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    ubtfl upstream binding transcription factor, like [ Danio rerio (zebrafish) ]

    Gene ID: 393978, updated on 9-Dec-2024

    Summary

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    Official Symbol
    ubtflprovided by ZNC
    Official Full Name
    upstream binding transcription factor, likeprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1159
    See related
    Ensembl:ENSDARG00000038780 AllianceGenome:ZFIN:ZDB-GENE-040426-1159
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    Tcfubf; zgc:63557
    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. Is expressed in adaxial cell; musculature system; and telencephalon. Human ortholog(s) of this gene implicated in childhood-onset neurodegeneration with brain atrophy. Orthologous to human UBTF (upstream binding transcription factor) and UBTFL1 (upstream binding transcription factor like 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See ubtfl in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (32357606..32387429, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (32374388..32405027, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene family with sequence similarity 49 member Ba Neighboring gene ArfGAP with SH3 domain, ankyrin repeat and PH domain 1a Neighboring gene solute carrier family 4 member 2a Neighboring gene tetratricopeptide repeat domain 19

    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. The African coelacanth genome provides insights into tetrapod evolution. Amemiya CT, et al. Nature, 2013 Apr 18. PMID 23598338, Free PMC Article
    2. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    3. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. Diotel N, et al. J Comp Neurol, 2015 Jun 1. PMID 25556858, 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 (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC63557

    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
    upstream binding transcription factor, 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_201003.1 → NP_957297.1  upstream binding transcription factor, like

      See identical proteins and their annotated locations for NP_957297.1

      Status: PROVISIONAL

      Source sequence(s)
      BC055140
      UniProtKB/TrEMBL
      Q7SY36
      Related
      ENSDARP00000056633.3, ENSDART00000056634.5
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 509
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    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
      32357606..32387429 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068223456.1 → XP_068079557.1  upstream binding transcription factor, like isoform X18

    2. XM_068223454.1 → XP_068079555.1  upstream binding transcription factor, like isoform X17

    3. XM_068223433.1 → XP_068079534.1  upstream binding transcription factor, like isoform X8

    4. XM_068223429.1 → XP_068079530.1  upstream binding transcription factor, like isoform X7

    5. XM_068223450.1 → XP_068079551.1  upstream binding transcription factor, like isoform X16

    6. XM_068223442.1 → XP_068079543.1  upstream binding transcription factor, like isoform X14

    7. XM_068223439.1 → XP_068079540.1  upstream binding transcription factor, like isoform X12

    8. XM_068223426.1 → XP_068079527.1  upstream binding transcription factor, like isoform X6

    9. XM_005163487.4 → XP_005163544.1  upstream binding transcription factor, like isoform X4

      UniProtKB/TrEMBL
      A0A8M2BAL3
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:428 → 504
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    10. XM_005163490.4 → XP_005163547.1  upstream binding transcription factor, like isoform X15

      UniProtKB/TrEMBL
      A0A8M2BAP6
      Related
      ENSDARP00000123462.1, ENSDART00000141757.3
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 503
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    11. XM_068223440.1 → XP_068079541.1  upstream binding transcription factor, like isoform X13

    12. XM_005163488.4 → XP_005163545.1  upstream binding transcription factor, like isoform X5

      UniProtKB/TrEMBL
      A0A8M2BAY0
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 503
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    13. XM_068223437.1 → XP_068079538.1  upstream binding transcription factor, like isoform X11

    14. XM_009298612.3 → XP_009296887.1  upstream binding transcription factor, like isoform X2

      UniProtKB/TrEMBL
      A0A8M3APU0
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 508
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    15. XM_009298614.3 → XP_009296889.1  upstream binding transcription factor, like isoform X10

      UniProtKB/TrEMBL
      A0A8M3AQA2
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 509
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    16. XM_005163489.4 → XP_005163546.1  upstream binding transcription factor, like isoform X9

      UniProtKB/TrEMBL
      A0A8M2BAL7
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 509
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    17. XM_009298613.3 → XP_009296888.1  upstream binding transcription factor, like isoform X3

      UniProtKB/TrEMBL
      A0A8M3B7S2
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 509
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    18. XM_005163486.4 → XP_005163543.1  upstream binding transcription factor, like isoform X1

      UniProtKB/TrEMBL
      A0A8M2BAT3, B0S7C3
      Conserved Domains (2) summary
      cd01390
      Location:198 → 263
      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 ...
      cl00082
      Location:433 → 509
      HMG-box; High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I ...

    19. XM_068223401.1 → XP_068079502.1  upstream binding transcription factor, like isoform X1

      UniProtKB/TrEMBL
      A0A8M2BAT3, B0S7C3
    Nucleotide Protein Strain
    Heading Accession and Version

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