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Aliases for USF1 Gene

Aliases for USF1 Gene

  • Upstream Transcription Factor 1 2 3 5
  • Class B Basic Helix-Loop-Helix Protein 11 3 4
  • Major Late Transcription Factor 1 3 4
  • BHLHb11 3 4
  • HYPLIP1 3
  • FCHL1 3
  • MLTFI 3
  • FCHL 3
  • MLTF 3
  • UEF 3
  • USF 4

External Ids for USF1 Gene

Previous GeneCards Identifiers for USF1 Gene

  • GC01M158720
  • GC01M156741
  • GC01M157786
  • GC01M158225
  • GC01M158208
  • GC01M157822
  • GC01M159275
  • GC01M132366

Summaries for USF1 Gene

Entrez Gene Summary for USF1 Gene

  • This gene encodes a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor. The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs. This gene has been linked to familial combined hyperlipidemia (FCHL). Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been defined on chromosome 21. [provided by RefSeq, Feb 2013]

GeneCards Summary for USF1 Gene

USF1 (Upstream Transcription Factor 1) is a Protein Coding gene. Diseases associated with USF1 include Hyperlipidemia, Familial Combined and Photokeratitis. Among its related pathways are Signaling mediated by p38-alpha and p38-beta. GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding and sequence-specific DNA binding. An important paralog of this gene is USF2.

UniProtKB/Swiss-Prot for USF1 Gene

  • Transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5-CACGTG-3) that is found in a variety of viral and cellular promoters.

Gene Wiki entry for USF1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USF1 Gene

Genomics for USF1 Gene

Regulatory Elements for USF1 Gene

Enhancers for USF1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around USF1 on UCSC Golden Path with GeneCards custom track

Promoters for USF1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USF1 on UCSC Golden Path with GeneCards custom track

Genomic Location for USF1 Gene

161,039,251 bp from pter
161,045,979 bp from pter
6,729 bases
Minus strand

Genomic View for USF1 Gene

Genes around USF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USF1 Gene

Proteins for USF1 Gene

  • Protein details for USF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Upstream stimulatory factor 1
    Protein Accession:
    Secondary Accessions:
    • B2RBZ4
    • Q5SY46
    • Q7Z5Y1

    Protein attributes for USF1 Gene

    310 amino acids
    Molecular mass:
    33538 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Binds DNA as a homodimer or a heterodimer (USF1/USF2). Interacts with varicella-zoster virus IE62 protein.

    Three dimensional structures from OCA and Proteopedia for USF1 Gene

    Alternative splice isoforms for USF1 Gene


neXtProt entry for USF1 Gene

Proteomics data for USF1 Gene at MOPED

Post-translational modifications for USF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USF1 Gene

Domains & Families for USF1 Gene

Gene Families for USF1 Gene

Protein Domains for USF1 Gene

Suggested Antigen Peptide Sequences for USF1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 bHLH (basic helix-loop-helix) domain.
  • Contains 1 bHLH (basic helix-loop-helix) domain.
genes like me logo Genes that share domains with USF1: view

Function for USF1 Gene

Molecular function for USF1 Gene

GENATLAS Biochemistry:
upstream stimulatory transcription factor,ubiquitous (43 kDa),binding the AP-1/AP-4 site on the APP promoter
UniProtKB/Swiss-Prot Function:
Transcription factor that binds to a symmetrical DNA sequence (E-boxes) (5-CACGTG-3) that is found in a variety of viral and cellular promoters.

Gene Ontology (GO) - Molecular Function for USF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003690 double-stranded DNA binding IEA --
GO:0005515 protein binding IEA,IPI 19303849
GO:0019901 protein kinase binding IPI 19303849
GO:0043565 sequence-specific DNA binding IEA,IDA 2249772
GO:0046983 protein dimerization activity IEA --
genes like me logo Genes that share ontologies with USF1: view
genes like me logo Genes that share phenotypes with USF1: view

Animal Models for USF1 Gene

MGI Knock Outs for USF1:

Animal Model Products

  • Taconic Biosciences Mouse Models for USF1

miRNA for USF1 Gene

miRTarBase miRNAs that target USF1

Transcription Factor Targets for USF1 Gene

Selected GeneGlobe predicted Target genes for USF1
Targeted motifs for USF1 Gene
HOMER Transcription Factor Regulatory Elements motif USF1
  • Consensus sequence: GGTCACGTGA Submotif: canonical Cell Type: GM12878 GEO ID: GSE32465

No data available for Enzyme Numbers (IUBMB) and Human Phenotype Ontology for USF1 Gene

Localization for USF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USF1 Gene

Subcellular locations from

Jensen Localization Image for USF1 Gene COMPARTMENTS Subcellular localization image for USF1 gene
Compartment Confidence
nucleus 5
extracellular 2
golgi apparatus 2

No data available for Gene Ontology (GO) - Cellular Components for USF1 Gene

Pathways & Interactions for USF1 Gene

genes like me logo Genes that share pathways with USF1: view

Pathways by source for USF1 Gene

1 BioSystems pathway for USF1 Gene

SIGNOR curated interactions for USF1 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for USF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000432 positive regulation of transcription from RNA polymerase II promoter by glucose IEA,ISS --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0009411 response to UV IEA,ISS --
GO:0019086 late viral transcription IDA 2249772
GO:0042593 glucose homeostasis TAS 15054483
genes like me logo Genes that share ontologies with USF1: view

Drugs & Compounds for USF1 Gene

(10) Drugs for USF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(8) Additional Compounds for USF1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with USF1: view

Transcripts for USF1 Gene

Unigene Clusters for USF1 Gene

Upstream transcription factor 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USF1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c
SP1: - - -
SP2: - - -
SP3: -
SP4: - -
SP5: - -

Relevant External Links for USF1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USF1 Gene

mRNA expression in normal human tissues for USF1 Gene

mRNA differential expression in normal tissues according to GTEx for USF1 Gene

This gene is overexpressed in Whole Blood (x5.4).

