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si:dkey-34m19.3 si:dkey-34m19.3 [ Danio rerio (zebrafish) ]

Gene ID: 100005466, updated on 2-Nov-2024

Summary

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Official Symbol
si:dkey-34m19.3provided by ZNC
Official Full Name
si:dkey-34m19.3provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-2206
See related
Ensembl:ENSDARG00000078814 AllianceGenome:ZFIN:ZDB-GENE-030131-2206
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fb99f06; wu:fb99f06
Summary
Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
all
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Genomic context

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See si:dkey-34m19.3 in Genome Data Viewer
Location:
chromosome: 6
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (10701396..10715109, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (10465969..10479701, complement)

Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene potassium channel, voltage gated eag related subfamily H, member 7 Neighboring gene dynein, axonemal, heavy polypeptide 9 like Neighboring gene Sp3b transcription factor Neighboring gene Obg-like ATPase 1

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. The THAP domain of THAP1 is a large C2CH module with zinc-dependent sequence-specific DNA-binding activity. Clouaire T, et al. Proc Natl Acad Sci U S A, 2005 May 10. PMID 15863623, Free PMC Article
  2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
  3. 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
  4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
  5. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-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
  

General protein information

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Preferred Names
zinc finger protein 260

NCBI Reference Sequences (RefSeq)

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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_007117.7 Reference GRCz11 Primary Assembly

    Range
    10701396..10715109 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_068221896.1 → XP_068077997.1  zinc finger protein 260 isoform X3

  2. XM_005165797.5 → XP_005165854.1  zinc finger protein 260 isoform X5

    UniProtKB/TrEMBL
    A0A8M2BD67
    Conserved Domains (3) summary
    sd00017
    Location:343 → 363
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam05485
    Location:16 → 96
    THAP; THAP domain
    pfam13465
    Location:495 → 520
    zf-H2C2_2; Zinc-finger double domain

  3. XM_005165795.5 → XP_005165852.1  zinc finger protein 260 isoform X4

    UniProtKB/TrEMBL
    A0A8M2BD27
    Conserved Domains (4) summary
    COG2916
    Location:264 → 348
    Hns; DNA-binding protein H-NS [Transcription]
    sd00017
    Location:380 → 400
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam05485
    Location:16 → 96
    THAP; THAP domain
    pfam13465
    Location:532 → 557
    zf-H2C2_2; Zinc-finger double domain

  4. XM_005165796.5 → XP_005165853.1  zinc finger protein 260 isoform X2

    UniProtKB/TrEMBL
    A0A8M2BD35
    Conserved Domains (3) summary
    sd00017
    Location:380 → 400
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam05485
    Location:16 → 96
    THAP; THAP domain
    pfam13465
    Location:532 → 557
    zf-H2C2_2; Zinc-finger double domain

  5. XM_002662300.6 → XP_002662346.1  zinc finger protein 260 isoform X1

    UniProtKB/TrEMBL
    A0A8M1RH95, F1R8F3
    Related
    ENSDARP00000099658.2, ENSDART00000108656.4
    Conserved Domains (3) summary
    sd00017
    Location:417 → 437
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam05485
    Location:16 → 96
    THAP; THAP domain
    pfam13465
    Location:569 → 594
    zf-H2C2_2; Zinc-finger double domain
Nucleotide Protein
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