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

Summary

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

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_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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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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)

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

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT6
NM_001404621.1 → NP_001391550.1 nucleolar transcription factor 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT6
NM_001404622.1 → NP_001391551.1 nucleolar transcription factor 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT6
NM_001404623.1 → NP_001391552.1 nucleolar transcription factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT5
NM_001404624.1 → NP_001391553.1 nucleolar transcription factor 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT6
NM_001404625.1 → NP_001391554.1 nucleolar transcription factor 1 isoform 2

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT6
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
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
NM_001404628.1 → NP_001391557.1 nucleolar transcription factor 1 isoform 1

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT5
NM_001404629.1 → NP_001391558.1 nucleolar transcription factor 1 isoform 3

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT7
NM_001404630.1 → NP_001391559.1 nucleolar transcription factor 1 isoform 3

Status: VALIDATED

Source sequence(s)

AL954730

UniProtKB/TrEMBL

A2AWT7
NM_001404633.1 → NP_001391562.1 nucleolar transcription factor 1 isoform 8

Status: VALIDATED

Source sequence(s)

AL954730
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

NC_000077.7 Reference GRCm39 C57BL/6J

Range

102195393..102214738 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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

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.
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.