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COL27A1 collagen type XXVII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 85301, updated on 20-Apr-2020

Summary

Official Symbol
COL27A1provided by HGNC
Official Full Name
collagen type XXVII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:22986
See related
Ensembl:ENSG00000196739 MIM:608461
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
STLS
Summary
This gene encodes a member of the fibrillar collagen family, and plays a role during the calcification of cartilage and the transition of cartilage to bone. The encoded protein product is a preproprotein. It includes an N-terminal signal peptide, which is followed by an N-terminal propetide, mature peptide and a C-terminal propeptide. The N-terminal propeptide contains thrombospondin N-terminal-like and laminin G-like domains. The mature peptide is a major triple-helical region. The C-terminal propeptide, also known as COLFI domain, plays crucial roles in tissue growth and repair. Mutations in this gene cause Steel syndrome. Alternatively spliced transcript variants have been found, but the full-length nature of some variants has not been determined. [provided by RefSeq, Sep 2014]
Expression
Ubiquitous expression in endometrium (RPKM 17.8), prostate (RPKM 8.1) and 23 other tissues See more
Orthologs

Genomic context

See COL27A1 in Genome Data Viewer
Location:
9q32
Exon count:
66
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (114154271..114312511)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116918231..117072975)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene kinesin family member 12 Neighboring gene uncharacterized LOC105376225 Neighboring gene microRNA 455 Neighboring gene uncharacterized LOC105376224 Neighboring gene orosomucoid 1 Neighboring gene orosomucoid 2

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Steel syndrome
MedGen: C3554594 OMIM: 615155 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study of Tourette's syndrome.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ11895, KIAA1870, MGC11337

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular matrix structural constituent conferring tensile strength HDA PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
extracellular matrix organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
growth plate cartilage chondrocyte development IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular matrix IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
fibrillar collagen trimer IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_034260.1 RefSeqGene

    Range
    4993..161967
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032888.4NP_116277.2  collagen alpha-1(XXVII) chain preproprotein

    See identical proteins and their annotated locations for NP_116277.2

    Status: REVIEWED

    Source sequence(s)
    AI808820, AL356796, AL445543, AY149237, BC035728, BU076480
    Consensus CDS
    CCDS6802.1
    UniProtKB/Swiss-Prot
    Q8IZC6
    Related
    ENSP00000348385.3, ENST00000356083.8
    Conserved Domains (3) summary
    pfam01391
    Location:694752
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16611859
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45220
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    114154271..114312511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011519138.2XP_011517440.1  collagen alpha-1(XXVII) chain isoform X1

    Conserved Domains (3) summary
    pfam01391
    Location:692750
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16591857
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:43218
    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_011519142.3XP_011517444.1  collagen alpha-1(XXVII) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:694752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45220
    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_017015239.1XP_016870728.1  collagen alpha-1(XXVII) chain isoform X7

  4. XM_011519143.2XP_011517445.1  collagen alpha-1(XXVII) chain isoform X5

    Conserved Domains (2) summary
    pfam01391
    Location:694752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45220
    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_011519144.2XP_011517446.1  collagen alpha-1(XXVII) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:694752
    Collagen; Collagen triple helix repeat (20 copies)
    cl22861
    Location:45220
    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_011519140.1XP_011517442.1  collagen alpha-1(XXVII) chain isoform X2

    Conserved Domains (3) summary
    pfam01391
    Location:694752
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16431841
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45220
    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_006717308.2XP_006717371.1  collagen alpha-1(XXVII) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:676734
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:16431841
    COLFI; Fibrillar collagen C-terminal domain
    cl22861
    Location:45220
    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_006717310.3XP_006717373.1  collagen alpha-1(XXVII) chain isoform X8

    Conserved Domains (2) summary
    pfam01391
    Location:603660
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:8881086
    COLFI; Fibrillar collagen C-terminal domain
  9. XM_011519145.3XP_011517447.1  collagen alpha-1(XXVII) chain isoform X9

    Conserved Domains (2) summary
    pfam01391
    Location:565622
    Collagen; Collagen triple helix repeat (20 copies)
    cl02436
    Location:8501048
    COLFI; Fibrillar collagen C-terminal domain

RNA

  1. XR_001746405.1 RNA Sequence

  2. XR_929861.2 RNA Sequence

  3. XR_929862.1 RNA Sequence

  4. XR_929863.1 RNA Sequence

  5. XR_929860.3 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_032161.1: Suppressed sequence

    Description
    NM_032161.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
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