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    Supt4a SPT4A, DSIF elongation factor subunit [ Mus musculus (house mouse) ]

    Gene ID: 20922, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Supt4aprovided by MGI
    Official Full Name
    SPT4A, DSIF elongation factor subunitprovided by MGI
    Primary source
    MGI:MGI:107416
    See related
    Ensembl:ENSMUSG00000020485 AllianceGenome:MGI:107416
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Supt4h; Supt4h1; Supt4h1a
    Summary
    Predicted to enable RNA polymerase II complex binding activity and protein heterodimerization activity. Acts upstream of or within negative regulation of transcription elongation from RNA polymerase II promoter. Predicted to be located in nucleoplasm. Predicted to be part of DSIF complex. Is expressed in several structures, including genitourinary system; heart; liver; lung; and spleen. Orthologous to human SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in liver E14 (RPKM 38.8), liver E14.5 (RPKM 36.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Supt4a in Genome Data Viewer
    Location:
    11 C; 11 52.2 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (87628377..87634449)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (87737551..87743623)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene ring finger protein 43 Neighboring gene RIKEN cDNA 1110028F11 gene Neighboring gene predicted gene, 25968 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87534506-87534735 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87539623-87539928 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87547776-87547885 Neighboring gene STARR-positive B cell enhancer ABC_E7039 Neighboring gene STARR-positive B cell enhancer ABC_E1838 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87563093-87563276 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87565164-87565417 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:87568144-87568342 Neighboring gene STARR-positive B cell enhancer ABC_E8440 Neighboring gene microRNA 142b Neighboring gene TSPO associated protein 1 Neighboring gene microRNA 142 Neighboring gene STARR-positive B cell enhancer ABC_E7040

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Effects on murine behavior and lifespan of selectively decreasing expression of mutant huntingtin allele by supt4h knockdown. Cheng HM, et al. PLoS Genet, 2015 Mar. PMID 25760041, Free PMC Article
    2. The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination. Stanlie A, et al. PLoS Genet, 2012. PMID 22570620, Free PMC Article
    3. Spt4 is selectively required for transcription of extended trinucleotide repeats. Liu CR, et al. Cell, 2012 Feb 17. PMID 22341442
    4. Comparison of murine Supt4h and a nearly identical expressed, processed gene: evidence of sequence conservation through gene conversion extending into the untranslated regions. Chiang PW, et al. Nucleic Acids Res, 1998 Nov 1. PMID 9776760, Free PMC Article
    5. Isolation and characterization of the human and mouse homologues (SUPT4H and Supt4h) of the yeast SPT4 gene. Chiang PW, et al. Genomics, 1996 Jun 15. PMID 8786137

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. reduction of SUPT4H in mouse brains is associated with decreased HTT protein aggregation, and in R6/2 mice, also with prolonged lifespan and delay of the motor impairment that normally develops in these animals.
      Title: Effects on murine behavior and lifespan of selectively decreasing expression of mutant huntingtin allele by supt4h knockdown.
    2. our findings indicate that Spt4 and Spt5 have essential functions in the DNA repair phase of immunoglobulin class switch recombination.
      Title: The DSIF subunits Spt4 and Spt5 have distinct roles at various phases of immunoglobulin class switch recombination.
    3. These findings indicate that Supt4h is differentially required for expression of the mutant Htt allele in mouse striatal neurons.
      Title: Spt4 is selectively required for transcription of extended trinucleotide repeats.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    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 MGI

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in negative regulation of DNA-templated transcription, elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of transcription elongation by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription, elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription elongation by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription elongation by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in transcription elongation-coupled chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of DSIF complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of DSIF complex 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
    		  

    General protein information

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    Preferred Names
    transcription elongation factor SPT4-A
    Names
    DRB sensitivity-inducing factor small subunit 1
    DSIF small subunit 1
    Transcription elongation factor SPT4-A
    suppressor of Ty 4 homolog 1
    suppressor of Ty 4A
    transcription elongation factor SPT4 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.

    mRNA and Protein(s)

    1. NM_001355753.1 → NP_001342682.1  transcription elongation factor SPT4-A isoform 2

      Status: VALIDATED

      Source sequence(s)
      AK002990, AL604022, BQ176059, W47755
      Conserved Domains (1) summary
      cd07973
      Location:42 → 90
      Spt4; Transcription elongation factor Spt4

    2. NM_009296.2 → NP_033322.1  transcription elongation factor SPT4-A isoform 1

      See identical proteins and their annotated locations for NP_033322.1

      Status: VALIDATED

      Source sequence(s)
      BQ176059, DV044501, DV061290
      Consensus CDS
      CCDS36270.1
      UniProtKB/Swiss-Prot
      B2KGH6, P63271, Q3TIA2, Q5NCP8, Q5NCP9, Q5NCQ0
      Related
      ENSMUSP00000091487.6, ENSMUST00000093955.12
      Conserved Domains (1) summary
      cd07973
      Location:11 → 108
      Spt4; Transcription elongation factor Spt4

    RNA

    1. NR_149756.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK002990, AL604022, BQ176059, DV061290, W47755
      Related
      ENSMUST00000152700.8

    2. NR_149757.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK002990, AL604022, BQ176059, DV061290
      Related
      ENSMUST00000141169.2

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      87628377..87634449
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P63271.1 GenPept UniProtKB/Swiss-Prot:P63271

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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