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ubtf upstream binding transcription factor [ Danio rerio (zebrafish) ]

Gene ID: 368509, updated on 27-Mar-2024

Summary

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Official Symbol
ubtfprovided by ZNC
Official Full Name
upstream binding transcription factorprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030616-252
See related
Ensembl:ENSDARG00000035066 AllianceGenome:ZFIN:ZDB-GENE-030616-252
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
wu:fj38c10; si:dz180g5.3
Summary
Predicted to enable DNA binding activity. Predicted to be located in nucleus. Orthologous to several human genes including UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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See ubtf in Genome Data Viewer
Location:
chromosome: 3
Exon count:
22
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (20041906..20064884, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (19892166..19915220, complement)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene transmembrane and ubiquitin-like domain containing 2 Neighboring gene ataxin 7 like 3a Neighboring gene solute carrier family 4 member 1a (Diego blood group) Neighboring gene uncharacterized LOC110438598 Neighboring gene selenoprotein W, 2b

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. A subtracted cDNA library from the zebrafish (Danio rerio) embryonic inner ear. Coimbra RS, et al. Genome Res, 2002 Jun. PMID 12045154, Free PMC Article
  2. Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment. Baraban SC, et al. Nat Commun, 2013. PMID 24002024, Free PMC Article
  3. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
  4. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
  5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

See all (8) 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 DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase I core promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase I general transcription initiation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in positive regulation of transcription by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase I 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
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nucleolar transcription factor 1
Names
upstream binding transcription factor, RNA polymerase I

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_001005395.1 → NP_001005395.1  nucleolar transcription factor 1

    See identical proteins and their annotated locations for NP_001005395.1

    Status: VALIDATED

    Source sequence(s)
    BX088544
    UniProtKB/TrEMBL
    A0A0R4IDG0, A0A8M1N2F7, F1QZ83
    Related
    ENSDARP00000056613.6, ENSDART00000056614.8
    Conserved Domains (2) summary
    cd01390
    Location:104 → 168
    HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
    pfam14887
    Location:469 → 552
    HMG_box_5; HMG (high mobility group) box 5

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007114.7 Reference GRCz11 Primary Assembly

    Range
    20041906..20064884 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009299333.3 → XP_009297608.1  nucleolar transcription factor 1 isoform X1

    See identical proteins and their annotated locations for XP_009297608.1

    UniProtKB/TrEMBL
    A0A0R4IDG0, A0A8M1N2F7, F1QZ83
    Related
    ENSDARP00000131061.2, ENSDART00000165695.2
    Conserved Domains (2) summary
    cd01390
    Location:104 → 168
    HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
    pfam14887
    Location:469 → 552
    HMG_box_5; HMG (high mobility group) box 5

  2. XM_005163867.4 → XP_005163924.1  nucleolar transcription factor 1 isoform X1

    See identical proteins and their annotated locations for XP_005163924.1

    UniProtKB/TrEMBL
    A0A0R4IDG0, A0A8M1N2F7, F1QZ83
    Conserved Domains (2) summary
    cd01390
    Location:104 → 168
    HMGB-UBF_HMG-box; HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone ...
    pfam14887
    Location:469 → 552
    HMG_box_5; HMG (high mobility group) box 5
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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