
    Collagen; Collagen triple helix repeat (20 copies)
    smart00038
    Location:11461341
    COLFI; Fibrillar collagens C-terminal domain

RNA

  1. XR_385275.3 RNA Sequence

  2. XR_385276.3 RNA Sequence

Reference GRCm38.p4 129X1/SvJ

Genomic

  1. NT_039662.3 Reference GRCm38.p4 129X1/SvJ

    Range
    288076..315620
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCm38.p4 NOD/MrkTac

Genomic

  1. NT_187027.1 Reference GRCm38.p4 NOD/MrkTac

    Range
    349745..377270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCm38.p4 NOD/ShiLtJ

Genomic

  1. NT_187004.1 Reference GRCm38.p4 NOD/ShiLtJ

    Range
    349857..377382
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center