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    Supt4h1 SPT4 homolog, DSIF elongation factor subunit [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287608, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Supt4h1provided by RGD
    Official Full Name
    SPT4 homolog, DSIF elongation factor subunitprovided by RGD
    Primary source
    RGD:1306372
    See related
    Ensembl:ENSRNOG00000007845 AllianceGenome:RGD:1306372
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Supt4h2
    Summary
    Predicted to enable RNA polymerase II complex binding activity and protein heterodimerization activity. Predicted to be involved in RNA metabolic process; chromatin organization; and regulation of transcription, DNA-templated. Predicted to act 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. Orthologous to human SUPT4H1 (SPT4 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 379.1), Spleen (RPKM 240.1) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Supt4h1 in Genome Data Viewer
    Location:
    10q26
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (73036560..73042821)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (72539323..72545582)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (75032365..75038547)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene heat shock transcription factor 5 Neighboring gene ring finger protein 43 Neighboring gene U6 spliceosomal RNA Neighboring gene uncharacterized LOC134480847 Neighboring gene TSPO associated protein 1 Neighboring gene microRNA 142 Neighboring gene myeloperoxidase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Identification and analysis of a functional human homolog of the SPT4 gene of Saccharomyces cerevisiae. Hartzog GA, et al. Mol Cell Biol, 1996 Jun. PMID 8649394, Free PMC Article
    2. Evidence that P-TEFb alleviates the negative effect of DSIF on RNA polymerase II-dependent transcription in vitro. Wada T, et al. EMBO J, 1998 Dec 15. PMID 9857195, Free PMC Article
    3. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Wada T, et al. Genes Dev, 1998 Feb 1. PMID 9450929, Free PMC Article
    4. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome. Flynn RA, et al. Proc Natl Acad Sci U S A, 2011 Jun 28. PMID 21670248, Free PMC Article
    5. Control of transcriptional elongation. Kwak H, et al. Annu Rev Genet, 2013. PMID 24050178, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC188814

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables RNA polymerase II complex binding IBA
    Inferred from Biological aspect of Ancestor
    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 biological_process ND
    No biological Data available
    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
    		  
    acts_upstream_of_or_within negative regulation of transcription elongation 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 transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    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
    Names
    suppressor of Ty 4 homolog 1
    suppressor of Ty 4 homolog 2

    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_001105828.3 → NP_001099298.2  transcription elongation factor SPT4

      See identical proteins and their annotated locations for NP_001099298.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A8I6GK12, B5DEM7, F7F5Z5
      Related
      ENSRNOP00000010448.4, ENSRNOT00000010448.8
      Conserved Domains (1) summary
      cd07973
      Location:11 → 108
      Spt4; Transcription elongation factor Spt4

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      73036560..73042821
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063268702.1 → XP_063124772.1  transcription elongation factor SPT4 isoform X4

      UniProtKB/TrEMBL
      A6HHV0

    2. XM_063268701.1 → XP_063124771.1  transcription elongation factor SPT4 isoform X2

    3. XM_039085570.2 → XP_038941498.1  transcription elongation factor SPT4 isoform X3

      Conserved Domains (1) summary
      cd07973
      Location:11 → 64
      Spt4; Transcription elongation factor Spt4

    4. XM_039085572.2 → XP_038941500.1  transcription elongation factor SPT4 isoform X6

      Conserved Domains (1) summary
      cd07973
      Location:21 → 69
      Spt4; Transcription elongation factor Spt4

    5. XM_039085571.2 → XP_038941499.1  transcription elongation factor SPT4 isoform X5

      Conserved Domains (1) summary
      cd07973
      Location:28 → 76
      Spt4; Transcription elongation factor Spt4

    6. XM_039085568.2 → XP_038941496.1  transcription elongation factor SPT4 isoform X1

      Conserved Domains (1) summary
      cd07973
      Location:11 → 125
      Spt4; Transcription elongation factor Spt4
    Nucleotide Protein Strain
    Heading Accession and Version

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