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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
  • 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 Limited Scleroderma and Gastric Antral Vascular Ectasia. Among its related pathways are MAPK Signaling: Mitogen Stimulation Pathway and Validated targets of C-MYC transcriptional activation. GO annotations related to this gene include poly(A) RNA binding and 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

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

Genomics for UBTF Gene

Regulatory Elements for UBTF Gene

Enhancers for UBTF Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH17G044344 1.8 FANTOM5 ENCODE dbSUPER 12.3 -125.5 -125532 5.5 CREB3L1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF416 ZNF263 DHX8 SLC25A39 MEOX1 EFTUD2 RUNDC3A-AS1 ASB16-AS1 UBTF RUNDC3A ENSG00000221496 RNU6-453P
GH17G044152 0.4 ENCODE 10.8 +68.6 68578 1.2 ZSCAN21 HDAC5 UBTF PPY ENSG00000221044 TMEM101 GC17P044157 C17orf53
GH17G044323 1.7 FANTOM5 ENCODE dbSUPER 2.4 -103.9 -103869 3.8 HDGF PKNOX1 MLX CREB3L1 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 SLC4A1 SLC25A39 UBTF ASB16-AS1 ITGA2B TMUB2 ENSG00000267211
GH17G044288 1.4 FANTOM5 ENCODE 2.9 -67.0 -66966 0.4 HDGF PKNOX1 CREB3L1 ARNT ZNF766 CBX5 FOS REST ZNF592 SMARCA4 SLC4A1 UBTF SLC25A39 RN7SL507P GC17M044291 LOC105371790
GH17G044266 1.3 VISTA FANTOM5 2.8 -45.3 -45303 1.7 HDGF CREB3L1 ARNT SIN3A YBX1 ZNF766 CBX5 KLF13 JUNB REST SLC4A1 FAM187A UBTF SLC25A39 GC17M044250
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around UBTF on UCSC Golden Path with GeneCards custom track

Promoters for UBTF Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000094734 1326 4201 HDGF FOXA2 CREB3L1 AGO1 ARID4B SIN3A ZNF2 YY1 ZNF143 ZNF207

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

Genomic Location for UBTF Gene

Chromosome:
17
Start:
44,205,033 bp from pter
End:
44,221,626 bp from pter
Size:
16,594 bases
Orientation:
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:
    P17480-UBF1_HUMAN
    Recommended name:
    Nucleolar transcription factor 1
    Protein Accession:
    P17480
    Secondary Accessions:
    • A8K6R8

    Protein attributes for UBTF Gene

    Size:
    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).

    Three dimensional structures from OCA and Proteopedia for UBTF Gene

    Alternative splice isoforms for UBTF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for UBTF Gene

Post-translational modifications for UBTF Gene

  • Phosphorylated and activated by PIK3CA.
  • Ubiquitination at Lys45, Lys71, isoforms=2132, Lys266, posLast=279279, isoforms=2333, and Lys216
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for UBTF Gene

Domains & Families for UBTF Gene

Protein Domains for UBTF Gene

InterPro:
ProtoNet:

Graphical View of Domain Structure for InterPro Entry

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

No data available for Gene Families and 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.

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 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

Clone Products

  • Addgene plasmids for UBTF

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

COMPARTMENTS
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

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 from RNA polymerase I promoter NAS,TAS 12498690
GO:0006360 transcription from RNA polymerase I promoter TAS 2330041
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

(5) Drugs for UBTF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(5) 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

Clone Products

  • Addgene plasmids for UBTF

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: - -
SP5:
SP6:
SP7: - - - -
SP8: -
SP9: -

ExUns: 23 ^ 24 ^ 25a · 25b ^ 26
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:

Relevant External Links for UBTF Gene

GeneLoc Exon Structure for
UBTF
ECgene alternative splicing isoforms for
UBTF

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:

UBTF

SOURCE GeneReport for Unigene cluster for UBTF Gene:

Hs.89781

Evidence on tissue expression from TISSUES for UBTF Gene

  • Nervous system(4.3)
  • 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
chimpanzee
(Pan troglodytes)
Mammalia UBTF 34 35
  • 97.28 (n)
cow
(Bos Taurus)
Mammalia UBF 35
  • 97 (a)
OneToOne
UBTF 34
  • 94.08 (n)
oppossum
(Monodelphis domestica)
Mammalia UBTF 35
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Ubtf 34 16 35
  • 91.97 (n)
rat
(Rattus norvegicus)
Mammalia Ubtf 34
  • 90.49 (n)
dog
(Canis familiaris)
Mammalia UBTF 35
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves -- 35
  • 89 (a)
OneToMany
UBTF 34
  • 88.46 (n)
-- 35
  • 88 (a)
OneToMany
lizard
(Anolis carolinensis)
Reptilia UBTF 35
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ubtf 34
  • 73.62 (n)
Str.10891 34
African clawed frog
(Xenopus laevis)
Amphibia MGC52607 34
zebrafish
(Danio rerio)
Actinopterygii ubtf 34 35
  • 69.86 (n)
zgc63557 34
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

ENSEMBL:
Gene Tree for UBTF (if available)
TreeFam:
Gene Tree for UBTF (if available)

Paralogs for UBTF Gene

Paralogs for UBTF Gene

Pseudogenes.org 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 Sequence Context AA Info Type
rs483352703 other 44,207,459(-) ATGGG(A/G/T)ATGAG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs1000025061 -- 44,221,386(+) CGGTC(G/T)CTTGG intron-variant, nc-transcript-variant, upstream-variant-2KB, utr-variant-5-prime
rs1000078563 -- 44,220,661(+) CTGCC(C/T)GGGCG intron-variant, upstream-variant-2KB
rs1000193031 -- 44,206,813(+) AGGTG(G/T)CAGGC intron-variant, nc-transcript-variant, downstream-variant-500B, utr-variant-3-prime
rs1000281464 -- 44,209,981(+) TTACT(A/G)ATGAG 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)

Relevant External Links for UBTF Gene

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

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

Disorders for UBTF Gene

MalaCards: The human disease database

(3) MalaCards diseases for UBTF Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
limited scleroderma
  • crest syndrome
gastric antral vascular ectasia
  • watermelon stomach
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

Relevant External Links for UBTF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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) MA1ller C. … Calkhoven C.F. (EMBO J. 2010) 3 4 22 64
  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 A.G. … Chan E.K. (Genomics 1997) 2 3 22 64
  3. Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. (PMID: 2330041) Jantzen H.M. … Tjian R. (Nature 1990) 3 4 22 64
  4. The Warsaw breakage syndrome-related protein DDX11 is required for ribosomal RNA synthesis and embryonic development. (PMID: 26089203) Sun X. … Ma L. (Hum. Mol. Genet. 2015) 3 4 64
  5. Identification of DHX33 as a mediator of rRNA synthesis and cell growth. (PMID: 21930779) Zhang Y. … Weber J.D. (Mol. Cell. Biol. 2011) 3 4 64

Products for UBTF Gene

  • Addgene plasmids for UBTF

Sources for UBTF Gene

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