U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    usf1 upstream transcription factor 1 [ Danio rerio (zebrafish) ]

    Gene ID: 393266, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    usf1provided by ZNC
    Official Full Name
    upstream transcription factor 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1072
    See related
    Ensembl:ENSDARG00000041689 AllianceGenome:ZFIN:ZDB-GENE-040426-1072
    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
    zgc:56547
    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. Is expressed in telencephalon. Human ortholog(s) of this gene implicated in cardiovascular system disease and type 2 diabetes mellitus. Orthologous to human USF1 (upstream transcription factor 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See usf1 in Genome Data Viewer
    Location:
    chromosome: 15
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 15 NC_007126.7 (21252558..21261192)
    105 previous assembly GRCz10 (GCF_000002035.5) 15 NC_007126.6 (21316441..21325460)

    Chromosome 15 - NC_007126.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137487745 Neighboring gene uncharacterized LOC101886465 Neighboring gene glucuronokinase with putative uridyl pyrophosphorylase Neighboring gene ubiquitin associated and SH3 domain containing Bb

    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. Comparative Analysis of Vertebrate Diurnal/Circadian Transcriptomes. Boyle G, et al. PLoS One, 2017. PMID 28076377, Free PMC Article
    2. A chemical screen in zebrafish embryonic cells establishes that Akt activation is required for neural crest development. Ciarlo C, et al. Elife, 2017 Aug 23. PMID 28832322, Free PMC Article
    3. Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors. Wang Y, et al. J Mol Evol, 2009 Jun. PMID 19449054
    4. 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
    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

    Go to the top of the page Help

    Homology

    Clone Names

    • MGC56547

    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 cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein dimerization activity 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

    Go to the top of the page Help
    Preferred Names
    upstream stimulatory factor 1

    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_200296.1 → NP_956590.1  upstream stimulatory factor 1

      See identical proteins and their annotated locations for NP_956590.1

      Status: PROVISIONAL

      Source sequence(s)
      BC049481
      UniProtKB/TrEMBL
      Q7ZWC6
      Related
      ENSDARP00000002107.8, ENSDART00000019636.10
      Conserved Domains (1) summary
      pfam00010
      Location:199 → 254
      HLH; Helix-loop-helix DNA-binding 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_007126.7 Reference GRCz11 Primary Assembly

      Range
      21252558..21261192
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005157507.5 → XP_005157564.1  upstream stimulatory factor 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M2B3U4, F1QUA1
      Conserved Domains (1) summary
      pfam00010
      Location:199 → 254
      HLH; Helix-loop-helix DNA-binding domain

    2. XM_005157509.5 → XP_005157566.1  upstream stimulatory factor 1 isoform X5

      UniProtKB/TrEMBL
      A0A8M2B4B2
      Conserved Domains (1) summary
      pfam00010
      Location:188 → 243
      HLH; Helix-loop-helix DNA-binding domain

    3. XM_005157508.5 → XP_005157565.1  upstream stimulatory factor 1 isoform X4

      See identical proteins and their annotated locations for XP_005157565.1

      UniProtKB/TrEMBL
      A0A0R4IXK2, A0A8M2B4D0
      Related
      ENSDARP00000139344.2, ENSDART00000162619.2
      Conserved Domains (1) summary
      pfam00010
      Location:189 → 244
      HLH; Helix-loop-helix DNA-binding domain

    4. XM_005157510.5 → XP_005157567.1  upstream stimulatory factor 1 isoform X9

      UniProtKB/TrEMBL
      A0A8M2B3M5
      Conserved Domains (1) summary
      pfam00010
      Location:178 → 233
      HLH; Helix-loop-helix DNA-binding domain

    5. XM_009291624.4 → XP_009289899.1  upstream stimulatory factor 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3APR4
      Conserved Domains (1) summary
      pfam00010
      Location:197 → 252
      HLH; Helix-loop-helix DNA-binding domain

    6. XM_068213485.1 → XP_068069586.1  upstream stimulatory factor 1 isoform X7

    7. XM_009291626.4 → XP_009289901.1  upstream stimulatory factor 1 isoform X6

      UniProtKB/TrEMBL
      A0A8M3B0Z9
      Related
      ENSDARP00000123553.2, ENSDART00000138676.3
      Conserved Domains (1) summary
      pfam00010
      Location:187 → 242
      HLH; Helix-loop-helix DNA-binding domain

    8. XM_068213488.1 → XP_068069589.1  upstream stimulatory factor 1 isoform X10

      Related
      ENSDARP00000122834.1, ENSDART00000142902.2

    9. XM_021481356.2 → XP_021337031.1  upstream stimulatory factor 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M9QLB1
      Conserved Domains (1) summary
      pfam00010
      Location:193 → 248
      HLH; Helix-loop-helix DNA-binding domain

    10. XM_021481357.2 → XP_021337032.1  upstream stimulatory factor 1 isoform X8

      UniProtKB/TrEMBL
      A0A8M9Q076
      Conserved Domains (1) summary
      pfam00010
      Location:183 → 238
      HLH; Helix-loop-helix DNA-binding domain

    11. XM_009291625.4 → XP_009289900.1  upstream stimulatory factor 1 isoform X4

      See identical proteins and their annotated locations for XP_009289900.1

      UniProtKB/TrEMBL
      A0A0R4IXK2, A0A8M2B4D0
      Conserved Domains (1) summary
      pfam00010
      Location:189 → 244
      HLH; Helix-loop-helix DNA-binding domain

    12. XM_021481355.2 → XP_021337030.1  upstream stimulatory factor 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M3APR4
      Conserved Domains (1) summary
      pfam00010
      Location:197 → 252
      HLH; Helix-loop-helix DNA-binding domain

    13. XM_068213486.1 → XP_068069587.1  upstream stimulatory factor 1 isoform X7

    14. XM_068213484.1 → XP_068069585.1  upstream stimulatory factor 1 isoform X6

      UniProtKB/TrEMBL
      A0A8M3B0Z9

    15. XM_068213487.1 → XP_068069588.1  upstream stimulatory factor 1 isoform X8

      UniProtKB/TrEMBL
      A0A8M9Q076
    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.