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Aliases for USF1 Gene

Aliases for USF1 Gene

  • Upstream Transcription Factor 1 2 3
  • Class B Basic Helix-Loop-Helix Protein 11 3 4
  • Major Late Transcription Factor 1 3 4
  • HYPLIP1 3 6
  • BHLHb11 3 4
  • Upstream Stimulatory Factor 1 3
  • FCHL1 3
  • MLTFI 3
  • FCHL 3
  • MLTF 3
  • UEF 3
  • USF 4

External Ids for USF1 Gene

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 familial hyperlipidemia. Among its related pathways are Signaling mediated by p38-alpha and p38-beta. GO annotations related to this gene include protein homodimerization activity and protein heterodimerization activity. 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

Genomic Location for USF1 Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for USF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USF1 Gene

Regulatory Elements 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

Proteomics data for USF1 Gene at MOPED

Post-translational modifications for USF1 Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys214

No data available for DME Specific Peptides for USF1 Gene

Domains for USF1 Gene

Gene Families for USF1 Gene

HGNC:
  • bHLH :Basic helix-loop-helix proteins

Protein Domains for USF1 Gene

UniProtKB/Swiss-Prot:

USF1_HUMAN
Domain:
  • Contains 1 bHLH (basic helix-loop-helix) domain.:
    • P22415
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 --
GO:0003690 double-stranded DNA binding IEA --
GO:0003700 sequence-specific DNA binding transcription factor activity --
GO:0003705 RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity IMP 18234320
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:

miRNA for USF1 Gene

miRTarBase miRNAs that target USF1
Targeting motifs for USF1 Gene
HOMER Transcription Factor Regulatory Elements motif USF1
  • Consensus sequence: GGTCACGTGA Submotif: canonical Cell Type: GM12878 GeoId: GSE32465

No data available for Enzyme Numbers (IUBMB) and Transcription Factor Targeting 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

Gene Ontology (GO) - Cellular Components for USF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm IDA --
GO:0005667 transcription factor complex IDA 19303849
genes like me logo Genes that share ontologies with USF1: view

Pathways 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

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 --
GO:0001666 response to hypoxia IMP 12917334
GO:0006006 glucose metabolic process IEA --
GO:0006355 regulation of transcription, DNA-templated --
genes like me logo Genes that share ontologies with USF1: view

Compounds for USF1 Gene

(18) Novoseek inferred chemical compound relationships for USF1 Gene

Compound -log(P) Hits PubMed IDs
leucine 56.9 19
oligonucleotide 30.6 9
glucose 25.1 31
lipid 21.4 27
deoxycytidine 17 2
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: - -
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 for USF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (5.4).

Integrated Proteomics: protein expression 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 expressions with USF1: view

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 36
  • 99.78 (n)
  • 99.68 (a)
USF1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USF1 36
  • 94.52 (n)
  • 99.35 (a)
USF1 37
  • 99 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USF1 36
  • 94.41 (n)
  • 99.68 (a)
USF1 37
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usf1 36
  • 90.43 (n)
  • 98.39 (a)
Usf1 16
Usf1 37
  • 98 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USF1 37
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usf1 36
  • 90.32 (n)
  • 98.39 (a)
chicken
(Gallus gallus)
Aves USF1 36
  • 78.57 (n)
  • 87.99 (a)
USF1 37
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.7020 36
zebrafish
(Danio rerio)
Actinopterygii -- 36
usf1 36
  • 63.98 (n)
  • 64.91 (a)
usf1 37
  • 59 (a)
OneToMany
usf1l 37
  • 47 (a)
OneToMany
fruit fly
(Drosophila melanogaster)
Insecta Usf 37
  • 17 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 31 (a)
OneToMany
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

ENSEMBL:
Gene Tree for USF1 (if available)
TreeFam:
Gene Tree for USF1 (if available)

Paralogs for USF1 Gene

Paralogs for USF1 Gene

Selected 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 MAF
rs1556259 -- 161,044,859(-) TTGTG(C/T)TGGGA intron-variant
rs1556260 -- 161,044,656(-) TTGGA(A/G)TTGTC intron-variant
rs2073653 -- 161,042,970(-) TGCCA(A/G)TGAGT intron-variant
rs2073654 -- 161,042,801(-) TAAGA(A/C)CCCAT intron-variant
rs2073655 -- 161,042,800(-) AAGAA(C/T)CCATC intron-variant

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

Relevant External Links for USF1 Gene

HapMap Linkage Disequilibrium report
USF1
Human Gene Mutation Database (HGMD)
USF1

Disorders for USF1 Gene

(1) OMIM Diseases for USF1 Gene (191523)

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.

(3) University of Copenhagen DISEASES for USF1 Gene

(17) Novoseek inferred disease relationships for USF1 Gene

Disease -log(P) Hits PubMed IDs
hyperlipidemia familial combined 87 29
dyslipidemia 38.1 9
glioblastoma 21.7 3
coronary heart disease 17.4 4
immunodeficiency 12 5

Relevant External Links for USF1

Genetic Association Database (GAD)
USF1
Human Genome Epidemiology (HuGE) Navigator
USF1
genes like me logo Genes that share disorders with USF1: view

Publications for USF1 Gene

  1. Structure and function of the b/HLH/Z domain of USF. (PMID: 8306960) Ferre-D'Amare A.R. … Burley S.K. (EMBO J. 1994) 3 4 23
  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. Variation in USF1 shows haplotype effects, gene : gene and gene : environment associations with glucose and lipid parameters in the European Atherosclerosis Research Study II. (PMID: 15175273) Putt W. … Talmud P.J. (Hum. Mol. Genet. 2004) 3 23 49
  4. Familial combined hyperlipidemia is associated with upstream transcription factor 1 (USF1). (PMID: 14991056) Pajukanta P. … Peltonen L. (Nat. Genet. 2004) 3 4 23
  5. The linkage and association of the gene encoding upstream stimulatory factor 1 with type 2 diabetes and metabolic syndrome in the Chinese population. (PMID: 16132950) Ng M.C. … Chan J.C. (Diabetologia 2005) 3 23 49

Products for USF1 Gene

Sources for USF1 Gene

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