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Aliases for UBTF Gene

Aliases for UBTF Gene

  • Upstream Binding Transcription Factor, RNA Polymerase I 2 3 5
  • Autoantigen NOR-90 3 4
  • UBF-1 3 4
  • UBF1 3 4
  • UBF 3 4
  • 90-KDa Nucleolus Organizer Region Autoantigen 3
  • Nucleolar Transcription Factor 1 3
  • Upstream-Binding Factor 1 4
  • CONDBA 3
  • NOR-90 3
  • UBF2 3

External Ids for UBTF Gene

Previous GeneCards Identifiers for UBTF Gene

  • GC17M042025
  • GC17M044461
  • GC17M042294
  • GC17M042757
  • GC17M042759
  • GC17M039637
  • GC17M038046
  • GC17M042282

Summaries for UBTF Gene

Entrez Gene Summary for UBTF Gene

  • 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]

GeneCards Summary for UBTF Gene

UBTF (Upstream Binding Transcription Factor, RNA Polymerase I) is a Protein Coding gene. Diseases associated with UBTF include Neurodegeneration, Childhood-Onset, With Brain Atrophy and Crest Syndrome. Among its related pathways are Ectoderm Differentiation and Gene Expression. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is UBTFL1.

UniProtKB/Swiss-Prot for UBTF Gene

  • Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element.

Gene Wiki entry for UBTF Gene

Additional gene information for UBTF Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for UBTF Gene

Genomics for UBTF Gene

GeneHancer (GH) Regulatory Elements for UBTF Gene

Promoters and enhancers for UBTF Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17I044214 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +2.4 2404 9.9 HDGF PKNOX1 ARID4B SIN3A ZNF2 IRF4 YY1 ZNF213 ZNF207 ZNF143 UBTF ENSG00000260793 ASB16-AS1 DBF4B MIR6782 LOC101926967 ENSG00000267394
GH17I043322 Enhancer 1.5 Ensembl ENCODE dbSUPER 244.6 +898.5 898463 1.6 CLOCK MLX ZFP64 YBX1 DMAP1 YY1 SLC30A9 ZNF213 ZNF416 ZNF143 ENSG00000267340 UBTF ASB16-AS1 ENSG00000267002 DHX8 HMGN1P29 TMUB2 NBR2 LINC00910 PLEKHH3
GH17I045143 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 110.8 -926.3 -926321 9.6 CLOCK MLX FEZF1 DMAP1 YBX1 IRF4 YY1 SLC30A9 ZNF213 E2F8 HEXIM1 ENSG00000276728 GC17M045149 ENSG00000262372 ASB16-AS1 UBTF TMUB2 ENSG00000224505 LINC02210 MAP3K14-AS1
GH17I044818 Enhancer 1.4 Ensembl ENCODE dbSUPER 107.2 -598.8 -598769 3.4 ARNT ZNF493 ZFP64 FEZF1 ZNF2 ZNF121 ZNF213 KLF7 FOS ZNF202 UBTF ASB16-AS1 TMUB2 GPATCH8 GJC1 MPP2 ENSG00000266918 LINC02210 ENSG00000260793 EFTUD2
GH17I045042 Enhancer 1.3 Ensembl ENCODE dbSUPER 71.8 -824.5 -824467 6.8 HDGF PKNOX1 CLOCK ZNF493 ZFP64 SIN3A ZNF121 ZNF213 FOS ZNF202 GC17M045043 UBTF ENSG00000262372 ASB16-AS1 TMUB2 DCAKD ENSG00000266918 ENSG00000224505 GPATCH8 LINC02210
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around UBTF on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the UBTF gene promoter:

Genomic Locations for UBTF Gene

Genomic Locations for UBTF Gene
16,594 bases
Minus strand

Genomic View for UBTF Gene

Genes around UBTF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
UBTF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for UBTF Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for UBTF Gene

Proteins for UBTF Gene

  • Protein details for UBTF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Nucleolar transcription factor 1
    Protein Accession:
    Secondary Accessions:
    • A8K6R8

    Protein attributes for UBTF Gene

    764 amino acids
    Molecular mass:
    89406 Da
    Quaternary structure:
    • Homodimer (By similarity). Interacts with TBP (PubMed:7982918). Interacts with TAF1A (PubMed:7491500). Interacts with RASL11A (By similarity). Binds to IRS1 and PIK3CA (By similarity). Interacts with DHX33 (PubMed:21930779). Interacts with PHF6 (PubMed:23229552). Interacts with CEBPA (isoform 1 and isoform 4) (PubMed:20075868). Interacts with DDX11 (PubMed:26089203). Interacts with NOP53 (PubMed:27729611).

