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Ubtf upstream binding transcription factor, RNA polymerase I [ Mus musculus (house mouse) ]

Gene ID: 21429, updated on 3-Apr-2024

Summary

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Official Symbol
Ubtfprovided by MGI
Official Full Name
upstream binding transcription factor, RNA polymerase Iprovided by MGI
Primary source
MGI:MGI:98512
See related
Ensembl:ENSMUSG00000020923 AllianceGenome:MGI:98512
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
UBF; UBF1; UBF-1; NOR-90; Tcfubf; A930005G04Rik
Summary
Predicted to enable several functions, including RNA polymerase I general transcription initiation factor activity; RNA polymerase I transcription regulatory region sequence-specific DNA binding activity; and scaffold protein binding activity. Involved in positive regulation of transcription by RNA polymerase I. Acts upstream of or within cellular response to leukemia inhibitory factor; rDNA heterochromatin assembly; and transcription elongation from RNA polymerase I promoter. Located in nucleolus. Is expressed in several structures, including brain; branchial arch; early conceptus; genitourinary system; and limb. Orthologous to human UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 28.0), liver E14 (RPKM 15.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Ubtf in Genome Data Viewer
Location:
11 66.29 cM; 11 D
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (102195393..102214738, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (102304560..102323649, complement)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E1432 Neighboring gene transmembrane and ubiquitin-like domain containing 2 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:102156604-102156807 Neighboring gene ataxin 7-like 3 Neighboring gene STARR-positive B cell enhancer ABC_E469 Neighboring gene predicted gene, 33851 Neighboring gene STARR-positive B cell enhancer ABC_E5281 Neighboring gene STARR-seq mESC enhancer starr_30800 Neighboring gene solute carrier family 4 (anion exchanger), member 1 Neighboring gene Bloodlinc, erythroid developmental long intergenic non-protein coding transcript Neighboring gene predicted gene, 34253

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Polymerase I pathway inhibitor ameliorates experimental autoimmune encephalomyelitis. Achiron A, et al. J Neuroimmunol, 2013 Oct 15. PMID 23998422
  2. The splice variants of UBF differentially regulate RNA polymerase I transcription elongation in response to ERK phosphorylation. Stefanovsky VY, et al. Nucleic Acids Res, 2008 Sep. PMID 18676449, Free PMC Article
  3. Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF. Hisatake K, et al. Nucleic Acids Res, 1991 Sep 11. PMID 1891354, Free PMC Article
  4. Behavioral and molecular effects of Ubtf knockout and knockdown in mice. Hori RT, et al. Brain Res, 2022 Oct 15. PMID 35973608, Free PMC Article
  5. A recurrent de novo missense mutation in UBTF causes developmental neuroregression. Toro C, et al. Hum Mol Genet, 2018 Feb 15. PMID 29300972, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. UBF and Nopp140 dynamic redistribution between the two-cell and blastocyst stages (time of implantation) is correlated with morphological and structural modifications that occur in embryonic nucleolar compartments.
    Title: Three-Dimensional Distribution of UBF and Nopp140 in Relationship to Ribosomal DNA Transcription During Mouse Preimplantation Development.
  2. inhibition of UBF function is a major factor in the cytotoxicity of cisplatin; its depletion selectively induces p53-independent apoptotic death in transformed cells
    Title: Depletion of the cisplatin targeted HMGB-box factor UBF selectively induces p53-independent apoptotic death in transformed cells.
  3. Loss of UBF also unexpectedly induced the formation in cells of a large sub-nuclear structure resembling the nucleolar precursor body (NPB) of oocytes and early embryos.
    Title: Conditional inactivation of Upstream Binding Factor reveals its epigenetic functions and the existence of a somatic nucleolar precursor body.
  4. we have uncovered a novel role for UBTF1 and UBTF2 in maintaining genome stability through coordinating the expression of highly transcribed Pol I (UBTF1 activity) and Pol II genes (UBTF2 activity).
    Title: A novel role for the Pol I transcription factor UBTF in maintaining genome stability through the regulation of highly transcribed Pol II genes.
  5. Inhibition of the POL1 pathway delays and suppresses the development of experimental autoimmune encephalomyelitis and ameliorates the disease in mice with persistent clinical signs.
    Title: Polymerase I pathway inhibitor ameliorates experimental autoimmune encephalomyelitis.
  6. UBF1 mutation (K352A, K352Q, and K352R) decreased rDNA transcriptional activity.
    Title: Dysregulation of upstream binding factor-1 acetylation at K352 is linked to impaired ribosomal DNA transcription in Huntington's disease.
  7. augmented ribosome biogenesis occurs in UBF-dependent manner during increased protein synthesis induced by high glucose in glomerular epithelial cells that correlates with UBF activation and renal hypertrophy in rodents with type 1 and type 2 diabetes.
    Title: Ribosomal biogenesis induction by high glucose requires activation of upstream binding factor in kidney glomerular epithelial cells.
  8. Myeloid cell IGF-1 receptor-mediated regulation of UBF-1 levels involves IRS-1 and ERK pathways.
    Title: Dual regulation of upstream binding factor 1 levels by IRS-1 and ERKs in IGF-1-receptor signaling.
  9. Phosphatidylinositol 3-kinase subunit directly phosphorylates and activates UBF1, an exclusively nucleolar protein.
    Title: Control of cell size through phosphorylation of upstream binding factor 1 by nuclear phosphatidylinositol 3-kinase.
  10. increased UBF levels correlate with elevated pressure load and increased cardiac growth rates
    Title: Cardiac hypertrophy in vivo is associated with increased expression of the ribosomal gene transcription factor UBF.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (5)  1 citation
  • Endonuclease-mediated (3) 

