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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, Familial Combined and Urethral Calculus. 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 Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01F161011 1.2 FANTOM5 ENCODE 17.6 +28.8 28766 11.7 MLX CREB3L1 ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 DUSP12 ARHGAP30 TSTD1 ENSG00000228606 FCGR2A USF1 RPSAP18 CD48 DEDD KLHDC9
GH01F161002 0.8 FANTOM5 13.2 +43.1 43089 0.3 ENSG00000232879 USF1 TSTD1 LOC105371471 KLHDC9 NECTIN4 DEDD ARHGAP30 SLAMF7 GC01M161000
GH01F161008 1.1 Ensembl ENCODE 12 +36.3 36267 2.1 ATF1 PKNOX1 ARNT FEZF1 ZNF2 ZNF121 GLIS2 GATA2 KLF7 ZNF263 ENSG00000232879 TSTD1 USF1 ARHGAP30 LOC105371471 NECTIN4 DEDD KLHDC9 ENSG00000228863 F11R
GH01F161079 1.1 FANTOM5 Ensembl ENCODE 4.9 -38.8 -38790 11.3 PKNOX1 ATF1 BRCA1 ZNF121 GLIS2 FOS ZNF263 SP3 ZHX2 NCOA1 F11R NECTIN4 DUSP12 TSTD1 NCSTN USF1 LOC105371471
GH01F161066 1 FANTOM5 ENCODE 4.6 -22.6 -22636 5.1 HDGF PKNOX1 WRNIP1 SIN3A YY1 GLIS2 ELK1 ZNF143 ZNF207 SP3 FCGR2A TSTD1 DUSP12 ENSG00000228606 ARHGAP30 F11R DEDD ATF6 NECTIN4 ENSG00000232879
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

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
ENSR00001040224 379 2801 MLX CREB3L1 FEZF1 DMAP1 YY1 ZNF143 SP3 NFYC TBX21 MEF2D

Genomic Location for USF1 Gene

Chromosome:
1
Start:
161,039,251 bp from pter
End:
161,045,979 bp from pter
Size:
6,729 bases
Orientation:
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:
    P22415-USF1_HUMAN
    Recommended name:
    Upstream stimulatory factor 1
    Protein Accession:
    P22415
    Secondary Accessions:
    • B2RBZ4
    • Q5SY46
    • Q7Z5Y1

    Protein attributes for USF1 Gene

    Size:
    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

    UniProtKB/Swiss-Prot:

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

Protein Domains for USF1 Gene

Suggested Antigen Peptide Sequences for USF1 Gene

Graphical View of Domain Structure for InterPro Entry

P22415

UniProtKB/Swiss-Prot:

USF1_HUMAN :
  • Contains 1 bHLH (basic helix-loop-helix) domain.
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:0003677 DNA binding IEA --
GO:0003690 double-stranded DNA binding IEA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding IEA,IMP 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

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

Inhibitory RNA Products

Flow Cytometry 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

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

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

Activates:
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 IEA,ISS --
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:

Inhibitory RNA Products

Flow Cytometry 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: - -
SP6:
SP7:

Relevant External Links for USF1 Gene

GeneLoc Exon Structure for
USF1
ECgene alternative splicing isoforms for
USF1

Expression for USF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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:

USF1

SOURCE GeneReport for Unigene cluster for USF1 Gene:

Hs.414880
genes like me logo Genes that share expression patterns with USF1: view

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
chimpanzee
(Pan troglodytes)
Mammalia USF1 34 35
  • 99.78 (n)
cow
(Bos Taurus)
Mammalia USF1 34 35
  • 94.52 (n)
dog
(Canis familiaris)
Mammalia USF1 34 35
  • 94.41 (n)
mouse
(Mus musculus)
Mammalia Usf1 34 16 35
  • 90.43 (n)
rat
(Rattus norvegicus)
Mammalia Usf1 34
  • 90.32 (n)
oppossum
(Monodelphis domestica)
Mammalia USF1 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves USF1 34 35
  • 78.57 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7020 34
zebrafish
(Danio rerio)
Actinopterygii usf1 34 35
  • 63.98 (n)
usf1l 35
  • 47 (a)
OneToMany
-- 34
fruit fly
(Drosophila melanogaster)
Insecta Usf 35
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 31 (a)
OneToMany
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

ENSEMBL:
Gene Tree for USF1 (if available)
TreeFam:
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.org 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
rs2073658 other 161,040,972(-) CATAA(A/G)TGGTC intron-variant, upstream-variant-2KB
rs3737787 other 161,039,733(-) GTGGA(C/T)GTGCA upstream-variant-2KB, utr-variant-3-prime
rs112080717 -- 161,039,306(+) GAAAA(A/G)AAAAA upstream-variant-2KB, utr-variant-3-prime
rs112388093 -- 161,047,971(+) GGGTT(C/T)GCCGA upstream-variant-2KB, reference, missense
rs112546711 -- 161,043,362(+) AGTCC(G/T)GGTAG splice-acceptor-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)

Relevant External Links for USF1 Gene

Human Gene Mutation Database (HGMD)
USF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
USF1

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

Disorders for USF1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
hyperlipidemia, familial combined
  • combined hyperlipidemia, familial
urethral calculus
  • urethral stone
photokeratitis
lower urinary tract calculus
  • calculus of lower urinary tract
lipid metabolism disorder
  • dyslipidemia
- elite association - COSMIC cancer census association via MalaCards
Search USF1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

USF1_HUMAN
  • 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)
USF1
Human Genome Epidemiology (HuGE) Navigator
USF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USF1
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 P.P. … Peltonen L. (Arterioscler. Thromb. Vasc. Biol. 2010) 3 22 46 64
  2. Association analysis of allelic variants of USF1 in coronary atherosclerosis. (PMID: 18276913) Kristiansson K. … Karhunen P.J. (Arterioscler. Thromb. Vasc. Biol. 2008) 3 22 46 64
  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. … LehtimAoki T.J. (Circ. J. 2008) 3 22 46 64
  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. (Eur. J. Endocrinol. 2008) 3 22 46 64
  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. (J. Mol. Med. 2007) 3 22 46 64

Products for USF1 Gene

Sources for USF1 Gene

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