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 [ Homo sapiens (human) ]

    Gene ID: 7343, updated on 9-Dec-2024

    Summary

    Official Symbol
    UBTFprovided by HGNC
    Official Full Name
    upstream binding transcription factorprovided by HGNC
    Primary source
    HGNC:HGNC:12511
    See related
    Ensembl:ENSG00000108312 MIM:600673; AllianceGenome:HGNC:12511
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    UBF; UBF1; UBF2; UBF-1; CONDBA; NOR-90
    Summary
    This gene encodes a member of the HMG-box DNA-binding protein family. The encoded protein plays a critical role in ribosomal RNA transcription as a key component of the pre-initiation complex, mediating the recruitment of RNA polymerase I to rDNA promoter regions. The encoded protein may also play important roles in chromatin remodeling and pre-rRNA processing, and its activity is regulated by both phosphorylation and acetylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. Pseudogenes of this gene are located on the short arm of chromosomes 3, 11 and X and the long arm of chromosome 11. [provided by RefSeq, Aug 2011]
    Expression
    Ubiquitous expression in lymph node (RPKM 22.2), thyroid (RPKM 21.0) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See UBTF in Genome Data Viewer
    Location:
    17q21.31
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (44205040..44221304, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (45058143..45074402, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42282408..42298672, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ASB16 antisense RNA 1 Neighboring gene ankyrin repeat and SOCS box containing 16 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42263664-42264198 Neighboring gene transmembrane and ubiquitin like domain containing 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42274223-42275146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42275147-42276069 Neighboring gene ataxin 7 like 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42276274-42276829 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42277555-42278093 Neighboring gene ATXN7L3 antisense RNA 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:42278094-42278631 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42284331-42284831 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:42285473-42286672 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8579 Neighboring gene Sharpr-MPRA regulatory region 7848 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8581 Neighboring gene microRNA 6782 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8582 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:42296769-42296933 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42299194-42299798 Neighboring gene SHC adaptor protein 1 pseudogene 2 Neighboring gene MPRA-validated peak2857 silencer Neighboring gene MPRA-validated peak2858 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:42315119-42315750 Neighboring gene solute carrier family 4 member 1 (Diego blood group) Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:42334442-42335398

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    nucleolar transcription factor 1
    Names
    90-kDa nucleolus organizer region autoantigen
    autoantigen NOR-90
    upstream binding transcription factor, RNA polymerase I

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_029864.1 RefSeqGene

      Range
      6952..21587
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001076683.2NP_001070151.1  nucleolar transcription factor 1 isoform b

      See identical proteins and their annotated locations for NP_001070151.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (b), which is shorter than isoform a.
      Source sequence(s)
      BC042297, BP230502
      Consensus CDS
      CCDS42346.1
      UniProtKB/TrEMBL
      A0A994J4N4
      Related
      ENSP00000345297.5, ENST00000343638.9
      Conserved Domains (3) summary
      cd01390
      Location:370433
      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 chromosomal ...
      pfam14887
      Location:442525
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112179
      HMG_box; HMG (high mobility group) box
    2. NM_001076684.3NP_001070152.1  nucleolar transcription factor 1 isoform b

      See identical proteins and their annotated locations for NP_001070152.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (b), which is shorter than isoform a.
      Source sequence(s)
      AC004596, BC042297, X56687
      Consensus CDS
      CCDS42346.1
      UniProtKB/TrEMBL
      A0A994J4N4
      Related
      ENSP00000377231.3, ENST00000393606.7
      Conserved Domains (3) summary
      cd01390
      Location:370433
      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 chromosomal ...
      pfam14887
      Location:442525
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112179
      HMG_box; HMG (high mobility group) box
    3. NM_014233.4NP_055048.1  nucleolar transcription factor 1 isoform a

      See identical proteins and their annotated locations for NP_055048.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AC004596, AK291733, BC042297
      Consensus CDS
      CCDS11480.1
      UniProtKB/Swiss-Prot
      A8K6R8, P17480
      UniProtKB/TrEMBL
      A8K962
      Related
      ENSP00000390669.1, ENST00000436088.6
      Conserved Domains (3) summary
      cd01390
      Location:407470
      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 chromosomal ...
      pfam14887
      Location:479562
      HMG_box_5; HMG (high mobility group) box 5
      pfam00505
      Location:112179
      HMG_box; HMG (high mobility group) box

    RNA

    1. NR_045058.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK292518, BC042297

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      44205040..44221304 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      45058143..45074402 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)