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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
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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

Gene LinkOut

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