U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 368509, updated on 4-Jan-2025

    Summary

    Go to the top of the page Help
    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 RNA polymerase I core promoter sequence-specific DNA binding activity and RNA polymerase I general transcription initiation factor activity. Predicted to be involved in positive regulation of transcription by RNA polymerase I and transcription by RNA polymerase I. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in childhood-onset neurodegeneration with brain atrophy. Orthologous to several human genes including UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See ubtf in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (20041906..20063633, 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 selenoprotein W, 2b

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Nucleolar GTPase Bms1 displaces Ttf1 from RFB-sites to balance progression of rDNA transcription and replication. Zhu Y, et al. J Mol Cell Biol, 2022 Jan 29. PMID 34791311, Free PMC Article
    2. 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
    3. 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
    4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    5. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    nucleolar transcription factor 1
    Names
    upstream binding transcription factor, RNA polymerase I

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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: 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_007114.7 Reference GRCz11 Primary Assembly

      Range
      20041906..20063633 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009299333.4 → 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_005163867.5 → 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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.