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

    Gene ID: 340267, updated on 27-Nov-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    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

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 extracellular matrix 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 XI 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

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

    NCBI Reference Sequences (RefSeq)

    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_001037763.3NP_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: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
      pfam01391
      Location:360419
      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_011515360.3XP_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: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
      pfam01391
      Location:360419
      Collagen; Collagen triple helix repeat (20 copies)
    2. XM_011515358.4XP_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: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
      pfam01391
      Location:360419
      Collagen; Collagen triple helix repeat (20 copies)
    3. 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
      A4D101, A4D106, A4D107, A8MVR2, B9EGX9, Q2UY07, Q2UY08, Q2UY09
      Conserved Domains (4) summary
      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
      pfam01391
      Location:360419
      Collagen; Collagen triple helix repeat (20 copies)
    4. XM_047420314.1XP_047276270.1  collagen alpha-1(XXVIII) chain isoform X5

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

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

    7. XM_011515364.3XP_011513666.1  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 ...
    8. XM_011515363.3XP_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: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_011515365.3XP_011513667.1  collagen alpha-1(XXVIII) chain isoform X8

      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_017012133.2XP_016867622.1  collagen alpha-1(XXVIII) chain isoform X7

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

      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_926936.4 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_054358093.1XP_054214068.1  collagen alpha-1(XXVIII) chain isoform X1

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

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