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spock3 SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 [ Danio rerio (zebrafish) ]

Gene ID: 562002, updated on 9-Dec-2024

Summary

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Official Symbol
spock3provided by ZNC
Official Full Name
SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3provided by ZNC
Primary source
ZFIN:ZDB-GENE-090311-24
See related
Ensembl:ENSDARG00000070266 AllianceGenome:ZFIN:ZDB-GENE-090311-24
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
im:7139568; si:dkey-285b22.1
Summary
Predicted to enable calcium ion binding activity. Predicted to be located in extracellular region. Is expressed in cardiovascular system; hypural; nervous system; and neural tube. Orthologous to human SPOCK3 (SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
human mouse all
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Genomic context

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See spock3 in Genome Data Viewer
Location:
chromosome: 1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (20635190..20706298)
105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (19942253..20013361)

Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3 Neighboring gene UDP glycosyltransferase 8 Neighboring gene tolloid-like 1 Neighboring gene carboxypeptidase E

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. Dynamic expression of sparc precedes formation of skeletal elements in the Medaka (Oryzias latipes). Renn J, et al. Gene, 2006 May 10. PMID 16545530
  2. Single-cell chromatin profiling reveals genetic programs activating proregenerative states in nonmyocyte cells. Dong Y, et al. Sci Adv, 2024 Feb 23. PMID 38381829, Free PMC Article
  3. Zebrafish models of skeletal dysplasia induced by cholesterol biosynthesis deficiency. Anderson RA, et al. Dis Model Mech, 2020 Jun 24. PMID 32430393, Free PMC Article
  4. An anti-inflammatory activation sequence governs macrophage transcriptional dynamics during tissue injury in zebrafish. Denans N, et al. Nat Commun, 2022 Sep 20. PMID 36127326, Free PMC Article
  5. Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish. Gomez GA, et al. PLoS One, 2009. PMID 19308258, 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 calcium ion binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
testican-3
Names
sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 3
testican 3

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_001327987.1 → NP_001314916.1  testican-3 isoform a precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a),
    Source sequence(s)
    CR381587, EB939186, EH433753, EH447295, EH458122, EH468737
    UniProtKB/TrEMBL
    A0A0R4IMY5, A0A8M1P8M2, A0A8M3BEW5
    Related
    ENSDARP00000135664.2, ENSDART00000166479.2
    Conserved Domains (4) summary
    smart00280
    Location:106 → 149
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:275 → 339
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:161 → 277
    SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
    pfam10591
    Location:160 → 265
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region

  2. NM_001327988.1 → NP_001314917.1  testican-3 isoform b precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    CR381587, EB939186, EH433753, EH447295, EH458122, EH468737
    UniProtKB/TrEMBL
    A0A8M1P451, A0A8M3BEW5, F1RAX3
    Related
    ENSDARP00000123781.1, ENSDART00000148518.3
    Conserved Domains (4) summary
    smart00280
    Location:103 → 146
    KAZAL; Kazal type serine protease inhibitors
    cd00191
    Location:272 → 336
    TY; Thyroglobulin type I repeats.; The N-terminal region of human thyroglobulin contains 11 type-1 repeats TY repeats are proposed to be inhibitors of cysteine proteases
    cd00252
    Location:158 → 274
    SPARC_EC; SPARC_EC; extracellular Ca2+ binding domain (containing 2 EF-hand motifs) of SPARC and related proteins (QR1, SC1/hevin, testican and tsc-36/FRP). SPARC (BM-40) is a multifunctional glycoprotein, a matricellular protein, that functions to regulate ...
    pfam10591
    Location:157 → 262
    SPARC_Ca_bdg; Secreted protein acidic and rich in cysteine Ca binding region

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_007112.7 Reference GRCz11 Primary Assembly

    Range
    20635190..20706298
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017355108.2 → XP_017210597.1  testican-3 isoform X1

    UniProtKB/TrEMBL
    A0A8M3BEW5, A0A8M6YZL5
    Related
    ENSDARP00000093744.4, ENSDART00000102969.5

Reference GRCz11 ALT_DRER_TU_2

Genomic

  1. NW_018395210.1 Reference GRCz11 ALT_DRER_TU_2

    Range
    581507..652614
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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