Usf1 upstream transcription factor 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Usf1provided by RGD
Official Full Name: upstream transcription factor 1provided by RGD
Primary source: RGD:620974
See related: AllianceGenome:RGD:620974
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA binding activity; DNA-binding transcription factor activity; and identical protein binding activity. Contributes to DNA-binding transcription factor activity, RNA polymerase II-specific. Involved in glucose metabolic process and positive regulation of transcription by RNA polymerase II. Located in nucleus. Human ortholog(s) of this gene implicated in cardiovascular system disease and type 2 diabetes mellitus. Orthologous to human USF1 (upstream transcription factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 234.5), Spleen (RPKM 196.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q24

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (86377679..86385523)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (83845230..83854875)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (89797750..89805561)

Chromosome 13 - NC_086031.1 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: 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?

Upstream stimulatory factors (USF1 and USF2) induce Nr5a1 and Shbg gene expression during the onset of rat Sertoli cell differentiation.
Title: Upstream stimulatory factor induces Nr5a1 and Shbg gene expression during the onset of rat Sertoli cell differentiation.
a novel signaling pathway inhibits hepatic gluconeogenesis through HGF/AMPK/USF-1/SHP
Title: Hepatocyte growth factor family negatively regulates hepatic gluconeogenesis via induction of orphan nuclear receptor small heterodimer partner in primary hepatocytes.
USF has a role in increasing TGF-beta1 protein levels, but not in indusing G1 phase arrest
Title: Overexpression of USF increases TGF-beta1 protein levels, but G1 phase arrest was not induced in FRTL-5 cells.
USF1 and USF2 are important contributors to neuronal-specific and mitogen-activated protein kinase regulation of the CGRP gene in trigeminal ganglion neurons
Title: Control of the calcitonin gene-related peptide enhancer by upstream stimulatory factor in trigeminal ganglion neurons.
USF1 and 2 transactivate rat and human PF4 promoters and may play an important role in megakaryocytic gene expression
Title: Upstream stimulatory factors stimulate transcription through E-box motifs in the PF4 gene in megakaryocytes.
osteopontin expression through a coordinate action of NFkappaB, activator protein-1, and upstream stimulatory factor in arterial smooth muscle cells
Title: UTP induces osteopontin expression through a coordinate action of NFkappaB, activator protein-1, and upstream stimulatory factor in arterial smooth muscle cells.
USF regulates osteopontin gene transcription aortic vascular smooth muscle cells, entrained to changes in cellular glucose metabolism
Title: Osteopontin transcription in aortic vascular smooth muscle cells is controlled by glucose-regulated upstream stimulatory factor and activator protein-1 activities.
Overexpression of upstream stimulatory factor 1 increases cyclic GMP-dependent protein kinase I promoter activity in human vascular smooth muscle cells.
Title: Upstream stimulatory factors (USF-1/USF-2) regulate human cGMP-dependent protein kinase I gene expression in vascular smooth muscle cells.

Submit: New GeneRIF Correction

General gene information

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Markers

MARC_4129-4130:996679399:1 (e-PCR)
- UniSTS:269327

RH133926 (e-PCR)
- UniSTS:217209

Usf1 (e-PCR), detects polymorphism
- UniSTS:527601

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
contributes_to DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables bHLH transcription factor binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to insulin stimulus	ISO Inferred from Sequence Orthology more info
involved_in glucose metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in late viral transcription	ISO Inferred from Sequence Orthology more info
involved_in lipid homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to UV	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: upstream stimulatory 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_031777.3 → NP_113965.1 upstream stimulatory factor 1

See identical proteins and their annotated locations for NP_113965.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A6JFZ3, O35410, Q5HZX6

Conserved Domains (1) summary

pfam00010
Location:200 → 255

HLH; Helix-loop-helix DNA-binding domain

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_086031.1 Reference GRCr8

Range

86377679..86385523

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063272640.1 → XP_063128710.1 upstream stimulatory factor 1 isoform X1

UniProtKB/TrEMBL

A6JFZ3, O35410, Q5HZX6
XM_006250266.4 → XP_006250328.1 upstream stimulatory factor 1 isoform X1

See identical proteins and their annotated locations for XP_006250328.1

UniProtKB/TrEMBL

A6JFZ3, O35410, Q5HZX6

Conserved Domains (1) summary

pfam00010
Location:200 → 255

HLH; Helix-loop-helix DNA-binding domain
XM_063272642.1 → XP_063128712.1 upstream stimulatory factor 1 isoform X1

UniProtKB/TrEMBL

A6JFZ3, O35410, Q5HZX6
XM_063272641.1 → XP_063128711.1 upstream stimulatory factor 1 isoform X1

UniProtKB/TrEMBL

A6JFZ3, O35410, Q5HZX6
XM_008769765.4 → XP_008767987.1 upstream stimulatory factor 1 isoform X2

Conserved Domains (1) summary

pfam00010
Location:141 → 196

HLH; Helix-loop-helix DNA-binding domain