    Three dimensional structures from OCA and Proteopedia for UBTF Gene

    Alternative splice isoforms for UBTF Gene


neXtProt entry for UBTF Gene

Post-translational modifications for UBTF Gene

  • Phosphorylated and activated by PIK3CA.
  • Ubiquitination at posLast=4545, isoforms=271, isoforms=2132, isoforms=2266, posLast=279279, isoforms=2333, and posLast=216216
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for UBTF Gene

Domains & Families for UBTF Gene

Gene Families for UBTF Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for UBTF Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with UBTF: view

No data available for UniProtKB/Swiss-Prot for UBTF Gene

Function for UBTF Gene

Molecular function for UBTF Gene

GENATLAS Biochemistry:
RNA polymerase 1,associated transcription factor 1,hUBF-NORGO essential for activation of transcription of 18S and 28S RNA
UniProtKB/Swiss-Prot Function:
Recognizes the ribosomal RNA gene promoter and activates transcription mediated by RNA polymerase I through cooperative interactions with the transcription factor SL1/TIF-IB complex. It binds specifically to the upstream control element.

Phenotypes From GWAS Catalog for UBTF Gene

Gene Ontology (GO) - Molecular Function for UBTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding IDA 22368283
GO:0001165 RNA polymerase I upstream control element sequence-specific DNA binding IDA 22368283
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IDA 26089203
GO:0003723 RNA binding IDA,HDA 22681889
genes like me logo Genes that share ontologies with UBTF: view
genes like me logo Genes that share phenotypes with UBTF: view

Animal Models for UBTF Gene

MGI Knock Outs for UBTF:

Animal Model Products

miRNA for UBTF Gene

miRTarBase miRNAs that target UBTF

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for UBTF Gene

Localization for UBTF Gene

Subcellular locations from UniProtKB/Swiss-Prot for UBTF Gene

Nucleus, nucleolus.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for UBTF gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for UBTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001650 fibrillar center IDA --
GO:0005634 nucleus IEA,IDA 22368283
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus TAS,ISS --
genes like me logo Genes that share ontologies with UBTF: view

Pathways & Interactions for UBTF Gene

genes like me logo Genes that share pathways with UBTF: view

SIGNOR curated interactions for UBTF Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for UBTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006356 regulation of transcription by RNA polymerase I NAS,TAS 12498690
GO:0006360 transcription by RNA polymerase I TAS,IMP 28777933
GO:0006361 transcription initiation from RNA polymerase I promoter TAS --
genes like me logo Genes that share ontologies with UBTF: view

Drugs & Compounds for UBTF Gene

(6) Drugs for UBTF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(4) Additional Compounds for UBTF Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with UBTF: view

Transcripts for UBTF Gene

Unigene Clusters for UBTF Gene

Upstream binding transcription factor, RNA polymerase I:
Representative Sequences:

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for UBTF Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: - - - - - -
SP2: - - - - -
SP3: - -
SP4: - -
SP7: - - - -
SP8: -
SP9: -

ExUns: 23 ^ 24 ^ 25a · 25b ^ 26

Relevant External Links for UBTF Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for UBTF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for UBTF Gene

Protein differential expression in normal tissues from HIPED for UBTF Gene

This gene is overexpressed in Peripheral blood mononuclear cells (22.9) and Blymphocyte (7.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for UBTF Gene

Protein tissue co-expression partners for UBTF Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of UBTF Gene:


SOURCE GeneReport for Unigene cluster for UBTF Gene:


Evidence on tissue expression from TISSUES for UBTF Gene

  • Nervous system(4.4)
  • Kidney(2.7)
  • Muscle(2.4)
  • Adrenal gland(2.3)
  • Bone marrow(2.3)
  • Gall bladder(2.3)
  • Heart(2.3)
  • Intestine(2.3)
  • Lung(2.3)
  • Lymph node(2.3)
  • Pancreas(2.3)
  • Skin(2.3)
  • Spleen(2.3)
  • Stomach(2.3)
  • Thyroid gland(2.3)
  • Blood(2.2)
genes like me logo Genes that share expression patterns with UBTF: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for UBTF Gene

Orthologs for UBTF Gene

This gene was present in the common ancestor of chordates.

