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    Supt5 suppressor of Ty 5, DSIF elongation factor subunit [ Mus musculus (house mouse) ]

    Gene ID: 20924, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Supt5provided by MGI
    Official Full Name
    suppressor of Ty 5, DSIF elongation factor subunitprovided by MGI
    Primary source
    MGI:MGI:1202400
    See related
    Ensembl:ENSMUSG00000003435 AllianceGenome:MGI:1202400
    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
    Spt5; Supt5h
    Summary
    Enables chromatin binding activity. Predicted to be involved in positive regulation of macroautophagy; regulation of RNA metabolic process; and 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; limb mesenchyme; and nervous system. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thymus adult (RPKM 68.8), adrenal adult (RPKM 67.5) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    7 A3; 7 16.68 cM
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (28014316..28038341, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (28314891..28338804, complement)

    Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene delta like canonical Notch ligand 3 Neighboring gene STARR-positive B cell enhancer ABC_E6527 Neighboring gene translocase of inner mitochondrial membrane 50 Neighboring gene predicted gene, 51445 Neighboring gene STARR-seq mESC enhancer starr_18409 Neighboring gene STARR-positive B cell enhancer ABC_E3708 Neighboring gene snoRNA AF357399 Neighboring gene ribosomal protein S16 Neighboring gene pleckstrin homology domain containing, family G (with RhoGef domain) member 2 Neighboring gene STARR-positive B cell enhancer ABC_E445 Neighboring gene nuclear encoded tRNA isoleucine 16 (anticodon TAT)

    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. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape. Hu S, et al. Mol Cell, 2021 Nov 4. PMID 34534457
    2. Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction. Fitz J, et al. Nat Genet, 2020 May. PMID 32251373
    3. Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation. Fitz J, et al. EMBO J, 2018 Apr 13. PMID 29514850, Free PMC Article
    4. Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5. Pavri R, et al. Cell, 2010 Oct 1. PMID 20887897, Free PMC Article
    5. 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

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
      Title: SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape.
    2. We propose that an important role of Spt5 in mammalian elongation is to promote the processivity of those Pol II complexes that are transitioning toward maximum elongation speed 15-20 kb from the promoter.
      Title: Regulation of RNA polymerase II processivity by Spt5 is restricted to a narrow window during elongation.
    3. Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo-activated cells.
      Title: Spt5 accumulation at variable genes distinguishes somatic hypermutation in germinal center B cells from ex vivo-activated cells.
    4. 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.
    5. Study reports that Spt5, a factor normally associated with stalled or paused Pol II, is required for class switch recombination.
      Title: Activation-induced cytidine deaminase targets DNA at sites of RNA polymerase II stalling by interaction with Spt5.
    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 chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein heterodimerization activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA-templated transcription elongation IEA
    Inferred from Electronic Annotation
    more info
    		  
    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
    		  
    involved_in positive regulation of DNA-templated transcription, elongation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of macroautophagy 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 elongation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II 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 SPT5
    Names
    DRB sensitivity-inducing factor large subunit
    DSIF large subunit
    suppressor of Ty 5 homolog

    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_001417308.1 → NP_001404237.1  transcription elongation factor SPT5 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC148986

    2. NM_001417309.1 → NP_001404238.1  transcription elongation factor SPT5 isoform b

      Status: VALIDATED

      Source sequence(s)
      AC148986
      Related
      ENSMUST00000207879.2

    3. NM_001417310.1 → NP_001404239.1  transcription elongation factor SPT5 isoform c

      Status: VALIDATED

      Source sequence(s)
      AC148986

    4. NM_013676.2 → NP_038704.1  transcription elongation factor SPT5 isoform a

      See identical proteins and their annotated locations for NP_038704.1

      Status: VALIDATED

      Source sequence(s)
      AC148986
      Consensus CDS
      CCDS39857.1
      UniProtKB/Swiss-Prot
      O55201, Q3UJ77, Q3UJH1, Q3UKD7, Q3UM54, Q6PB73, Q6PDP0, Q6PFR4
      Related
      ENSMUSP00000003527.9, ENSMUST00000003527.10
      Conserved Domains (12) summary
      PRK08559
      Location:173 → 314
      nusG; transcription antitermination protein NusG; Validated
      cd09888
      Location:176 → 263
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:332 → 959
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:274 → 311
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06082
      Location:418 → 468
      KOW_Spt5_2; KOW domain of Spt5, repeat 2
      cd06083
      Location:469 → 519
      KOW_Spt5_3; KOW domain of Spt5, repeat 3
      cd06084
      Location:595 → 637
      KOW_Spt5_4; KOW domain of Spt5, repeat 4
      cd06085
      Location:696 → 745
      KOW_Spt5_5; KOW domain of Spt5, repeat 5
      cd06086
      Location:1022 → 1079
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam04731
      Location:841 → 970
      Caudal_act; Caudal like protein activation region
      pfam11942
      Location:91 → 169
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal
      pfam12815
      Location:760 → 816
      CTD; Spt5 C-terminal nonapeptide repeat binding Spt4

    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_000073.7 Reference GRCm39 C57BL/6J

      Range
      28014316..28038341 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006539703.3 → XP_006539766.1  transcription elongation factor SPT5 isoform X2

      Conserved Domains (5) summary
      cd09888
      Location:176 → 263
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:332 → 906
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:274 → 311
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:969 → 1026
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:73 → 169
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    2. XM_036152859.1 → XP_036008752.1  transcription elongation factor SPT5 isoform X3

      Conserved Domains (4) summary
      cd09888
      Location:37 → 124
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:193 → 820
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:135 → 172
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:883 → 940
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O55201.1 GenPept UniProtKB/Swiss-Prot:O55201

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