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COL28A1 collagen type XXVIII alpha 1 chain [ Homo sapiens (human) ]

Gene ID: 340267, updated on 21-Apr-2019

Summary

Official Symbol
COL28A1provided by HGNC
Official Full Name
collagen type XXVIII alpha 1 chainprovided by HGNC
Primary source
HGNC:HGNC:22442
See related
Ensembl:ENSG00000215018 MIM:609996
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
COL28
Summary
COL28A1 belongs to a class of collagens containing von Willebrand factor (VWF; MIM 613160) type A (VWFA) domains (Veit et al., 2006 [PubMed 16330543]).[supplied by OMIM, Nov 2010]
Expression
Broad expression in salivary gland (RPKM 1.1), adrenal (RPKM 0.6) and 20 other tissues See more
Orthologs

Genomic context

See COL28A1 in Genome Data Viewer
Location:
7p21.3
Exon count:
46
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (7338542..7542094, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (7398244..7575460, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 Neighboring gene uncharacterized LOC101927354 Neighboring gene uncharacterized LOC107986764 Neighboring gene uncharacterized LOC101927391 Neighboring gene meiosis regulator for oocyte development

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder.
NHGRI GWA Catalog
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
NHGRI GWA Catalog

Pathways from BioSystems

  • Collagen biosynthesis and modifying enzymes, organism-specific biosystem (from REACTOME)
    Collagen biosynthesis and modifying enzymes, organism-specific biosystemThe biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proli...
  • Collagen chain trimerization, organism-specific biosystem (from REACTOME)
    Collagen chain trimerization, organism-specific biosystemThe C-propeptides of collagen propeptide chains are essential for the association of three peptide chains into a trimeric but non-helical procollagen. This initial binding event determines the compo...
  • Collagen formation, organism-specific biosystem (from REACTOME)
    Collagen formation, organism-specific biosystemCollagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in...
  • Extracellular matrix organization, organism-specific biosystem (from REACTOME)
    Extracellular matrix organization, organism-specific biosystemThe extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
extracellular matrix structural constituent conferring tensile strength RCA
inferred from Reviewed Computational Analysis
more info
PubMed 
serine-type endopeptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cell adhesion IEA
Inferred from Electronic Annotation
more info
 
negative regulation of endopeptidase activity IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
basement membrane IEA
Inferred from Electronic Annotation
more info
 
collagen trimer IEA
Inferred from Electronic Annotation
more info
 
collagen-containing extracellular matrix HDA PubMed 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
collagen alpha-1(XXVIII) chain
Names
collagen, type XXVIII, 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.

mRNA and Protein(s)

  1. NM_001037763.2NP_001032852.2  collagen alpha-1(XXVIII) chain precursor

    See identical proteins and their annotated locations for NP_001032852.2

    Status: VALIDATED

    Source sequence(s)
    AC004982, AJ890451
    Consensus CDS
    CCDS43553.1
    UniProtKB/Swiss-Prot
    Q2UY09
    Related
    ENSP00000382356.3, ENST00000399429.7
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

    Range
    7338542..7542094 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017012132.2XP_016867621.1  collagen alpha-1(XXVIII) chain isoform X1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain
  2. XM_011515360.2XP_011513662.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513662.1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain
  3. XM_011515358.3XP_011513660.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513660.1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain
  4. XM_017012131.2XP_016867620.1  collagen alpha-1(XXVIII) chain isoform X1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain
  5. XM_011515359.2XP_011513661.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513661.1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (4) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:10701123
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
    pfam00092
    Location:799974
    VWA; von Willebrand factor type A domain
  6. XM_011515362.2XP_011513664.1  collagen alpha-1(XXVIII) chain isoform X2

    Conserved Domains (3) summary
    pfam01391
    Location:198253
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:687740
    KU; BPTI/Kunitz family of serine protease inhibitors; Structure is a disulfide rich alpha+beta fold. BPTI (bovine pancreatic trypsin inhibitor) is an extensively studied model structure.
    pfam00092
    Location:416591
    VWA; von Willebrand factor type A domain
  7. XM_011515364.2XP_011513666.1  collagen alpha-1(XXVIII) chain isoform X4

    Conserved Domains (2) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  8. XM_011515363.2XP_011513665.1  collagen alpha-1(XXVIII) chain isoform X3

    See identical proteins and their annotated locations for XP_011513665.1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (2) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  9. XM_011515365.2XP_011513667.1  collagen alpha-1(XXVIII) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
  10. XM_017012133.1XP_016867622.1  collagen alpha-1(XXVIII) chain isoform X5

  11. XM_011515366.2XP_011513668.1  collagen alpha-1(XXVIII) chain isoform X7

    Conserved Domains (2) summary
    pfam01391
    Location:383442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47209
    vWFA_subfamily_ECM; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

RNA

  1. XR_926936.3 RNA Sequence

  2. XR_001744688.1 RNA Sequence

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