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    col28a2a collagen, type XXVIII, alpha 2a [ Danio rerio (zebrafish) ]

    Gene ID: 100294690, updated on 4-Jan-2025

    Summary

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    Official Symbol
    col28a2aprovided by ZNC
    Official Full Name
    collagen, type XXVIII, alpha 2aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-4444
    See related
    Ensembl:ENSDARG00000076321 AllianceGenome:ZFIN:ZDB-GENE-030131-4444
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    wu:fd06c09; si:dkey-211m23.2
    Summary
    Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within cell adhesion. Predicted to be located in extracellular region. Predicted to be part of collagen type IX trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. Is expressed in floor plate; integument; muscle; rhombomere 5; and white matter. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See col28a2a in Genome Data Viewer
    Location:
    chromosome: 9
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (48298473..48370606, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (48601078..48673211, complement)

    Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene kelch-like family member 41a Neighboring gene Bardet-Biedl syndrome 5 Neighboring gene zgc:172182 Neighboring gene low density lipoprotein receptor-related protein 2a Neighboring gene retinol dehydrogenase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol, 2016 Jan. PMID 26235539
    2. Fishing for collagen function: About development, regeneration and disease. Bretaud S, et al. Semin Cell Dev Biol, 2019 May. PMID 30312775
    3. A screen for hoxb1-regulated genes identifies ppp1r14al as a regulator of the rhombomere 4 Fgf-signaling center. Choe SK, et al. Dev Biol, 2011 Oct 15. PMID 21787765, Free PMC Article
    4. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables extracellular matrix structural constituent conferring tensile strength 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
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in extracellular matrix organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of collagen type IX trimer IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in collagen-containing extracellular matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    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, type XXVIII, alpha 2a

    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_001159842.2 → NP_001153314.2  collagen, type XXVIII, alpha 2a precursor

      Status: VALIDATED

      Source sequence(s)
      CU182074
      UniProtKB/TrEMBL
      A0A8M1NUC2, F1QAB3
      Related
      ENSDARP00000100078.2, ENSDART00000115121.5
      Conserved Domains (4) summary
      pfam01391
      Location:502 → 561
      Collagen; Collagen triple helix repeat (20 copies)
      pfam00014
      Location:1151 → 1203
      Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
      pfam03157
      Location:273 → 614
      Glutenin_hmw; High molecular weight glutenin subunit
      pfam00092
      Location:817 → 995
      VWA; von Willebrand factor type A domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007120.7 Reference GRCz11 Primary Assembly

      Range
      48298473..48370606 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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