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Usf1 upstream transcription factor 1 [ Mus musculus (house mouse) ]

Gene ID: 22278, updated on 5-Jan-2023

Summary

Official Symbol
Usf1provided by MGI
Official Full Name
upstream transcription factor 1provided by MGI
Primary source
MGI:MGI:99542
See related
Ensembl:ENSMUSG00000026641 AllianceGenome:MGI:99542
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
bHLHb11
Summary
This protein encoded by this gene is a member of the basic-Helix-Hoop-Helix-Leucine zipper (bHLH-LZ) family and encodes a protein that can act as a transcription factor. Studies indicate that the basic region interacts with DNA at E-Box motifs, while the helix-loop-helix and leucine zipper domains are involved in dimerization with different partners. This protein is involved in a wide array of biological pathways, including cell cycle regulation, immune response, and responses to ultraviolet radiation. Mice lacking most of the coding exons of this gene often lacked both whiskers and nasal fur, and were prone to epileptic seizures, while mice lacking both this gene and another family member, Usf2, displayed embryonic lethality (PMID:9520440). Mutations in the human ortholog of this gene have been associated with Familial Combined Hyperlipidemia (FCHL) in humans. Pseudogenes of this gene are found on chromosome 11 and the X chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2015]
Expression
Ubiquitous expression in whole brain E14.5 (RPKM 35.2), ovary adult (RPKM 33.6) and 28 other tissues See more
Orthologs
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Genomic context

See Usf1 in Genome Data Viewer
Location:
1 H3; 1 79.4 cM
Exon count:
12
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (171238875..171246327)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (171411307..171418954)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene nectin cell adhesion molecule 4 Neighboring gene Rho GTPase activating protein 30 Neighboring gene thiosulfate sulfurtransferase (rhodanese)-like domain containing 1 Neighboring gene predicted gene, 26641

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
contributes_to DNA-binding transcription factor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables bHLH transcription factor binding ISO
Inferred from Sequence Orthology
more info
 
enables double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables enzyme binding ISO
Inferred from Sequence Orthology
more info
 
enables histone deacetylase binding ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein dimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein heterodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein kinase binding ISO
Inferred from Sequence Orthology
more info
 
enables protein-containing complex binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in chromatin ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of transcription regulator complex IC
Inferred by Curator
more info
PubMed 
part_of transcription regulator complex ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
upstream stimulatory factor 1
Names
Upstream stimulatory factor 1 (Major late transcription factor 1)
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.

mRNA and Protein(s)

  1. NM_001305676.1NP_001292605.1  upstream stimulatory factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001292605.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in its 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AK142437, AW555090, BE995823, CJ050979
    Consensus CDS
    CCDS15495.1
    UniProtKB/Swiss-Prot
    Q61069
    UniProtKB/TrEMBL
    A0A8C6HZ27, Q3UQH7
    Related
    ENSMUSP00000125729.2, ENSMUST00000161241.8
    Conserved Domains (2) summary
    pfam15744
    Location:145284
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:196260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
  2. NM_001305677.1NP_001292606.1  upstream stimulatory factor 1 isoform 1

    See identical proteins and their annotated locations for NP_001292606.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AK142437, AW555090, BE995823, CJ050979
    Consensus CDS
    CCDS15495.1
    UniProtKB/Swiss-Prot
    Q61069
    UniProtKB/TrEMBL
    A0A8C6HZ27, Q3UQH7
    Conserved Domains (2) summary
    pfam15744
    Location:145284
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:196260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
  3. NM_001305678.1NP_001292607.1  upstream stimulatory factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001292607.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site at an internal exon compared to variant 1. This variant represents translation initiation at a downstream AUG compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream AUG to encode an isoform (2) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK142437, AW555090, BE995823, CJ050979, DV653810
    UniProtKB/TrEMBL
    A0A6P5PBF1, Q3UQH7, Q8R4E5
    Conserved Domains (2) summary
    pfam15744
    Location:86225
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:137201
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
  4. NM_009480.3NP_033506.1  upstream stimulatory factor 1 isoform 1

    See identical proteins and their annotated locations for NP_033506.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. The 5' terminal exon of this transcript was described in PMID:8938446, and is supported by RNASeq data. Variants 1, 2, and 3 encode the same isoform (1).
    Source sequence(s)
    AC087229, AK142437, AW555090, BE995823
    Consensus CDS
    CCDS15495.1
    UniProtKB/Swiss-Prot
    Q61069
    UniProtKB/TrEMBL
    A0A8C6HZ27, Q3UQH7
    Related
    ENSMUSP00000128913.2, ENSMUST00000167546.2
    Conserved Domains (2) summary
    pfam15744
    Location:145284
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:196260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    171238875..171246327
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030253053.2XP_030108913.1  upstream stimulatory factor 1 isoform X2

    UniProtKB/TrEMBL
    A0A6P5PBF1, Q8R4E5
    Conserved Domains (2) summary
    pfam15744
    Location:86225
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:137201
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
  2. XM_030253052.2XP_030108912.1  upstream stimulatory factor 1 isoform X1

    UniProtKB/Swiss-Prot
    Q61069
    UniProtKB/TrEMBL
    A0A8C6HZ27, Q3UQH7
    Conserved Domains (2) summary
    pfam15744
    Location:145284
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:196260
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins
  3. XM_030253055.1XP_030108915.1  upstream stimulatory factor 1 isoform X2

    UniProtKB/TrEMBL
    A0A6P5PBF1, Q8R4E5
    Conserved Domains (2) summary
    pfam15744
    Location:86225
    UPF0492; Uncharacterized protein family UPF0492
    cd18924
    Location:137201
    bHLHzip_USF1; basic Helix-Loop-Helix-zipper (bHLHzip) domain found in upstream stimulatory factor 1 (USF1) and similar proteins