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... See more...

Aliases for UBTF Gene

Aliases for UBTF Gene

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

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) is a Protein Coding gene. Diseases associated with UBTF include Neurodegeneration, Childhood-Onset, With Brain Atrophy and Retinoblastoma. Among its related pathways are RNA Polymerase I Promoter Escape and Assembly of RNA Polymerase-I Initiation Complex. Gene Ontology (GO) annotations related to this gene include binding. An important paralog of this gene is UBTFL1.

UniProtKB/Swiss-Prot Summary 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 , Rfam classification and piRNA Summary for UBTF Gene

Genomics for UBTF Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for UBTF Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around UBTF on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for UBTF

Top Transcription factor binding sites by QIAGEN in the UBTF gene promoter:
  • AP-1
  • Sp1
  • TBP

Genomic Locations for UBTF Gene

Genomic Locations for UBTF Gene
chr17:44,205,033-44,221,626
(GRCh38/hg38)
Size:
16,594 bases
Orientation:
Minus strand
chr17:42,282,401-42,298,994
(GRCh37/hg19)
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). Interacts with NOP53 (PubMed:27729611).

    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, Lys132, Lys266, Lys279, and Lys333
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for UBTF Gene

Domains & Families for UBTF Gene

Gene Families for UBTF Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for UBTF Gene

Suggested Antigen Peptide Sequences for UBTF Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ53802, highly similar to Nucleolar transcription factor 1 (B4DLB0_HUMAN)
  • Ribosomal RNA upstream binding transcription factor (O00164_HUMAN)
  • UBTF protein (Q05BZ1_HUMAN)
  • Upstream binding transcription factor, RNA polymerase I (Q9BQR2_HUMAN)
  • Upstream-binding factor 1 (UBF1_HUMAN)
genes like me logo Genes that share domains with UBTF: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for UBTF Gene

Function for UBTF Gene

Molecular function for UBTF Gene

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.
GENATLAS Biochemistry:
RNA polymerase 1,associated transcription factor 1,hUBF-NORGO essential for activation of transcription of 18S and 28S RNA

Phenotypes From GWAS Catalog for UBTF Gene

Gene Ontology (GO) - Molecular Function for UBTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
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
genes like me logo Genes that share ontologies with UBTF: view
genes like me logo Genes that share phenotypes with UBTF: view

Human Phenotype Ontology for UBTF Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for UBTF Gene

MGI Knock Outs for UBTF:
  • Ubtf Ubtf<tm1.2Tmss>
  • Ubtf Ubtf<tm1Tmss>

Animal Model Products

CRISPR Products

miRNA for UBTF Gene

miRTarBase miRNAs that target UBTF

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for UBTF

Clone Products

  • Addgene plasmids for UBTF

No data available for Enzyme Numbers (IUBMB) , 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 3
cytoskeleton 2
plasma membrane 1
extracellular 1
mitochondrion 1
endoplasmic reticulum 1
golgi apparatus 1

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 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

Pathways by source for UBTF Gene

1 R&D Systems pathway for UBTF Gene
2 Qiagen pathways for UBTF Gene
  • Assembly of RNA Polymerase-I Initiation Complex
  • ERK Signaling

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:0001188 RNA polymerase I preinitiation complex assembly IEA --
GO:0006356 regulation of transcription by RNA polymerase I NAS 12498690
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0006360 transcription by RNA polymerase I 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

(7) Drugs for UBTF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) 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

mRNA/cDNA for UBTF Gene

3 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
14 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for UBTF

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

Expression for UBTF Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for UBTF Gene



Protein tissue co-expression partners for UBTF Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for UBTF

SOURCE GeneReport for Unigene cluster for UBTF Gene:

Hs.89781

Evidence on tissue expression from TISSUES for UBTF Gene

  • Nervous system(4.5)
  • Skin(3.3)
  • Kidney(3.1)
  • Intestine(3)
  • Lung(2.9)
  • Muscle(2.8)
  • Pancreas(2.8)
  • Thyroid gland(2.7)
  • Bone marrow(2.7)
  • Adrenal gland(2.7)
  • Spleen(2.6)
  • Heart(2.6)
  • Blood(2.6)
  • Lymph node(2.6)
  • Liver(2.4)
  • Gall bladder(2.3)
  • Stomach(2.3)
genes like me logo Genes that share expression patterns with UBTF: view

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 30 31
  • 97.28 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia UBF 31
  • 97 (a)
OneToOne
UBTF 30
  • 94.08 (n)
Oppossum
(Monodelphis domestica)
Mammalia UBTF 31
  • 94 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ubtf 30 17 31
  • 91.97 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ubtf 30
  • 90.49 (n)
Dog
(Canis familiaris)
Mammalia UBTF 31
  • 76 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 89 (a)
OneToMany
UBTF 30
  • 88.46 (n)
-- 31
  • 88 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia UBTF 31
  • 85 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ubtf 30
  • 73.62 (n)
Str.10891 30
African clawed frog
(Xenopus laevis)
Amphibia MGC52607 30
Zebrafish
(Danio rerio)
Actinopterygii ubtf 30 31
  • 69.86 (n)
OneToOne
zgc63557 30
Species where no ortholog for UBTF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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)
Aminode:
Evolutionary constrained regions (ECRs) for UBTF: view image

Paralogs for UBTF Gene

(4) SIMAP similar genes for UBTF Gene using alignment to 9 proteins:

  • UBF1_HUMAN
  • B4DLB0_HUMAN
  • E9PKP7_HUMAN
  • E9PLT2_HUMAN
  • E9PMM2_HUMAN
  • H0YDH7_HUMAN
  • O00164_HUMAN
  • Q05BZ1_HUMAN
  • Q9BQR2_HUMAN

Pseudogenes.org Pseudogenes for UBTF Gene

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

Variants for UBTF Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for UBTF Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
780067 Likely Benign: not provided 44,207,502(-) G/A NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS_VARIANT
rs1236405535 Likely Pathogenic: not provided 44,211,605(-) C/T SPLICE_DONOR_VARIANT
rs1555577265 Likely Pathogenic: not provided 44,207,710(-) G/A NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
rs1555582065 Pathogenic/Likely Pathogenic: Infantile or childhood onset neurodegenerative disease, global developmental delay, and intellectual disability; UBTF E210K Neuroregression Syndrome; UBTF-Related Disorder; Childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder. Neurodegeneration, childhood-onset, with brain atrophy (CONDBA) [MIM:617672] 44,212,851(-) C/Tp.Glu210Lys MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
rs1567797466 Likely Pathogenic: not provided 44,211,729(-) G/C NONSENSE,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for UBTF Gene

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)
UBTF
SNPedia medical, phenotypic, and genealogical associations of SNPs for
UBTF

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

(8) MalaCards diseases for UBTF Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search UBTF in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

UBF1_HUMAN
  • Neurodegeneration, childhood-onset, with brain atrophy (CONDBA) [MIM:617672]: An autosomal dominant neurodegenerative disease with onset in childhood, characterized by progressive cortical atrophy, developmental delay, developmental regression, loss of motor skills and ambulation, absence of language, and intellectual disability. {ECO:0000269 PubMed:28777933}. Note=The disease is caused by mutations affecting the gene represented in this entry.
genes like me logo Genes that share disorders with UBTF: view

No data available for 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 23
  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 23
  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 23
  4. A recurrent de novo missense mutation in UBTF causes developmental neuroregression. (PMID: 29300972) Toro C … LeDoux MS (Human molecular genetics 2018) 2 3
  5. Heterozygous De Novo UBTF Gain-of-Function Variant Is Associated with Neurodegeneration in Childhood. (PMID: 28777933) Edvardson S … Elpeleg O (American journal of human genetics 2017) 3 4

Products for UBTF Gene