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Col27a1 collagen, type XXVII, alpha 1 [ Mus musculus (house mouse) ]

Gene ID: 373864, updated on 12-May-2024

Summary

Official Symbol
Col27a1provided by MGI
Official Full Name
collagen, type XXVII, alpha 1provided by MGI
Primary source
MGI:MGI:2672118
See related
Ensembl:ENSMUSG00000045672 AllianceGenome:MGI:2672118
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
Also known as
5730512J02Rik
Summary
This gene encodes the alpha-1 subunit of type XXVII collagen, one of the low abundance fibril-forming collagens found in cartilage. The encoded protein forms a homotrimeric triple helical procollagen that undergoes proteolytic processing during fibril formation. Transgenic mice lacking a portion of the collagenous domain in the encoded protein exhibit skeletal abnormalities, chondrodysplasia and die at birth because of a lung defect. [provided by RefSeq, Dec 2015]
Expression
Broad expression in limb E14.5 (RPKM 27.8), ovary adult (RPKM 7.1) and 17 other tissues See more
Orthologs
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Genomic context

See Col27a1 in Genome Data Viewer
Location:
4 B3; 4 33.96 cM
Exon count:
65
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (63132246..63253228)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (63214009..63334991)

Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene alpha 1 microglobulin/bikunin precursor Neighboring gene kinesin family member 12 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:62883492-62883675 Neighboring gene microRNA 455 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:62968523-62968632 Neighboring gene STARR-seq mESC enhancer starr_10435 Neighboring gene predicted gene, 52743 Neighboring gene orosomucoid 1 pseudogene Neighboring gene orosomucoid 1

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (2)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Process Evidence Code Pubs
involved_in angiogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in collagen fibril organization IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in endothelial cell morphogenesis IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within extracellular matrix organization IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within growth plate cartilage chondrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in notochord development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
part_of collagen trimer IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in collagen-containing extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of fibrillar collagen trimer IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
collagen alpha-1(XXVII) chain
Names
procollagen, type XXVII, alpha 1

NCBI Reference Sequences (RefSeq)

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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_025685.3NP_079961.3  collagen alpha-1(XXVII) chain preproprotein

    See identical proteins and their annotated locations for NP_079961.3

    Status: REVIEWED

    Source sequence(s)
    AK157951, AL683828, AL691496, AY167568
    Consensus CDS
    CCDS18250.1
    UniProtKB/Swiss-Prot
    Q5QNQ9, Q69Z83, Q80UA8
    Related
    ENSMUSP00000043816.7, ENSMUST00000036300.13
    Conserved Domains (3) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16461844
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000070.7 Reference GRCm39 C57BL/6J

    Range
    63132246..63253228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030253629.1XP_030109489.1  collagen alpha-1(XXVII) chain isoform X2

    Conserved Domains (4) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:16471845
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  2. XM_030253631.2XP_030109491.1  collagen alpha-1(XXVII) chain isoform X5

    Conserved Domains (3) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  3. XM_011250057.4XP_011248359.1  collagen alpha-1(XXVII) chain isoform X6

    Conserved Domains (3) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  4. XM_006538039.5XP_006538102.1  collagen alpha-1(XXVII) chain isoform X9

    Conserved Domains (3) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  5. XM_011250058.4XP_011248360.1  collagen alpha-1(XXVII) chain isoform X8

    Conserved Domains (3) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  6. XM_006538035.5XP_006538098.1  collagen alpha-1(XXVII) chain isoform X1

    Conserved Domains (4) summary
    pfam01391
    Location:679737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:16471845
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  7. XM_036164207.1XP_036020100.1  collagen alpha-1(XXVII) chain isoform X3

    Conserved Domains (5) summary
    PRK12678
    Location:12651445
    PRK12678; transcription termination factor Rho; Provisional
    pfam05109
    Location:269567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam01391
    Location:745801
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16291827
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43221
    LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
  8. XM_030253630.2XP_030109490.1  collagen alpha-1(XXVII) chain isoform X4

    Conserved Domains (3) summary
    pfam01391
    Location:509567
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:99397
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:14771675
    COLFI; Fibrillar collagen C-terminal domain
  9. XM_030253632.1XP_030109492.1  collagen alpha-1(XXVII) chain isoform X7

    Conserved Domains (2) summary
    pfam01391
    Location:609666
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:8891087
    COLFI; Fibrillar collagen C-terminal domain
  10. XM_030253634.1XP_030109494.1  collagen alpha-1(XXVII) chain isoform X10

    Conserved Domains (2) summary
    pfam01391
    Location:457514
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:737935
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_390328.4 RNA Sequence

  2. XR_003954978.2 RNA Sequence