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    Supt5h SPT5 homolog, DSIF elongation factor subunit [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308472, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Supt5hprovided by RGD
    Official Full Name
    SPT5 homolog, DSIF elongation factor subunitprovided by RGD
    Primary source
    RGD:1563807
    See related
    EnsemblRapid:ENSRNOG00000032034 AllianceGenome:RGD:1563807
    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
    Summary
    Predicted to enable several functions, including chromatin binding activity; mRNA binding activity; and protein heterodimerization activity. Involved in positive regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of DSIF complex. Orthologous to human SUPT5H (SPT5 homolog, DSIF elongation factor subunit). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 284.4), Thymus (RPKM 233.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Supt5h in Genome Data Viewer
    Location:
    1q21
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (92714276..92745489, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (83586713..83616971, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (85437780..85466854)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene delta like canonical Notch ligand 3 Neighboring gene translocase of inner mitochondrial membrane 50 Neighboring gene 40S ribosomal protein S28 pseudogene Neighboring gene small nucleolar RNA SNORA40 Neighboring gene ribosomal protein S16

    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. Transcription elongation factors are involved in programming hormone production in pituitary neuroendocrine GH4C1 cells. Fujita T, et al. Mol Cell Endocrinol, 2010 May 5. PMID 20097260
    2. Structure and function of the human transcription elongation factor DSIF. Yamaguchi Y, et al. J Biol Chem, 1999 Mar 19. PMID 10075709
    3. A monoclonal autoantibody which promotes central nervous system remyelination is highly polyreactive to multiple known and novel antigens. Asakura K, et al. J Neuroimmunol, 1996 Mar. PMID 8642059
    4. 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
    5. 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

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    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 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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 SPT5
    Names
    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_001107497.2 → NP_001100967.2  transcription elongation factor SPT5

      See identical proteins and their annotated locations for NP_001100967.2

      Status: VALIDATED

      Source sequence(s)
      BC166741, CB751273, CR755056, DY319730
      UniProtKB/TrEMBL
      A0A8I5ZQE4, E9PTB2
      Related
      ENSRNOP00000076183.3, ENSRNOT00000093384.3
      Conserved Domains (5) summary
      cd09888
      Location:177 → 264
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:333 → 960
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:275 → 312
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:1023 → 1080
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:92 → 171
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    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_086019.1 Reference GRCr8

      Range
      92714276..92745489 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063261526.1 → XP_063117596.1  transcription elongation factor SPT5 isoform X4

      UniProtKB/TrEMBL
      E9PTB2

    2. XM_039111569.2 → XP_038967497.1  transcription elongation factor SPT5 isoform X2

      UniProtKB/TrEMBL
      A0A1W2Q689, E9PTB2
      Conserved Domains (5) summary
      cd09888
      Location:173 → 260
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:329 → 956
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:271 → 308
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:1019 → 1076
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:74 → 167
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    3. XM_039111570.2 → XP_038967498.1  transcription elongation factor SPT5 isoform X3

      UniProtKB/TrEMBL
      A0A1W2Q6F0, E9PTB2
      Related
      ENSRNOP00000076244.2, ENSRNOT00000093740.3
      Conserved Domains (5) summary
      cd09888
      Location:177 → 264
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:333 → 907
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:275 → 312
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:970 → 1027
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:92 → 171
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    4. XM_063261518.1 → XP_063117588.1  transcription elongation factor SPT5 isoform X2

      UniProtKB/TrEMBL
      A0A1W2Q689, E9PTB2
      Related
      ENSRNOP00000081111.2, ENSRNOT00000093383.3

    5. XM_039111567.2 → XP_038967495.1  transcription elongation factor SPT5 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQE4, E9PTB2
      Conserved Domains (5) summary
      cd09888
      Location:177 → 264
      NGN_Euk; Eukaryotic N-Utilization Substance G (NusG) N-terminal (NGN) domain, including plant KTF1 (KOW domain-containing Transcription Factor 1)
      COG5164
      Location:333 → 960
      SPT5; Transcription elongation factor [Transcription]
      cd06081
      Location:275 → 312
      KOW_Spt5_1; KOW domain of Spt5, repeat 1
      cd06086
      Location:1023 → 1080
      KOW_Spt5_6; KOW domain of Spt5, repeat 6
      pfam11942
      Location:92 → 171
      Spt5_N; Spt5 transcription elongation factor, acidic N-terminal

    6. XM_063261515.1 → XP_063117585.1  transcription elongation factor SPT5 isoform X2

      UniProtKB/TrEMBL
      A0A1W2Q689, E9PTB2

    7. XM_063261507.1 → XP_063117577.1  transcription elongation factor SPT5 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQE4, E9PTB2

    8. XM_063261528.1 → XP_063117598.1  transcription elongation factor SPT5 isoform X5

      UniProtKB/TrEMBL
      A6J9H9, E9PTB2
    Nucleotide Protein Strain
    Heading Accession and Version

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