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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
  • Upstream Stimulatory Factor 1 3
  • 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, Combined, 1 and Hyperlipidemia, Familial Combined. Among its related pathways are Signaling mediated by p38-alpha and p38-beta. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity 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

Additional gene information for USF1 Gene

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

Genomics for USF1 Gene

GeneHancer (GH) Regulatory Elements for USF1 Gene

Promoters and enhancers for USF1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I161043 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 -0.9 -910 5.8 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 GC01P161046 PIR33280 USF1 DEDD TSTD1 LOC100287049 ARHGAP30 LOC105371471 NECTIN4 KLHDC9
GH01I161011 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE dbSUPER 17.7 +28.8 28766 11.7 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 DUSP12 USP21 LOC100287049 DEDD PPOX TSTD1 LOC148430 B4GALT3 ARHGAP30 KLHDC9
GH01I161008 Enhancer 1.3 Ensembl ENCODE dbSUPER 12 +36.3 36267 2.1 PKNOX1 ATF1 ARNT NCOA2 TCF12 ZNF121 ZNF766 GATA2 ATF7 NCOA1 ENSG00000232879 TSTD1 USF1 ARHGAP30 LOC105371471 NECTIN4 DEDD KLHDC9 ENSG00000228863 F11R
GH01I161066 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.6 -22.6 -22636 5.1 HDGF PKNOX1 BMI1 ZBTB40 KLF5 IRF4 ZNF207 ZNF143 ATF7 ETV6 ARHGAP30 FCGR2A TSTD1 DUSP12 USP21 PPOX F11R DEDD NECTIN4 ENSG00000232879
GH01I161079 Promoter/Enhancer 2.1 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 5 -38.8 -38774 11.2 PKNOX1 CLOCK ATF1 NEUROD1 SIN3A BRCA1 GLIS2 ATF7 FOS ZNF263 NECTIN4 LOC105371471 F11R TSTD1 NCSTN USF1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USF1 gene promoter:

Genomic Locations for USF1 Gene

Genomic Locations for USF1 Gene
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

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

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for USF1 Gene

Suggested Antigen Peptide Sequences for USF1 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for USF1 Gene

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.

Phenotypes From GWAS Catalog for USF1 Gene

Gene Ontology (GO) - Molecular Function for USF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IEA --
GO:0003700 DNA binding transcription factor activity IEA --
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding IMP,IEA 8576131
GO:0005515 protein binding IPI 19303849
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

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

Clone Products

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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USF1 gene
Compartment Confidence
nucleus 5
extracellular 2
golgi apparatus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for USF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin IDA 27141965
GO:0005634 nucleus IDA 2249772
GO:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex IDA 19303849
GO:0016589 colocalizes_with NURF complex IDA 27141965
genes like me logo Genes that share ontologies with USF1: view

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:0000430 regulation of transcription from RNA polymerase II promoter by glucose IC 8576131
GO:0000432 positive regulation of transcription from RNA polymerase II promoter by glucose ISS,IEA --
GO:0001666 response to hypoxia IMP 12917334
GO:0006006 glucose metabolic process IEA --
GO:0006351 transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with USF1: view

Drugs & Compounds for USF1 Gene

(11) Drugs for USF1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(7) 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for USF1 Gene

Protein tissue co-expression partners for USF1 Gene

NURSA nuclear receptor signaling pathways regulating expression of USF1 Gene:


SOURCE GeneReport for Unigene cluster for USF1 Gene:


Evidence on tissue expression from TISSUES for USF1 Gene

  • Kidney(4.4)
  • Liver(2.6)
  • Blood(2.3)
  • Skin(2.3)
  • Intestine(2.2)
  • Nervous system(2.2)
  • Lung(2)
  • Muscle(2)
genes like me logo Genes that share expression patterns with USF1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
(Pan troglodytes)
Mammalia USF1 33 34
  • 99.78 (n)
(Bos Taurus)
Mammalia USF1 33 34
  • 94.52 (n)
(Canis familiaris)
Mammalia USF1 33 34
  • 94.41 (n)
(Mus musculus)
Mammalia Usf1 33 16 34
  • 90.43 (n)
(Rattus norvegicus)
Mammalia Usf1 33
  • 90.32 (n)
(Monodelphis domestica)
Mammalia USF1 34
  • 85 (a)
(Gallus gallus)
Aves USF1 33 34
  • 78.57 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7020 33
(Danio rerio)
Actinopterygii usf1 33 34
  • 63.98 (n)
usf1l 34
  • 47 (a)
-- 33
fruit fly
(Drosophila melanogaster)
Insecta Usf 34
  • 17 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 31 (a)
Species where no ortholog for USF1 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs2073658 risk-factor, Hyperlipidemia, familial combined, susceptibility to 161,040,972(-) C/T intron_variant
rs3737787 risk-factor, Hyperlipidemia, familial combined, susceptibility to 161,039,733(-) G/A 3_prime_UTR_variant
rs1000010156 -- 161,040,145(-) A/G intron_variant
rs1000105620 -- 161,045,569(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000550967 -- 161,040,479(-) A/G intron_variant

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

Variant ID Type Subtype PubMed ID
nsv1145376 CNV deletion 24896259
nsv3221 CNV deletion 18451855
nsv548059 CNV gain 21841781

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)

Additional Variant Information for USF1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for USF1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for USF1 Gene - From: HGMD, OMIM, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
hyperlipidemia, combined, 1
  • hyperlipidemia, familial combined
hyperlipidemia, familial combined
  • fchl
urethral calculus
  • urethral stone
lower urinary tract calculus
  • calculus of lower urinary tract
- 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.

Additional Disease Information for USF1

Genetic Association Database
Human Genome Epidemiology 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. Genetic association and interaction analysis of USF1 and APOA5 on lipid levels and atherosclerosis. (PMID: 19910639) Laurila PP … Peltonen L (Arteriosclerosis, thrombosis, and vascular biology 2010) 3 22 44 58
  2. Association analysis of allelic variants of USF1 in coronary atherosclerosis. (PMID: 18276913) Kristiansson K … Karhunen PJ (Arteriosclerosis, thrombosis, and vascular biology 2008) 3 22 44 58
  3. Allelic variants of upstream transcription factor 1 associate with carotid artery intima-media thickness: the Cardiovascular Risk in Young Finns study. (PMID: 18577828) Collings A … Lehtimäki TJ (Circulation journal : official journal of the Japanese Circulation Society 2008) 3 22 44 58
  4. Genetic variants in the USF1 gene are associated with low-density lipoprotein cholesterol levels and incident type 2 diabetes mellitus in women: results from the MONICA/KORA Augsburg case-cohort study, 1984-2002. (PMID: 18593823) Holzapfel C … Klopp N (European journal of endocrinology 2008) 3 22 44 58
  5. Upstream transcription factor 1 gene polymorphisms are associated with high antilipolytic insulin sensitivity and show gene-gene interactions. (PMID: 17016691) Kantartzis K … Stefan N (Journal of molecular medicine (Berlin, Germany) 2007) 3 22 44 58

Products for USF1 Gene

Sources for USF1 Gene

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