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UBTF upstream binding transcription factor [ Homo sapiens (human) ]

Gene ID: 7343, updated on 18-Sep-2018

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; Vega:OTTHUMG00000167585
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

Genomic context

See UBTF in Genome Data Viewer
Location:
17q21.31
Exon count:
26
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 17 NC_000017.11 (44205033..44221626, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (42282401..42298994, 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 transmembrane and ubiquitin like domain containing 2 Neighboring gene ataxin 7 like 3 Neighboring gene uncharacterized LOC101926967 Neighboring gene microRNA 6782 Neighboring gene SHC adaptor protein 1 pseudogene 2 Neighboring gene solute carrier family 4 member 1 (Diego blood group)

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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Component Evidence Code Pubs
fibrillar center IDA
Inferred from Direct Assay
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
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)

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
    5745..21594
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001076683.1NP_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/Swiss-Prot
    P17480
    Related
    ENSP00000345297.5, OTTHUMP00000236247, ENST00000343638.9, OTTHUMT00000395204
    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  2. NM_001076684.2NP_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/Swiss-Prot
    P17480
    Related
    ENSP00000377231.3, OTTHUMP00000236259, ENST00000393606.7, OTTHUMT00000395215
    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  3. NM_014233.3NP_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
    P17480
    Related
    ENSP00000390669.1, OTTHUMP00000236258, ENST00000436088.5, OTTHUMT00000395214
    Conserved Domains (3) summary
    cd01390
    Location:407470
    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 ...
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
    pfam14887
    Location:479563
    HMG_box_5; HMG (high mobility group) box 5

RNA

  1. NR_045058.1 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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p12 Primary Assembly

    Range
    44205033..44221626 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017024997.2XP_016880486.1  nucleolar transcription factor 1 isoform X1

  2. XM_017025002.2XP_016880491.1  nucleolar transcription factor 1 isoform X3

    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  3. XM_017025000.2XP_016880489.1  nucleolar transcription factor 1 isoform X3

    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  4. XM_006722059.4XP_006722122.1  nucleolar transcription factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006722122.1

    UniProtKB/Swiss-Prot
    P17480
    Related
    ENSP00000302640.4, ENST00000302904.8
    Conserved Domains (3) summary
    cd01390
    Location:407470
    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 ...
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
    pfam14887
    Location:479563
    HMG_box_5; HMG (high mobility group) box 5
  5. XM_017024995.2XP_016880484.1  nucleolar transcription factor 1 isoform X1

  6. XM_017024999.1XP_016880488.1  nucleolar transcription factor 1 isoform X1

  7. XM_017025001.1XP_016880490.1  nucleolar transcription factor 1 isoform X3

    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  8. XM_017024996.1XP_016880485.1  nucleolar transcription factor 1 isoform X1

  9. XM_024450907.1XP_024306675.1  nucleolar transcription factor 1 isoform X3

    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  10. XM_017024998.1XP_016880487.1  nucleolar transcription factor 1 isoform X1

  11. XM_017025003.2XP_016880492.1  nucleolar transcription factor 1 isoform X4

    UniProtKB/Swiss-Prot
    P17480
    Related
    ENSP00000432925.1, OTTHUMP00000236257, ENST00000526094.5
    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  12. XM_017025004.2XP_016880493.1  nucleolar transcription factor 1 isoform X4

    UniProtKB/Swiss-Prot
    P17480
    Related
    ENSP00000437180.1, ENST00000533177.5
    Conserved Domains (2) summary
    cd01390
    Location:112177
    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:442526
    HMG_box_5; HMG (high mobility group) box 5
  13. XM_006722060.3XP_006722123.1  nucleolar transcription factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006722123.1

    UniProtKB/Swiss-Prot
    P17480
    Related
    ENSP00000435708.1, OTTHUMP00000236261, ENST00000529383.5
    Conserved Domains (3) summary
    cd01390
    Location:407470
    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 ...
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
    pfam14887
    Location:479563
    HMG_box_5; HMG (high mobility group) box 5
  14. XM_006722061.3XP_006722124.1  nucleolar transcription factor 1 isoform X2

    See identical proteins and their annotated locations for XP_006722124.1

    UniProtKB/Swiss-Prot
    P17480
    Conserved Domains (3) summary
    cd01390
    Location:407470
    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 ...
    pfam00505
    Location:112179
    HMG_box; HMG (high mobility group) box
    pfam14887
    Location:479563
    HMG_box_5; HMG (high mobility group) box 5
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