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    col28a1a collagen, type XXVIII, alpha 1a [ Danio rerio (zebrafish) ]

    Gene ID: 555428, updated on 9-Dec-2024

    Summary

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    Official Symbol
    col28a1aprovided by ZNC
    Official Full Name
    collagen, type XXVIII, alpha 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-070705-84
    See related
    Ensembl:ENSDARG00000077084 AllianceGenome:ZFIN:ZDB-GENE-070705-84
    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
    col28a1; col28a1c; si:ch211-174d12.1; si:ch211-174d12.4
    Summary
    Predicted to enable serine-type endopeptidase inhibitor activity. Predicted to act upstream of or within cell adhesion. Predicted to be located in extracellular region. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Is expressed in intestine; liver; and muscle. Orthologous to human COL28A1 (collagen type XXVIII alpha 1 chain). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See col28a1a in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    36
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (25476220..25512695)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (25891997..25928472)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene UBAP1-MVB12-associated (UMA) domain containing 1 Neighboring gene replication protein A3 Neighboring gene core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase 1a Neighboring gene succinate dehydrogenase complex assembly factor 3

    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. Loss of the adaptor protein Sh3bgrl initiates ovarian fibrosis in zebrafish. Jin Z, et al. FEBS Lett, 2023 Nov. PMID 37698355
    2. Hyperactivation of mTORC1 in a double hit mutant zebrafish model of tuberous sclerosis complex causes increased seizure susceptibility and neurodevelopmental abnormalities. De Meulemeester AS, et al. Front Cell Dev Biol, 2022. PMID 36238691, Free PMC Article
    3. microRNA-29b knocks down collagen type I production in cultured rainbow trout (Oncorhynchus mykiss) cardiac fibroblasts. Johnston EF, et al. J Exp Biol, 2019 Sep 6. PMID 31439649
    4. Tissue-Specific Transcriptomes Reveal Gene Expression Trajectories in Two Maturing Skin Epithelial Layers in Zebrafish Embryos. Cokus SJ, et al. G3 (Bethesda), 2019 Oct 7. PMID 31431477, Free PMC Article
    5. Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol, 2016 Jan. PMID 26235539

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    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
    is_active_in basement membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of collagen trimer IEA
    Inferred from Electronic Annotation
    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 1a
    Names
    collagen type XXVIII alpha 1 c
    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_001348047.1 → NP_001334976.1  collagen, type XXVIII, alpha 1a precursor

      Status: VALIDATED

      Source sequence(s)
      BX927077, CR318650
      UniProtKB/TrEMBL
      A0A8M1P9N3, C0H5W1, F6NTC3
      Related
      ENSDARP00000102543.4, ENSDART00000112808.5
      Conserved Domains (4) summary
      pfam01391
      Location:491 → 548
      Collagen; Collagen triple helix repeat (20 copies)
      cd01450
      Location:49 → 214
      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 ...
      pfam00014
      Location:1117 → 1168
      Kunitz_BPTI; Kunitz/Bovine pancreatic trypsin inhibitor domain
      pfam00092
      Location:803 → 980
      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_007130.7 Reference GRCz11 Primary Assembly

      Range
      25476220..25512695
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068215131.1 → XP_068071232.1  collagen, type XXVIII, alpha 1a isoform X1

    Nucleotide Protein
    Heading Accession and Version

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