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

Gene ID: 553590, updated on 17-Sep-2024

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) and SSBP4 (single stranded DNA binding protein 4). [provided by Alliance of Genome Resources, Apr 2022]
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 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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