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

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

    Summary

    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
    NEW
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    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Hyperlipidemia, combined, 1
    MedGen: C1865289 OMIM: 602491 GeneReviews: Not available
    Compare labs

    EBI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001276373.2NP_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:196260
      bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
    2. NM_007122.5NP_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:196260
      bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
    3. NM_207005.3NP_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:137201
      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_047429959.1XP_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_054338612.1XP_054194587.1  upstream stimulatory factor 1 isoform X1