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

Gene ID: 287608, updated on 2-Nov-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
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 regulation of DNA-templated transcription and transcription elongation by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription elongation by RNA polymerase II. 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, Nov 2024]
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 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
    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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