Ubtf upstream binding transcription factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ubtfprovided by RGD
Official Full Name: upstream binding transcription factorprovided by RGD
Primary source: RGD:3927
See related: EnsemblRapid:ENSRNOG00000020937 AllianceGenome:RGD:3927
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Tcfubf
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. Predicted to be involved in positive regulation of transcription by RNA polymerase I and transcription initiation at RNA polymerase I promoter. Predicted to act upstream of or within cellular response to leukemia inhibitory factor and transcription elongation by RNA polymerase I. Located in fibrillar center. Human ortholog(s) of this gene implicated in childhood-onset neurodegeneration with brain atrophy. Orthologous to human UBTF (upstream binding transcription factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 125.6), Spleen (RPKM 118.7) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q32.1

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (87758346..87775377, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (87258217..87274291, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (90250275..90265772, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Growth factor stimulation induces an increase in rRNA transcriptional activity via phosphorylation of UBF at serine 389 in part by facilitating a rate-limiting step in the recruitment of RNA polymerase I: i.e., recruitment of SL1.
Title: Mass spectrometric identification of phosphorylation sites of rRNA transcription factor upstream binding factor.
competitive recruitment of CBP and Rb-HDAC regulates UBF acetylation and ribosomal transcription
Title: Competitive recruitment of CBP and Rb-HDAC regulates UBF acetylation and ribosomal transcription.

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General gene information

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Gene Ontology Provided by RGD

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 chromatin binding	ISS Inferred from Sequence or Structural Similarity 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
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase I	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in regulation of glucose mediated signaling pathway	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in transcription initiation at RNA polymerase I promoter	ISO Inferred from Sequence Orthology more info
involved_in transcription initiation at RNA polymerase I promoter	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in fibrillar center	IDA Inferred from Direct Assay more info	PubMed
located_in fibrillar center	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation 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: UBF-1; transcription factor UBF; upstream binding transcription factor, RNA polymerase I; 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_001105723.3 → NP_001099193.2 nucleolar transcription factor 1 isoform 1

See identical proteins and their annotated locations for NP_001099193.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1).

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P25977

Related

ENSRNOP00000044305.3, ENSRNOT00000048418.6

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_001127690.2 → NP_001121162.1 nucleolar transcription factor 1 isoform 2

See identical proteins and their annotated locations for NP_001121162.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) includes an alternate exon in the coding region compared to variant 1. The resulting protein (isoform 2) is longer but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P25977, P25978

Related

ENSRNOP00000063740.1, ENSRNOT00000064283.5

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

87758346..87775377 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063268481.1 → XP_063124551.1 nucleolar transcription factor 1 isoform X2
XM_006247264.5 → XP_006247326.1 nucleolar transcription factor 1 isoform X1

See identical proteins and their annotated locations for XP_006247326.1

UniProtKB/Swiss-Prot

P25977, P25978

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_063268479.1 → XP_063124549.1 nucleolar transcription factor 1 isoform X2
XM_006247262.5 → XP_006247324.1 nucleolar transcription factor 1 isoform X1

See identical proteins and their annotated locations for XP_006247324.1

UniProtKB/Swiss-Prot

P25977, P25978

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_063268480.1 → XP_063124550.1 nucleolar transcription factor 1 isoform X2
XM_063268478.1 → XP_063124548.1 nucleolar transcription factor 1 isoform X1

UniProtKB/Swiss-Prot

P25977, P25978