Protein differential expression in normal tissues from HIPED for USF1 Gene

This gene is overexpressed in Monocytes (17.0), Peripheral blood mononuclear cells (15.0), and Fetal ovary (7.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for USF1 Gene

SOURCE GeneReport for Unigene cluster for USF1 Gene Hs.414880

genes like me logo Genes that share expression patterns with USF1: view

Protein tissue co-expression partners for USF1 Gene

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for USF1 Gene

Orthologs for USF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for USF1 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia USF1 35
  • 94.52 (n)
  • 99.35 (a)
USF1 36
  • 99 (a)
(Canis familiaris)
Mammalia USF1 35
  • 94.41 (n)
  • 99.68 (a)
USF1 36
  • 92 (a)
(Mus musculus)
Mammalia Usf1 35
  • 90.43 (n)
  • 98.39 (a)
Usf1 16
Usf1 36
  • 98 (a)
(Pan troglodytes)
Mammalia USF1 35
  • 99.78 (n)
  • 99.68 (a)
USF1 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Usf1 35
  • 90.32 (n)
  • 98.39 (a)
(Monodelphis domestica)
Mammalia USF1 36
  • 85 (a)
(Gallus gallus)
Aves USF1 35
  • 78.57 (n)
  • 87.99 (a)
USF1 36
  • 71 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7020 35
(Danio rerio)
Actinopterygii -- 35
usf1 35
  • 63.98 (n)
  • 64.91 (a)
usf1 36
  • 59 (a)
usf1l 36
  • 47 (a)
fruit fly
(Drosophila melanogaster)
Insecta Usf 36
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 31 (a)
Species with no ortholog for USF1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for USF1 Gene

Gene Tree for USF1 (if available)
Gene Tree for USF1 (if available)

Paralogs for USF1 Gene

Paralogs for USF1 Gene

(3) SIMAP similar genes for USF1 Gene using alignment to 6 proteins: Pseudogenes for USF1 Gene

genes like me logo Genes that share paralogs with USF1: view

Variants for USF1 Gene

Sequence variations from dbSNP and Humsavar for USF1 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1556259 -- 161,044,859(-) TTGTG(C/T)TGGGA intron-variant
rs1556260 -- 161,044,656(-) TTGGA(A/G)TTGTC intron-variant
rs2774273 -- 161,044,195(-) GAGGC(C/G)GAGGC intron-variant
rs2774276 -- 161,041,926(-) CCCAA(C/G)GGATA intron-variant
rs2774278 -- 161,045,749(+) CAAAG(C/G)CTTCC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for USF1 Gene

Variant ID Type Subtype PubMed ID
nsv3221 CNV Loss 18451855
nsv872492 CNV Gain 21882294

Variation tolerance for USF1 Gene

Residual Variation Intolerance Score: 18.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.27; 6.01% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USF1 Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USF1 Gene

Disorders for USF1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for USF1 Gene - From: OMIM, GeneTests, DISEASES, and Novoseek

Disorder Aliases PubMed IDs
hyperlipidemia, familial combined
  • combined hyperlipidemia, familial
pilomyxoid astrocytoma
lipid metabolism disorder
  • dyslipidemia
inherited metabolic disorder
  • inborn errors of metabolism
- elite association - COSMIC cancer census association via MalaCards
Search USF1 in MalaCards View complete list of genes associated with diseases


  • Hyperlipidemia combined 1 (HYPLIP1) [MIM:602491]: A disorder characterized by a variable pattern of elevated levels of serum total cholesterol, triglycerides or both. It is observed in a percentage of individuals with premature coronary heart disease. {ECO:0000269 PubMed:14991056}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Relevant External Links for USF1

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with USF1: view

No data available for Genatlas for USF1 Gene

Publications for USF1 Gene

  1. Risk alleles of USF1 gene predict cardiovascular disease of women in two prospective studies. (PMID: 16699592) Komulainen K. … Peltonen L. (PLoS Genet. 2006) 3 23 48 67
  2. Localization of the gene-encoding upstream stimulatory factor (USF) to human chromosome 1q22-q23. (PMID: 8486371) Shieh B.H. … Lusis A.J. (Genomics 1993) 2 3 23
  3. Genetic association and interaction analysis of USF1 and APOA5 on lipid levels and atherosclerosis. (PMID: 19910639) Laurila P.P. … Peltonen L. (Arterioscler. Thromb. Vasc. Biol. 2010) 3 23
  4. Upstream transcription factor 1 influences plasma lipid and metabolic traits in mice. (PMID: 19995791) Wu S. … Drake T.A. (Hum. Mol. Genet. 2010) 3 23
  5. Target gene specificity of USF-1 is directed via p38-mediated phosphorylation-dependent acetylation. (PMID: 19389701) Corre S. … Galibert M.D. (J. Biol. Chem. 2009) 3 23

Products for USF1 Gene

Sources for USF1 Gene