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase I cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase I core promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase I core promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase I general transcription initiation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase I general transcription initiation factor activity ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding ISO
Inferred from Sequence Orthology
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables scaffold protein binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within cellular response to leukemia inhibitory factor IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of transcription by RNA polymerase I IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription by RNA polymerase I IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase I ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within transcription elongation by RNA polymerase I IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in transcription initiation at RNA polymerase I promoter ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in fibrillar center ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
nucleolar transcription factor 1
Names
transcription factor UBF
upstream-binding factor 1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001044383.4 → NP_001037848.1  nucleolar transcription factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001037848.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT6
    Related
    ENSMUSP00000102736.3, ENSMUST00000107119.9
    Conserved Domains (2) summary
    cd01390
    Location:112 → 177
    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 chromosomal ...
    pfam14887
    Location:442 → 525
    HMG_box_5; HMG (high mobility group) box 5

  2. NM_001302954.3 → NP_001289883.1  nucleolar transcription factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001289883.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT6
    Related
    ENSMUSP00000136310.2, ENSMUST00000178839.8
    Conserved Domains (2) summary
    cd01390
    Location:112 → 177
    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 chromosomal ...
    pfam14887
    Location:442 → 525
    HMG_box_5; HMG (high mobility group) box 5

  3. NM_001302955.3 → NP_001289884.1  nucleolar transcription factor 1 isoform 3

    See identical proteins and their annotated locations for NP_001289884.1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS79056.1
    UniProtKB/TrEMBL
    A2AWT7, Q9DBH1
    Related
    ENSMUSP00000006754.8, ENSMUST00000006754.14
    Conserved Domains (3) summary
    COG5648
    Location:311 → 510
    NHP6B; Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
    cd01390
    Location:112 → 177
    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:442 → 525
    HMG_box_5; HMG (high mobility group) box 5

  4. NM_001362544.2 → NP_001349473.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT5
    Related
    ENSMUSP00000133611.2, ENSMUST00000173870.8
    Conserved Domains (3) summary
    cd01390
    Location:407 → 470
    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 chromosomal ...
    pfam14887
    Location:479 → 562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112 → 179
    HMG_box; HMG (high mobility group) box

  5. NM_001362545.2 → NP_001349474.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT5
    Related
    ENSMUSP00000078539.5, ENSMUST00000079589.11
    Conserved Domains (3) summary
    cd01390
    Location:407 → 470
    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 chromosomal ...
    pfam14887
    Location:479 → 562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112 → 179
    HMG_box; HMG (high mobility group) box

