UBTF upstream binding transcription factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: UBTFprovided by HGNC
Official Full Name: upstream binding transcription factorprovided by HGNC
Primary source: HGNC:HGNC:12511
See related: Ensembl:ENSG00000108312 MIM:600673; AllianceGenome:HGNC:12511
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: UBF; UBF1; UBF2; UBF-1; CONDBA; NOR-90
Summary: 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]
Expression: Ubiquitous expression in lymph node (RPKM 22.2), thyroid (RPKM 21.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 17q21.31

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	17	NC_000017.11 (44205040..44221304, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	17	NC_060941.1 (45058143..45074402, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (42282408..42298672, complement)

Chromosome 17 - NC_000017.11 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: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

FGF13A interacts with NPM1 and UBF and inhibits the invasion of bladder cancer cells.
Title: FGF13A interacts with NPM1 and UBF and inhibits the invasion of bladder cancer cells.
UBTF tandem duplications define a distinct subtype of adult de novo acute myeloid leukemia.
Title: UBTF tandem duplications define a distinct subtype of adult de novo acute myeloid leukemia.
UBTF tandem duplications are rare but recurrent alterations in adult AML and associated with younger age, myelodysplasia, and inferior outcome.
Title: UBTF tandem duplications are rare but recurrent alterations in adult AML and associated with younger age, myelodysplasia, and inferior outcome.
UBTF-internal tandem duplication as a novel poor prognostic factor in pediatric acute myeloid leukemia.
Title: UBTF-internal tandem duplication as a novel poor prognostic factor in pediatric acute myeloid leukemia.
Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL.
Title: Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL.
Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.
Title: Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia.
Protein kinase Ciota promotes UBF1-ECT2 binding on ribosomal DNA to drive rRNA synthesis and transformed growth of non-small-cell lung cancer cells.
Title: Protein kinase Cι promotes UBF1-ECT2 binding on ribosomal DNA to drive rRNA synthesis and transformed growth of non-small-cell lung cancer cells.
These results demonstrate the role of pNO40 in ribosomal RNA biosynthesis regulation by compromising UBF function in ribosomal DNA transcription activation with subsequent ribosomal RNA synthesis inhibition.
Title: Ectopically expressed pNO40 suppresses ribosomal RNA synthesis by inhibiting UBF-dependent transcription activation.
mutant SEC23B binds to UBF transcription factor, with increased UBF transcription factor binding at the ribosomal DNA promoter. Our data indicate SEC23B has potential non-canonical COPII-independent function, particularly within the ribosome biogenesis pathway, and that may contribute to the pathogenesis of cancer-predisposition.
Title: Non-canonical role of cancer-associated mutant SEC23B in the ribosome biogenesis pathway.
Data underscore the importance of including UBTF E210K in the differential diagnosis of neuroregression and suggest that mainly gain-of-function mechanisms contribute to the pathogenesis of the UBTF E210K neuroregression syndrome.
Title: A recurrent de novo missense mutation in UBTF causes developmental neuroregression.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Childhood-onset motor and cognitive regression syndrome with extrapyramidal movement disorder MedGen: C4540086 OMIM: 617672 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UBTF__5182 (e-PCR)
- UniSTS:468782

D17S2047 (e-PCR)
- UniSTS:23598

SHGC-30675 (e-PCR)
- UniSTS:35147

A009G46 (e-PCR)
- UniSTS:42590

MARC_10313-10314:998934876:1 (e-PCR)
- UniSTS:267108

MARC_17735-17736:1031759262:1 (e-PCR)
- UniSTS:268389

G32535 (e-PCR)
- UniSTS:117119

G15974 (e-PCR)
- UniSTS:29350

RH93951 (e-PCR)
- UniSTS:91609

RH70694 (e-PCR)
- UniSTS:36593

STS-N39596 (e-PCR)
- UniSTS:766

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA polymerase I cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables scaffold protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA polymerase I preinitiation complex assembly	IEA Inferred from Electronic Annotation 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	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in regulation of glucose mediated signaling pathway	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription initiation at RNA polymerase I promoter	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: nucleolar transcription factor 1

Names: 90-kDa nucleolus organizer region autoantigen; autoantigen NOR-90; upstream binding transcription factor, RNA polymerase I

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.

Genomic

NG_029864.1 RefSeqGene

Range

6952..21587

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001076683.2 → NP_001070151.1 nucleolar transcription factor 1 isoform b

See identical proteins and their annotated locations for NP_001070151.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (b), which is shorter than isoform a.

Source sequence(s)

BC042297, BP230502

Consensus CDS

CCDS42346.1

UniProtKB/TrEMBL

A0A994J4N4

Related

ENSP00000345297.5, ENST00000343638.9

Conserved Domains (3) summary

cd01390
Location:370 → 433

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

pfam00505
Location:112 → 179

HMG_box; HMG (high mobility group) box
NM_001076684.3 → NP_001070152.1 nucleolar transcription factor 1 isoform b

See identical proteins and their annotated locations for NP_001070152.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks an exon in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (b), which is shorter than isoform a.

Source sequence(s)

AC004596, BC042297, X56687

Consensus CDS

CCDS42346.1

UniProtKB/TrEMBL

A0A994J4N4

Related

ENSP00000377231.3, ENST00000393606.7

Conserved Domains (3) summary

cd01390
Location:370 → 433

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

pfam00505
Location:112 → 179

HMG_box; HMG (high mobility group) box
NM_014233.4 → NP_055048.1 nucleolar transcription factor 1 isoform a

See identical proteins and their annotated locations for NP_055048.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a).

Source sequence(s)

AC004596, AK291733, BC042297

Consensus CDS

CCDS11480.1

UniProtKB/Swiss-Prot

A8K6R8, P17480

UniProtKB/TrEMBL

A8K962

Related

ENSP00000390669.1, ENST00000436088.6

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

RNA

NR_045058.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK292518, BC042297