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Rtf1 Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) [ Rattus norvegicus (Norway rat) ]

Gene ID: 366169, updated on 13-Apr-2024

Summary

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Official Symbol
Rtf1provided by RGD
Official Full Name
Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)provided by RGD
Primary source
RGD:1310654
See related
Ensembl:ENSRNOG00000005183 AllianceGenome:RGD:1310654
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
Gtl7
Summary
Predicted to enable RNA polymerase II C-terminal domain phosphoserine binding activity and single-stranded DNA binding activity. Predicted to be involved in several processes, including histone H3-K4 trimethylation; positive regulation of histone H3-K4 methylation; and transcription elongation from RNA polymerase II promoter. Predicted to act upstream of or within blastocyst growth. Predicted to be located in nucleolus. Predicted to be part of Cdc73/Paf1 complex. Orthologous to human RTF1 (RTF1 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Spleen (RPKM 54.2), Adrenal (RPKM 53.1) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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Location:
3q35
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (127113171..127172761)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (106659363..106718956)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (111478350..111537941)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene Opa interacting protein 5 Neighboring gene nucleolar and spindle associated protein 1 Neighboring gene 40S ribosomal protein S20 pseudogene Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene inositol-trisphosphate 3-kinase A Neighboring gene leukocyte receptor tyrosine kinase

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. Structure and DNA binding of the human Rtf1 Plus3 domain. de Jong RN, et al. Structure, 2008 Jan. PMID 18184592
  2. The Paf1 complex: platform or player in RNA polymerase II transcription? Jaehning JA. Biochim Biophys Acta, 2010 May-Jun. PMID 20060942, Free PMC Article
  3. Regulation of transcriptional elongation in pluripotency and cell differentiation by the PHD-finger protein Phf5a. Strikoudis A, et al. Nat Cell Biol, 2016 Nov. PMID 27749823, Free PMC Article
  4. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Kim J, et al. Cell, 2010 Feb 19. PMID 20178742, Free PMC Article
  5. Capturing novel mouse genes encoding chromosomal and other nuclear proteins. Tate P, et al. J Cell Sci, 1998 Sep. PMID 9701556

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables RNA polymerase II C-terminal domain phosphoserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables single-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
acts_upstream_of_or_within blastocyst growth ISO
Inferred from Sequence Orthology
more info
  
involved_in chromatin organization ISO
Inferred from Sequence Orthology
more info
  
involved_in endodermal cell fate commitment 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 stem cell population maintenance ISO
Inferred from Sequence Orthology
more info
  
involved_in transcription elongation by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of Cdc73/Paf1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Cdc73/Paf1 complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
RNA polymerase-associated protein RTF1 homolog
Names
gene trap locus 7

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_001401979.1 → NP_001388908.1  RNA polymerase-associated protein RTF1 homolog precursor

    Status: VALIDATED

    Source sequence(s)
    JAXUCZ010000003
    UniProtKB/TrEMBL
    A0A8I6AGX2
    Related
    ENSRNOP00000094041.1, ENSRNOT00000105159.1

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_086021.1 Reference GRCr8

    Range
    127113171..127172761
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063284277.1 → XP_063140347.1  RNA polymerase-associated protein RTF1 homolog isoform X1

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001108958.1: Suppressed sequence

    Description
    NM_001108958.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein Strain
Heading Accession and Version

Gene LinkOut

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