  6. NM_001362547.2 → NP_001349476.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT6
    Conserved Domains (2) summary
    cd01390
    Location:112 → 177
    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 chromosomal ...
    pfam14887
    Location:442 → 525
    HMG_box_5; HMG (high mobility group) box 5

  7. NM_001362548.2 → NP_001349477.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS36343.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT6
    Related
    ENSMUSP00000102734.3, ENSMUST00000107117.9
    Conserved Domains (2) summary
    cd01390
    Location:112 → 177
    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 chromosomal ...
    pfam14887
    Location:442 → 525
    HMG_box_5; HMG (high mobility group) box 5

  8. NM_001362549.2 → NP_001349478.1  nucleolar transcription factor 1 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Conserved Domains (2) summary
    cd01390
    Location:308 → 371
    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 chromosomal ...
    pfam14887
    Location:380 → 464
    HMG_box_5; HMG (high mobility group) box 5

  9. NM_001362552.2 → NP_001349481.1  nucleolar transcription factor 1 isoform 7

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS88262.1
    UniProtKB/TrEMBL
    E9Q4A8
    Related
    ENSMUSP00000131930.2, ENSMUST00000128016.2
    Conserved Domains (1) summary
    cd01390
    Location:112 → 158
    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 chromosomal ...

  10. NM_001404620.1 → NP_001391549.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6

  11. NM_001404621.1 → NP_001391550.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6

  12. NM_001404622.1 → NP_001391551.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6

  13. NM_001404623.1 → NP_001391552.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT5

  14. NM_001404624.1 → NP_001391553.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6

  15. NM_001404625.1 → NP_001391554.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6

  16. NM_001404626.1 → NP_001391555.1  nucleolar transcription factor 1 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT6
    Related
    ENSMUSP00000102732.2, ENSMUST00000107115.8

  17. NM_001404627.1 → NP_001391556.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT5
    Related
    ENSMUSP00000102740.4, ENSMUST00000107123.10

  18. NM_001404628.1 → NP_001391557.1  nucleolar transcription factor 1 isoform 1

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT5

  19. NM_001404629.1 → NP_001391558.1  nucleolar transcription factor 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT7

  20. NM_001404630.1 → NP_001391559.1  nucleolar transcription factor 1 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL954730
    UniProtKB/TrEMBL
    A2AWT7

  21. NM_001404633.1 → NP_001391562.1  nucleolar transcription factor 1 isoform 8

    Status: VALIDATED

    Source sequence(s)
    AL954730

  22. NM_011551.8 → NP_035681.2  nucleolar transcription factor 1 isoform 1

    See identical proteins and their annotated locations for NP_035681.2

    Status: VALIDATED

    Source sequence(s)
    AL954730
    Consensus CDS
    CCDS25495.1
    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT5
    Related
    ENSMUSP00000133844.2, ENSMUST00000174302.8
    Conserved Domains (3) summary
    cd01390
    Location:407 → 470
    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 chromosomal ...
    pfam14887
    Location:479 → 562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112 → 179
    HMG_box; HMG (high mobility group) box

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    102195393..102214738 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036156510.1 → XP_036012403.1  nucleolar transcription factor 1 isoform X1

    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT5
    Conserved Domains (3) summary
    cd01390
    Location:407 → 470
    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 chromosomal ...
    pfam14887
    Location:479 → 562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112 → 179
    HMG_box; HMG (high mobility group) box

  2. XM_030245777.2 → XP_030101637.1  nucleolar transcription factor 1 isoform X1

    UniProtKB/Swiss-Prot
    P25976
    UniProtKB/TrEMBL
    A2AWT5
    Conserved Domains (3) summary
    cd01390
    Location:407 → 470
    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 chromosomal ...
    pfam14887
    Location:479 → 562
    HMG_box_5; HMG (high mobility group) box 5
    pfam00505
    Location:112 → 179
    HMG_box; HMG (high mobility group) box

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001362550.1: Suppressed sequence

    Description
    NM_001362550.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.

  2. NM_001362551.1: Suppressed sequence

    Description
    NM_001362551.1: This RefSeq was removed because currently there is support for the transcript but not for the protein.
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P25976.1 GenPept UniProtKB/Swiss-Prot:P25976

Gene LinkOut

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