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

Gene ID: 340267, updated on 2-Nov-2024

Summary

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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; AllianceGenome:HGNC:22442
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
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Genomic context

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See COL28A1 in Genome Data Viewer
Location:
7p21.3
Exon count:
47
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (7338194..7543870, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (7477054..7655035, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (7397506..7575504, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17961 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17962 Neighboring gene core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:7240975-7241493 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25638 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:7249044-7249615 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:7249616-7250186 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr7:7250187-7250758 Neighboring gene uncharacterized LOC107986764 Neighboring gene long intergenic non-protein coding RNA 3016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25639 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25640 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr7:7478283-7479482 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:7505040-7505723 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:7596439-7596940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:7596941-7597440 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25641 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25642 Neighboring gene MPRA-validated peak6360 silencer Neighboring gene MIOS divergent transcript Neighboring gene meiosis regulator for oocyte development

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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

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Related articles in PubMed

  1. COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells. Li L, et al. Ren Fail, 2023 Dec. PMID 36883360, Free PMC Article
  2. Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain. Veit G, et al. J Biol Chem, 2006 Feb 10. PMID 16330543
  3. A genome-wide meta-analysis identifies novel loci associated with schizophrenia and bipolar disorder. Wang KS, et al. Schizophr Res, 2010 Dec. PMID 20889312
  4. Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. Kennedy RB, et al. Hum Genet, 2012 Sep. PMID 22610502, Free PMC Article
  5. Characterization of the Extracellular Matrix of Normal and Diseased Tissues Using Proteomics. Naba A, et al. J Proteome Res, 2017 Aug 4. PMID 28675934, Free PMC Article

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
    Title: COL28 promotes proliferation, migration, and EMT of renal tubular epithelial cells.
  2. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Collagen XXVIII is a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain
    Title: Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain.
Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 heparin binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables serine-type endopeptidase inhibitor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in cell adhesion 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 negative regulation of peptidase activity IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in basement membrane IEA
Inferred from Electronic Annotation
more info
  
part_of collagen type V 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 endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
  
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
collagen alpha-1(XXVIII) chain
Names
collagen, type XXVIII, 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_001037763.3 → NP_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, AC006356, AJ890451
    Consensus CDS
    CCDS43553.1
    UniProtKB/Swiss-Prot
    A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09
    Related
    ENSP00000382356.3, ENST00000399429.8
    Conserved Domains (4) summary
    cd00109
    Location:1070 → 1123
    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:47 → 209
    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:799 → 974
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:360 → 419
    Collagen; Collagen triple helix repeat (20 copies)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    7338194..7543870 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011515360.3 → XP_011513662.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513662.1

    UniProtKB/Swiss-Prot
    A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09
    Conserved Domains (4) summary
    cd00109
    Location:1070 → 1123
    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:47 → 209
    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:799 → 974
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:360 → 419
    Collagen; Collagen triple helix repeat (20 copies)

  2. XM_011515358.4 → XP_011513660.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513660.1

    UniProtKB/Swiss-Prot
    A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09
    Conserved Domains (4) summary
    cd00109
    Location:1070 → 1123
    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:47 → 209
    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:799 → 974
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:360 → 419
    Collagen; Collagen triple helix repeat (20 copies)

  3. XM_011515359.2 → XP_011513661.1  collagen alpha-1(XXVIII) chain isoform X1

    See identical proteins and their annotated locations for XP_011513661.1

    UniProtKB/Swiss-Prot
    A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09
    Conserved Domains (4) summary
    cd00109
    Location:1070 → 1123
    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:47 → 209
    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:799 → 974
    VWA; von Willebrand factor type A domain
    pfam01391
    Location:360 → 419
    Collagen; Collagen triple helix repeat (20 copies)

  4. XM_047420314.1 → XP_047276270.1  collagen alpha-1(XXVIII) chain isoform X5

  5. XM_011515362.2 → XP_011513664.1  collagen alpha-1(XXVIII) chain isoform X3

    Conserved Domains (3) summary
    pfam01391
    Location:198 → 253
    Collagen; Collagen triple helix repeat (20 copies)
    cd00109
    Location:687 → 740
    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:416 → 591
    VWA; von Willebrand factor type A domain

  6. XM_047420313.1 → XP_047276269.1  collagen alpha-1(XXVIII) chain isoform X2

  7. XM_011515364.3 → XP_011513666.1  collagen alpha-1(XXVIII) chain isoform X6

    Conserved Domains (2) summary
    pfam01391
    Location:383 → 442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47 → 209
    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_011515363.3 → XP_011513665.1  collagen alpha-1(XXVIII) chain isoform X4

    See identical proteins and their annotated locations for XP_011513665.1

    UniProtKB/Swiss-Prot
    Q2UY09
    Conserved Domains (2) summary
    pfam01391
    Location:383 → 442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47 → 209
    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_011515365.3 → XP_011513667.1  collagen alpha-1(XXVIII) chain isoform X8

    Conserved Domains (2) summary
    pfam01391
    Location:383 → 442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47 → 209
    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_017012133.2 → XP_016867622.1  collagen alpha-1(XXVIII) chain isoform X7

  11. XM_011515366.3 → XP_011513668.1  collagen alpha-1(XXVIII) chain isoform X9

    Conserved Domains (2) summary
    pfam01391
    Location:383 → 442
    Collagen; Collagen triple helix repeat (20 copies)
    cd01450
    Location:47 → 209
    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_926936.4 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    7477054..7655035 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054358093.1 → XP_054214068.1  collagen alpha-1(XXVIII) chain isoform X1

  2. XM_054358095.1 → XP_054214070.1  collagen alpha-1(XXVIII) chain isoform X5

  3. XM_054358094.1 → XP_054214069.1  collagen alpha-1(XXVIII) chain isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q2UY09.2 GenPept UniProtKB/Swiss-Prot:Q2UY09

Gene LinkOut

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