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USF1 upstream transcription factor 1 [ Homo sapiens (human) ]

Gene ID: 7391, updated on 5-Mar-2024

Summary

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Official Symbol
USF1provided by HGNC
Official Full Name
upstream transcription factor 1provided by HGNC
Primary source
HGNC:HGNC:12593
See related
Ensembl:ENSG00000158773 MIM:191523; AllianceGenome:HGNC:12593
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UEF; FCHL; MLTF; FCHL1; MLTFI; HYPLIP1; bHLHb11
Summary
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]
Expression
Ubiquitous expression in spleen (RPKM 29.9), lymph node (RPKM 25.8) and 25 other tissues See more
Orthologs
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Genomic context

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See USF1 in Genome Data Viewer
Location:
1q23.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (161039251..161045977, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (160176758..160183484, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (161009041..161015767, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:161004943-161005449 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:161005450-161005955 Neighboring gene GLR5 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1971 Neighboring gene thiosulfate sulfurtransferase like domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1972 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:161015335-161016534 Neighboring gene Rho GTPase activating protein 30 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:161038974-161039520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1974 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:161044543-161045219 Neighboring gene nectin cell adhesion molecule 4 Neighboring gene NECTIN4 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. [USF1 Suppresses Expression of Fibrillar Type I, II, and III Collagen and pNP Adamts-3 in Osteosarcoma Cells]. Alper M, et al. Mol Biol (Mosk), 2021 Jul-Aug. PMID 34432781
  2. Polymorphism rs3737787 of Upstream Stimulatory Factor 1 gene is associated with serum lipid phenotype in Nigerian population. Onadeko OT, et al. Mol Cell Probes, 2021 Feb. PMID 33307180
  3. The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1. Wang J, et al. Biosci Rep, 2020 Aug 28. PMID 32776110, Free PMC Article
  4. A novel mutation in USF1 gene is associated with familial combined hyperlipidemia. Taghizadeh E, et al. IUBMB Life, 2020 Apr. PMID 31725952
  5. The rs2516839 variation of USF1 gene is associated with 4-year mortality of nonagenarian women: The Vitality 90+ study. Ozsait-Selcuk B, et al. Ann Hum Genet, 2019 Jan. PMID 30203836

