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si:ch211-198a12.6 si:ch211-198a12.6 [ Danio rerio (zebrafish) ]

Gene ID: 563253, updated on 9-Dec-2024

Summary

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Official Symbol
si:ch211-198a12.6provided by ZNC
Official Full Name
si:ch211-198a12.6provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-1683
See related
Ensembl:ENSDARG00000074624 AllianceGenome:ZFIN:ZDB-GENE-030131-1683
Gene type
protein coding
RefSeq status
PREDICTED
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fa08f12; fb72e11; fb77h12; fc06d05; fe14e05; id:ibd2708; wu:fa08f12; wu:fb72e11; wu:fb77h12; wu:fc06d05; wu:fe14e05
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Is expressed in brain; immature eye; midbrain; and otic vesicle. [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
all
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Genomic context

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See si:ch211-198a12.6 in Genome Data Viewer
Location:
chromosome: 13
Exon count:
2
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (18507592..18512836)
105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (18376600..18381844)

Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene cell division cycle and apoptosis regulator 1 Neighboring gene storkhead box 1 Neighboring gene toll-like receptor 4b, duplicate a Neighboring gene toll-like receptor 4a, like

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. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. Sreenivasan R, et al. PLoS One, 2008 Mar 12. PMID 18335061, Free PMC Article
  2. A Toolbox for Efficient Proximity-Dependent Biotinylation in Zebrafish Embryos. Rosenthal SM, et al. Mol Cell Proteomics, 2021. PMID 34332124, Free PMC Article
  3. A gene expression screen in zebrafish embryogenesis. Kudoh T, et al. Genome Res, 2001 Dec. PMID 11731487
  4. 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
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in 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 LOC563253

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_001145579.1 → NP_001139051.1  uncharacterized protein LOC563253

    Status: PREDICTED

    Source sequence(s)
    BX908770
    UniProtKB/TrEMBL
    A0A8N1Z0T1, B8A688
    Related
    ENSDARP00000117362.1, ENSDART00000142622.2
    Conserved Domains (3) summary
    COG5048
    Location:247 → 523
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:282 → 302
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:323 → 347
    zf-H2C2_2; Zinc-finger double 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_007124.7 Reference GRCz11 Primary Assembly

    Range
    18507592..18512836
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394876.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    133685..138934
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

Gene LinkOut

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