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    zgc:110158 zgc:110158 [ Danio rerio (zebrafish) ]

    Gene ID: 553590, updated on 4-Jan-2025

    Summary

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    Official Symbol
    zgc:110158provided by ZNC
    Official Full Name
    zgc:110158provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-050522-195
    See related
    Ensembl:ENSDARG00000056490 AllianceGenome:ZFIN:ZDB-GENE-050522-195
    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
    Summary
    Predicted to enable single-stranded DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human SSBP3 (single stranded DNA binding protein 3). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    all
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    Genomic context

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    See zgc:110158 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (41576922..41723165, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (41728167..41873838, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene D-2-hydroxyglutarate dehydrogenase Neighboring gene zinc finger protein 622 Neighboring gene uncharacterized LOC103910218 Neighboring gene uncharacterized LOC137488067

    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    2. 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
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC110158

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    uncharacterized protein LOC553590
    Names
    single-stranded DNA binding protein like

    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_001020567.2 → NP_001018403.1  uncharacterized protein LOC553590 isoform 2

      See identical proteins and their annotated locations for NP_001018403.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      CABZ01046039, CT476817, FO818670, FQ377997
      UniProtKB/TrEMBL
      A0A8M1N5Z1, Q503T8, X1WDX6
      Related
      ENSDARP00000128426.2, ENSDART00000155577.3
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 334
      SSDP; Single-stranded DNA binding protein, SSDP

    2. NM_001362582.1 → NP_001349511.1  uncharacterized protein LOC553590 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      CABZ01046039, CT476817, FO818670, FQ377997
      UniProtKB/TrEMBL
      A0A0R4IGD1, A0A8M3APY7
      Related
      ENSDARP00000134550.1, ENSDART00000170171.3
      Conserved Domains (2) summary
      smart00667
      Location:17 → 43
      LisH; Lissencephaly type-1-like homology motif
      pfam04503
      Location:81 → 362
      SSDP; Single-stranded DNA binding protein, SSDP

    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_007113.7 Reference GRCz11 Primary Assembly

      Range
      41576922..41723165 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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