U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 373864, updated on 27-Nov-2024

Summary

Go to the top of the page Help
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
human all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1. Pace JM, et al. Matrix Biol, 2003 Mar. PMID 12714037
  2. A novel and highly conserved collagen (pro(alpha)1(XXVII)) with a unique expression pattern and unusual molecular characteristics establishes a new clade within the vertebrate fibrillar collagen family. Boot-Handford RP, et al. J Biol Chem, 2003 Aug 15. PMID 12766169
  3. Collagen XXVII is developmentally regulated and forms thin fibrillar structures distinct from those of classical vertebrate fibrillar collagens. Plumb DA, et al. J Biol Chem, 2007 Apr 27. PMID 17331945, Free PMC Article
  4. The transcription factor Lc-Maf participates in Col27a1 regulation during chondrocyte maturation. Mayo JL, et al. Exp Cell Res, 2009 Aug 1. PMID 19414009, Free PMC Article
  5. Collagen XXVII organises the pericellular matrix in the growth plate. Plumb DA, et al. PLoS One, 2011. PMID 22206015, Free PMC Article

See all (24) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results suggest that Lc-Maf may affect the process of endochondral ossification by participating in the regulation of Col27a1 expression.
    Title: The transcription factor Lc-Maf participates in Col27a1 regulation during chondrocyte maturation.
  2. molecular cloning
    Title: Identification, characterization and expression analysis of a new fibrillar collagen gene, COL27A1.
  3. type XXVII collagen has unusual molecular features such as no minor helical domain, a major helical domain that is short and interrupted, and a short chain selection sequence within the NC1 domain (COLLAGEN TYPE XXVII)
    Title: A novel and highly conserved collagen (pro(alpha)1(XXVII)) with a unique expression pattern and unusual molecular characteristics establishes a new clade within the vertebrate fibrillar collagen family.
Submit: New GeneRIF Correction

Variation

Go to the top of the page Help

Alleles

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

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables extracellular matrix structural constituent IDA
Inferred from Direct Assay
more info
 PubMed 
enables extracellular matrix structural constituent conferring tensile strength IBA
Inferred from Biological aspect of Ancestor
more info
  
enables extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in extracellular matrix organization 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 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

Go to the top of the page Help
Preferred Names
collagen alpha-1(XXVII) chain
Names
procollagen, type XXVII, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_025685.3 → NP_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:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1646 → 1844
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43 → 221
    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_030253629.1 → XP_030109489.1  collagen alpha-1(XXVII) chain isoform X2

    Conserved Domains (4) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:1647 → 1845
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43 → 221
    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_030253631.2 → XP_030109491.1  collagen alpha-1(XXVII) chain isoform X5

    Conserved Domains (3) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43 → 221
    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_011250057.4 → XP_011248359.1  collagen alpha-1(XXVII) chain isoform X6

    Conserved Domains (3) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43 → 221
    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_006538039.5 → XP_006538102.1  collagen alpha-1(XXVII) chain isoform X9

    Conserved Domains (3) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43 → 221
    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_011250058.4 → XP_011248360.1  collagen alpha-1(XXVII) chain isoform X8

    Conserved Domains (3) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl22861
    Location:43 → 221
    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_006538035.5 → XP_006538098.1  collagen alpha-1(XXVII) chain isoform X1

    Conserved Domains (4) summary
    pfam01391
    Location:679 → 737
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:1647 → 1845
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43 → 221
    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_036164207.1 → XP_036020100.1  collagen alpha-1(XXVII) chain isoform X3

    Conserved Domains (5) summary
    PRK12678
    Location:1265 → 1445
    PRK12678; transcription termination factor Rho; Provisional
    pfam05109
    Location:269 → 567
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    pfam01391
    Location:745 → 801
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:1629 → 1827
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43 → 221
    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_030253630.2 → XP_030109490.1  collagen alpha-1(XXVII) chain isoform X4

    Conserved Domains (3) summary
    pfam01391
    Location:509 → 567
    Collagen; Collagen triple helix repeat (20 copies)
    pfam05109
    Location:99 → 397
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)
    cl02436
    Location:1477 → 1675
    COLFI; Fibrillar collagen C-terminal domain

  9. XM_030253632.1 → XP_030109492.1  collagen alpha-1(XXVII) chain isoform X7

    Conserved Domains (2) summary
    pfam01391
    Location:609 → 666
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:889 → 1087
    COLFI; Fibrillar collagen C-terminal domain

  10. XM_030253634.1 → XP_030109494.1  collagen alpha-1(XXVII) chain isoform X10

    Conserved Domains (2) summary
    pfam01391
    Location:457 → 514
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:737 → 935
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_390328.4 RNA Sequence

  2. XR_003954978.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5QNQ9.1 GenPept UniProtKB/Swiss-Prot:Q5QNQ9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools