Human Gene UBTF (uc010czs.3) Description and Page Index
  Description: Homo sapiens upstream binding transcription factor, RNA polymerase I (UBTF), transcript variant 1, mRNA.
RefSeq Summary (NM_014233): 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].
Transcript (Including UTRs)
   Position: hg19 chr17:42,282,401-42,297,041 Size: 14,641 Total Exon Count: 21 Strand: -
Coding Region
   Position: hg19 chr17:42,284,610-42,295,597 Size: 10,988 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:42,282,401-42,297,041)mRNA (may differ from genome)Protein (764 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: UBF1_HUMAN
DESCRIPTION: RecName: Full=Nucleolar transcription factor 1; AltName: Full=Autoantigen NOR-90; AltName: Full=Upstream-binding factor 1; Short=UBF-1;
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.
SUBUNIT: Homodimer. Interacts with TBP. Interacts with RASL11A, TAF1A and TAF1D. Binds to IRS1 and PIK3CA (By similarity). Interacts with DHX33.
INTERACTION: P01106:MYC; NbExp=2; IntAct=EBI-396235, EBI-447544;
SUBCELLULAR LOCATION: Nucleus, nucleolus (By similarity).
PTM: Phosphorylated and activated by PIK3CA (By similarity).
SIMILARITY: Contains 6 HMG box DNA-binding domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: UBTF
Diseases sorted by gene-association score: neurodegeneration, childhood-onset, with brain atrophy* (500), warsaw breakage syndrome (9), dyskinesia of esophagus (9), retinitis pigmentosa 11 (8), gastric antral vascular ectasia (7), limited scleroderma (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 29.38 RPKM in Brain - Cerebellum
Total median expression: 885.18 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -154.70296-0.523 Picture PostScript Text
3' UTR -882.142209-0.399 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain
PF14887 - HMG (high mobility group) box 5

SCOP Domains:
47095 - HMG-box

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1K99
- NMR MuPIT

1L8Y
- NMR MuPIT

1L8Z
- NMR MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2HDZ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P17480
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001164 RNA polymerase I CORE element sequence-specific DNA binding
GO:0001165 RNA polymerase I upstream control element sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0097110 scaffold protein binding

Biological Process:
GO:0001188 RNA polymerase I transcriptional preinitiation complex assembly
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006356 regulation of transcription from RNA polymerase I promoter
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006360 transcription from RNA polymerase I promoter
GO:0006361 transcription initiation from RNA polymerase I promoter
GO:0006363 termination of RNA polymerase I transcription
GO:0045943 positive regulation of transcription from RNA polymerase I promoter
GO:1902659 regulation of glucose mediated signaling pathway

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  BC042297 - Homo sapiens upstream binding transcription factor, RNA polymerase I, mRNA (cDNA clone MGC:48801 IMAGE:4509695), complete cds.
AF289595 - Homo sapiens clone pp7879 unknown mRNA.
X53390 - Human mRNA for upstream binding factor (hUBF).
X53461 - Human mRNA for upstream binding factor (hUBF).
JD338783 - Sequence 319807 from Patent EP1572962.
JD270760 - Sequence 251784 from Patent EP1572962.
JD372548 - Sequence 353572 from Patent EP1572962.
JD362403 - Sequence 343427 from Patent EP1572962.
JD362402 - Sequence 343426 from Patent EP1572962.
JD381236 - Sequence 362260 from Patent EP1572962.
JD423214 - Sequence 404238 from Patent EP1572962.
AK291733 - Homo sapiens cDNA FLJ75058 complete cds, highly similar to Homo sapiens upstream binding transcription factor, RNA polymerase I (UBTF), mRNA.
JD105043 - Sequence 86067 from Patent EP1572962.
JD205745 - Sequence 186769 from Patent EP1572962.
JD388590 - Sequence 369614 from Patent EP1572962.
AK296917 - Homo sapiens cDNA FLJ53802 complete cds, highly similar to Nucleolar transcription factor 1.
X56688 - H.sapiens mRNA autoantigen NOR-90 3'-untranslated region.
AK298008 - Homo sapiens cDNA FLJ53818 complete cds, highly similar to Nucleolar transcription factor 1.
X56687 - H.sapiens mRNA for autoantigen NOR-90.
AK292577 - Homo sapiens cDNA FLJ77827 complete cds, highly similar to Human mRNA for upstream binding factor (hUBF).
JD389592 - Sequence 370616 from Patent EP1572962.
AK292518 - Homo sapiens cDNA FLJ77758 complete cds, highly similar to Homo sapiens upstream binding transcription factor, RNA polymerase I (UBTF), mRNA.
JD100164 - Sequence 81188 from Patent EP1572962.
JD380374 - Sequence 361398 from Patent EP1572962.
AK308321 - Homo sapiens cDNA, FLJ98269.
BC031423 - Homo sapiens upstream binding transcription factor, RNA polymerase I, mRNA (cDNA clone IMAGE:4341587), partial cds.
M61724 - Human UBF2 transcription factor mRNA.
JD172691 - Sequence 153715 from Patent EP1572962.
JD137749 - Sequence 118773 from Patent EP1572962.
JD382990 - Sequence 364014 from Patent EP1572962.
JD343975 - Sequence 324999 from Patent EP1572962.
JD271289 - Sequence 252313 from Patent EP1572962.
JD458507 - Sequence 439531 from Patent EP1572962.
JD458512 - Sequence 439536 from Patent EP1572962.
JD458511 - Sequence 439535 from Patent EP1572962.
JD056228 - Sequence 37252 from Patent EP1572962.
JD458513 - Sequence 439537 from Patent EP1572962.
JD458514 - Sequence 439538 from Patent EP1572962.
JD056229 - Sequence 37253 from Patent EP1572962.
JD317504 - Sequence 298528 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P17480 (Reactome details) participates in the following event(s):

R-HSA-73718 UBF-1 Binds rDNA Promoter
R-HSA-73722 Phosphorylation of UBF-1:rDNA Promoter
R-HSA-74994 Polymerase I Transcription Complex/Nascent Pre rRNA Complex pauses at the TTF-I:Sal Box
R-HSA-73769 Loss of Rrn3 from RNA Polymerase I promoter escape complex
R-HSA-74992 Dissociation of PTRF:Polymerase I/Nascent Pre rRNA Complex:TTF-I:Sal Box
R-HSA-73739 Recruitment of Acetylated SL1 to phosUBF-1:rDNA Promoter
R-HSA-74993 PTRF Binds the Polymerase I Transcription Complex/Nascent Pre rRNA Complex paused at the TTF-I:Sal Box
R-HSA-74986 Elongation of pre-rRNA transcript
R-HSA-427366 Transcription of intergenic spacer of the rRNA gene
R-HSA-73758 Recruitment of Active RNA Polymerase I to SL1:phos.UBF-1:rDNA Promoter
R-HSA-73728 RNA Polymerase I Promoter Opening
R-HSA-73863 RNA Polymerase I Transcription Termination
R-HSA-73772 RNA Polymerase I Promoter Escape
R-HSA-73854 RNA Polymerase I Promoter Clearance
R-HSA-73762 RNA Polymerase I Transcription Initiation
R-HSA-73864 RNA Polymerase I Transcription
R-HSA-73777 RNA Polymerase I Chain Elongation
R-HSA-427413 NoRC negatively regulates rRNA expression
R-HSA-74160 Gene expression (Transcription)
R-HSA-5250941 Negative epigenetic regulation of rRNA expression
R-HSA-212165 Epigenetic regulation of gene expression

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6R8, NM_014233, NP_055048, P17480, UBF, UBF1, UBF1_HUMAN
UCSC ID: uc010czs.3
RefSeq Accession: NM_014233
Protein: P17480 (aka UBF1_HUMAN)
CCDS: CCDS11480.1, CCDS42346.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014233.3
exon count: 21CDS single in 3' UTR: no RNA size: 4832
ORF size: 2295CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4076.00frame shift in genome: no % Coverage: 99.34
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.