Human Gene USF1 (ENST00000368021.7) from GENCODE V44
  Description: Homo sapiens upstream transcription factor 1 (USF1), transcript variant 1, mRNA. (from RefSeq NM_007122)
RefSeq Summary (NM_007122): 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].
Gencode Transcript: ENST00000368021.7
Gencode Gene: ENSG00000158773.14
Transcript (Including UTRs)
   Position: hg38 chr1:161,039,251-161,045,977 Size: 6,727 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg38 chr1:161,039,920-161,043,275 Size: 3,356 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:161,039,251-161,045,977)mRNA (may differ from genome)Protein (310 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: USF1_HUMAN
DESCRIPTION: RecName: Full=Upstream stimulatory factor 1; AltName: Full=Class B basic helix-loop-helix protein 11; Short=bHLHb11; AltName: Full=Major late transcription factor 1;
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.
SUBUNIT: 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.
INTERACTION: Q92831:KAT2B; NbExp=5; IntAct=EBI-1054489, EBI-477430;
SUBCELLULAR LOCATION: Nucleus.
DISEASE: Genetic variations in USF1 are associated with hyperlipidemia combined type 1 (HYPLIP1) [MIM:602491]; also known as familial combined hyperlipidemia type 1 (FCHL1). HYPLIP1 is characterized by elevated levels of serum total cholesterol, triglycerides or both, and is observed in about 20% of individuals with premature coronary heart disease.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/usf1/";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: USF1
Diseases sorted by gene-association score: hyperlipidemia, familial combined* (481), urethral calculus (11), photokeratitis (10), lower urinary tract calculus (7), lipid metabolism disorder (3), inherited metabolic disorder (2)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 76.49 RPKM in Spleen
Total median expression: 1351.72 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -61.00205-0.298 Picture PostScript Text
3' UTR -236.20669-0.353 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011598 - HLH_dom

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1AN4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P22415
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003690 double-stranded DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0005515 protein binding
GO:0019899 enzyme binding
GO:0019901 protein kinase binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0042826 histone deacetylase binding
GO:0043425 bHLH transcription factor binding
GO:0043565 sequence-specific DNA binding
GO:0046982 protein heterodimerization activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0000430 regulation of transcription from RNA polymerase II promoter by glucose
GO:0000432 positive regulation of transcription from RNA polymerase II promoter by glucose
GO:0001666 response to hypoxia
GO:0006006 glucose metabolic process
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0009411 response to UV
GO:0019086 late viral transcription
GO:0032869 cellular response to insulin stimulus
GO:0042593 glucose homeostasis
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0045990 carbon catabolite regulation of transcription
GO:0051918 negative regulation of fibrinolysis
GO:0055088 lipid homeostasis

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005667 transcription factor complex
GO:0016589 NURF complex
GO:0048188 Set1C/COMPASS complex


-  Descriptions from all associated GenBank mRNAs
  X55666 - Human usf mRNA for late upstream transcription factor.
BC035505 - Homo sapiens upstream transcription factor 1, mRNA (cDNA clone MGC:23147 IMAGE:4559819), complete cds.
AL832119 - Homo sapiens mRNA; cDNA DKFZp686K19103 (from clone DKFZp686K19103).
JD168576 - Sequence 149600 from Patent EP1572962.
JD353325 - Sequence 334349 from Patent EP1572962.
JD535058 - Sequence 516082 from Patent EP1572962.
JD222032 - Sequence 203056 from Patent EP1572962.
JD183236 - Sequence 164260 from Patent EP1572962.
JD551744 - Sequence 532768 from Patent EP1572962.
JD163452 - Sequence 144476 from Patent EP1572962.
JD507637 - Sequence 488661 from Patent EP1572962.
JD058555 - Sequence 39579 from Patent EP1572962.
JD232579 - Sequence 213603 from Patent EP1572962.
JD348094 - Sequence 329118 from Patent EP1572962.
JD391448 - Sequence 372472 from Patent EP1572962.
JD331590 - Sequence 312614 from Patent EP1572962.
AB098540 - Homo sapiens usf1-bd mRNA for upstream stimulatory factor 1 BD, complete cds.
AK314876 - Homo sapiens cDNA, FLJ95777, Homo sapiens upstream transcription factor 1 (USF1), mRNA.
KJ897731 - Synthetic construct Homo sapiens clone ccsbBroadEn_07125 USF1 gene, encodes complete protein.
KU178379 - Homo sapiens upstream transcription factor 1 isoform 1 (USF1) mRNA, partial cds.
KU178380 - Homo sapiens upstream transcription factor 1 isoform 2 (USF1) mRNA, complete cds.
AB464339 - Synthetic construct DNA, clone: pF1KB8339, Homo sapiens USF1 gene for upstream transcription factor 1, without stop codon, in Flexi system.
AM392755 - Synthetic construct Homo sapiens clone IMAGE:100002162 for hypothetical protein (USF1 gene).
AM393836 - Synthetic construct Homo sapiens clone IMAGE:100002161 for hypothetical protein (USF1 gene).
CU690092 - Synthetic construct Homo sapiens gateway clone IMAGE:100021899 5' read USF1 mRNA.
JD442212 - Sequence 423236 from Patent EP1572962.
JD560314 - Sequence 541338 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P22415 (Reactome details) participates in the following event(s):

R-HSA-9023840 HATs and coactivators are recruited to the CTSD gene
R-HSA-9018519 Estrogen-dependent gene expression
R-HSA-8939211 ESR-mediated signaling
R-HSA-9006931 Signaling by Nuclear Receptors
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: B2RBZ4, BHLHB11, ENST00000368021.1, ENST00000368021.2, ENST00000368021.3, ENST00000368021.4, ENST00000368021.5, ENST00000368021.6, NM_007122, P22415, Q5SY46, uc001fxi.1, uc001fxi.2, uc001fxi.3, uc001fxi.4, uc001fxi.5, USF, USF1_HUMAN
UCSC ID: ENST00000368021.7
RefSeq Accession: NM_007122
Protein: P22415 (aka USF1_HUMAN)
CCDS: CCDS1214.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.