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

    Gene ID: 340267, updated on 5-Mar-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
    mouse all
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    Genomic context

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    Location:
    7p21.3
    Exon count:
    47
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (7338194..7543870, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (7477054..7655035, complement)
    105.20220307 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
    • 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 (15) 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
    		  
    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_2023_10

    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

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

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