See all (184) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Hepatitis B virus suppresses complement C9 synthesis by limiting the availability of transcription factor USF-1 and inhibits formation of membrane attack complex: implications in disease pathogenesis.
    Title: Hepatitis B virus suppresses complement C9 synthesis by limiting the availability of transcription factor USF-1 and inhibits formation of membrane attack complex: implications in disease pathogenesis.
  2. USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
    Title: USF1-ATRAP-PBX3 Axis Promote Breast Cancer Glycolysis and Malignant Phenotype by Activating AKT/mTOR Signaling.
  3. Polymorphism rs3737787 of Upstream Stimulatory Factor 1 gene is associated with serum lipid phenotype in Nigerian population.
    Title: Polymorphism rs3737787 of Upstream Stimulatory Factor 1 gene is associated with serum lipid phenotype in Nigerian population.
  4. [USF1 Suppresses Expression of Fibrillar Type I, II, and III Collagen and pNP Adamts-3 in Osteosarcoma Cells].
    Title: [USF1 Suppresses Expression of Fibrillar Type I, II, and III Collagen and pNP Adamts-3 in Osteosarcoma Cells].
  5. A novel mutation in USF1 gene is associated with familial combined hyperlipidemia.
    Title: A novel mutation in USF1 gene is associated with familial combined hyperlipidemia.
  6. Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen.
    Title: Functional interrogation of HOXA9 regulome in MLLr leukemia via reporter-based CRISPR/Cas9 screen.
  7. The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1.
    Title: The transcription factor USF1 promotes glioma cell invasion and migration by activating lncRNA HAS2-AS1.
  8. USF1-induced overexpression of long noncoding RNA WDFY3-AS2 promotes lung adenocarcinoma progression via targeting miR-491-5p/ZNF703 axis.
    Title: USF1-induced overexpression of long noncoding RNA WDFY3-AS2 promotes lung adenocarcinoma progression via targeting miR-491-5p/ZNF703 axis.
  9. Up-regulation of ZFAS1 indicates dismal prognosis for cholangiocarcinoma and promotes proliferation and metastasis by modulating USF1 via miR-296-5p.
    Title: Up-regulation of ZFAS1 indicates dismal prognosis for cholangiocarcinoma and promotes proliferation and metastasis by modulating USF1 via miR-296-5p.
  10. USF1-induced upregulation of LINC01048 promoted cutaneous squamous cell carcinoma by interacting with TAF15 to upregulate YAP1.
    Title: USF1-induced upregulation of LINC01048 promotes cell proliferation and apoptosis in cutaneous squamous cell carcinoma by binding to TAF15 to transcriptionally activate YAP1.
Submit: New GeneRIF Correction See all GeneRIFs (120)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hyperlipidemia, combined, 1
MedGen: C1865289 OMIM: 602491 GeneReviews: Not available
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EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Asp asp Analysis of point mutations in the USF1 and NF-kappaB sites in the cis-acting elements of ASP promoter region shows that USF1 and NF-kappaB are required for ASP activity PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables bHLH transcription factor binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables enzyme binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables histone deacetylase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-containing complex binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in carbon catabolite regulation of transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in cellular response to insulin stimulus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in glucose homeostasis TAS
Traceable Author Statement
more info
 PubMed 
involved_in late viral transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in lipid homeostasis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of fibrinolysis IC
Inferred by Curator
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription from RNA polymerase II promoter by glucose ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription from RNA polymerase II promoter by glucose IC
Inferred by Curator
more info
 PubMed 
involved_in response to UV ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to hypoxia IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
part_of transcription regulator complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
upstream stimulatory factor 1
Names
class B basic helix-loop-helix protein 11
major late transcription factor 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011612.1 RefSeqGene

    Range
    4991..11717
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001276373.2 → NP_001263302.1  upstream stimulatory factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001263302.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform 1.
    Source sequence(s)
    AL591806, AL832119, X55666
    Consensus CDS
    CCDS1214.1
    UniProtKB/Swiss-Prot
    B2RBZ4, P22415, Q5SY46, Q7Z5Y1
    UniProtKB/TrEMBL
    A0A0S2Z4U5
    Related
    ENSP00000356999.1, ENST00000368020.5
    Conserved Domains (1) summary
    cd18924
    Location:196 → 260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins

  2. NM_007122.5 → NP_009053.1  upstream stimulatory factor 1 isoform 1

    See identical proteins and their annotated locations for NP_009053.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Both variants 1 and 3 encode isoform 1.
    Source sequence(s)
    AL591806, AL832119, BP280296
    Consensus CDS
    CCDS1214.1
    UniProtKB/Swiss-Prot
    B2RBZ4, P22415, Q5SY46, Q7Z5Y1
    UniProtKB/TrEMBL
    A0A0S2Z4U5
    Related
    ENSP00000357000.3, ENST00000368021.7
    Conserved Domains (1) summary
    cd18924
    Location:196 → 260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins

  3. NM_207005.3 → NP_996888.1  upstream stimulatory factor 1 isoform 2

    See identical proteins and their annotated locations for NP_996888.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as USF1/BD) uses an alternate splice site in its 5' UTR, and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AB098540, AL591806, AL832119, BP280296
    UniProtKB/Swiss-Prot
    P22415
    Conserved Domains (1) summary
    cd18924
    Location:137 → 201
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    161039251..161045977 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429959.1 → XP_047285915.1  upstream stimulatory factor 1 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    160176758..160183484 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338612.1 → XP_054194587.1  upstream stimulatory factor 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P22415.1 GenPept UniProtKB/Swiss-Prot:P22415

Gene LinkOut

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