Orthologs for UBTF Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia UBTF 33 34
  • 97.28 (n)
(Bos Taurus)
Mammalia UBF 34
  • 97 (a)
  • 94.08 (n)
(Monodelphis domestica)
Mammalia UBTF 34
  • 94 (a)
(Mus musculus)
Mammalia Ubtf 33 16 34
  • 91.97 (n)
(Rattus norvegicus)
Mammalia Ubtf 33
  • 90.49 (n)
(Canis familiaris)
Mammalia UBTF 34
  • 76 (a)
(Gallus gallus)
Aves -- 34
  • 89 (a)
  • 88.46 (n)
-- 34
  • 88 (a)
(Anolis carolinensis)
Reptilia UBTF 34
  • 85 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ubtf 33
  • 73.62 (n)
Str.10891 33
African clawed frog
(Xenopus laevis)
Amphibia MGC52607 33
(Danio rerio)
Actinopterygii ubtf 33 34
  • 69.86 (n)
zgc63557 33
Species where no ortholog for UBTF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for UBTF Gene

Gene Tree for UBTF (if available)
Gene Tree for UBTF (if available)

Paralogs for UBTF Gene

Paralogs for UBTF Gene Pseudogenes for UBTF Gene

genes like me logo Genes that share paralogs with UBTF: view

Variants for UBTF Gene

Sequence variations from dbSNP and Humsavar for UBTF Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs483352703 conflicting-interpretations-of-pathogenicity, not provided 44,207,459(-) C/A/T coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1000025061 -- 44,221,386(-) G/T 5_prime_UTR_variant, genic_upstream_transcript_variant, non_coding_transcript_variant, upstream_transcript_variant
rs1000078563 -- 44,220,661(-) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000193031 -- 44,206,813(-) G/T 3_prime_UTR_variant, downstream_transcript_variant, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1000281464 -- 44,209,981(-) G/A intron_variant

Structural Variations from Database of Genomic Variants (DGV) for UBTF Gene

Variant ID Type Subtype PubMed ID
dgv1469n106 CNV deletion 24896259
dgv529n67 CNV gain 20364138
dgv5602n54 CNV gain 21841781
dgv5603n54 CNV gain+loss 21841781
dgv5604n54 CNV loss 21841781
dgv5605n54 CNV loss 21841781
esv29087 CNV loss 19812545
nsv1071387 CNV deletion 25765185
nsv1146669 OTHER inversion 26484159
nsv510713 CNV deletion 20534489
nsv575067 CNV gain 21841781
nsv575071 CNV gain+loss 21841781
nsv575085 CNV loss 21841781
nsv833455 CNV loss 17160897

Variation tolerance for UBTF Gene

Residual Variation Intolerance Score: 8.15% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.39; 8.55% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for UBTF Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for UBTF Gene

Disorders for UBTF Gene

MalaCards: The human disease database

(7) MalaCards diseases for UBTF Gene - From: HGMD, OMIM, ClinVar, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
neurodegeneration, childhood-onset, with brain atrophy
  • condba
crest syndrome
  • calcinosis - raynaud phenomenon - esophageal involvement - sclerodactyly - telangiectasia
warsaw breakage syndrome
  • wabs
retinitis pigmentosa 11
  • rp11
dyskinesia of esophagus
  • dyskinesia of oesophagus
- elite association - COSMIC cancer census association via MalaCards
Search UBTF in MalaCards View complete list of genes associated with diseases

Additional Disease Information for UBTF

genes like me logo Genes that share disorders with UBTF: view

No data available for UniProtKB/Swiss-Prot and Genatlas for UBTF Gene

Publications for UBTF Gene

  1. Nucleolar retention of a translational C/EBPalpha isoform stimulates rDNA transcription and cell size. (PMID: 20075868) Müller C … Calkhoven CF (The EMBO journal 2010) 3 4 22 58
  2. Molecular cloning of the RNA polymerase I transcription factor hUBF/NOR-90 (UBTF) gene and localization to 17q21.3 by fluorescence in situ hybridization and radiation hybrid mapping. (PMID: 9126496) Matera AG … Chan EK (Genomics 1997) 2 3 22 58
  3. Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. (PMID: 2330041) Jantzen HM … Tjian R (Nature 1990) 3 4 22 58
  4. PICT-1 triggers a pro-death autophagy through inhibiting rRNA transcription and AKT/mTOR/p70S6K signaling pathway. (PMID: 27729611) Chen H … Huang L (Oncotarget 2016) 3 4 58
  5. The Warsaw breakage syndrome-related protein DDX11 is required for ribosomal RNA synthesis and embryonic development. (PMID: 26089203) Sun X … Ma L (Human molecular genetics 2015) 3 4 58

Products for UBTF Gene

  • Addgene plasmids for UBTF

Sources for UBTF Gene

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