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Rtf1 RTF1, Paf1/RNA polymerase II complex component [ Mus musculus (house mouse) ]

Gene ID: 76246, updated on 5-Mar-2024

Summary

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Official Symbol
Rtf1provided by MGI
Official Full Name
RTF1, Paf1/RNA polymerase II complex componentprovided by MGI
Primary source
MGI:MGI:1309480
See related
Ensembl:ENSMUSG00000027304 AllianceGenome:MGI:1309480
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
Gtl7; cbp82; 2900005O08Rik; 6530416A09Rik
Summary
Predicted to enable RNA polymerase II C-terminal domain phosphoserine binding activity and single-stranded DNA binding activity. Involved in several processes, including endodermal cell fate commitment; histone H3-K4 trimethylation; and positive regulation of histone H3-K4 methylation. Acts upstream of or within blastocyst growth. Located in nucleolus. Part of Cdc73/Paf1 complex. Is expressed in several structures, including brain and retina nuclear layer. Orthologous to human RTF1 (RTF1 homolog, Paf1/RNA polymerase II complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 14.6), CNS E14 (RPKM 12.6) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Rtf1 in Genome Data Viewer
Location:
2 E5; 2 59.97 cM
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (119505549..119565888)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (119675068..119735407)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 1 Neighboring gene STARR-positive B cell enhancer ABC_E9201 Neighboring gene H3 histone, family 3C Neighboring gene STARR-positive B cell enhancer ABC_E7852 Neighboring gene STARR-seq mESC enhancer starr_05489 Neighboring gene predicted gene, 25857 Neighboring gene inositol 1,4,5-trisphosphate 3-kinase A

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. Structure and DNA binding of the human Rtf1 Plus3 domain. de Jong RN, et al. Structure, 2008 Jan. PMID 18184592
  2. 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
  3. Capturing novel mouse genes encoding chromosomal and other nuclear proteins. Tate P, et al. J Cell Sci, 1998 Sep. PMID 9701556
  4. CTR9/PAF1c regulates molecular lineage identity, histone H3K36 trimethylation and genomic imprinting during preimplantation development. Zhang K, et al. Dev Biol, 2013 Nov 1. PMID 24036311, Free PMC Article
  5. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. Ding L, et al. Cell Stem Cell, 2009 May 8. PMID 19345177

See all (28) citations in PubMed

GeneRIFs: Gene References Into Functions

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (2)  1 citation
  • Endonuclease-mediated (1) 

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 DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II C-terminal domain phosphoserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within blastocyst growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromatin organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in endodermal cell fate commitment IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of Cdc73/Paf1 complex ISO
Inferred from Sequence Orthology
more info
  
located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
RNA polymerase-associated protein RTF1 homolog
Names
Rtf1, Paf1/RNA polymerase II complex component, homolog
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_030112.2 → NP_084388.2  RNA polymerase-associated protein RTF1 homolog

    See identical proteins and their annotated locations for NP_084388.2

    Status: VALIDATED

    Source sequence(s)
    AK019305, AL844536, AW491091, BC117849, BY270385, CN532066, CN839001
    Consensus CDS
    CCDS50673.1
    UniProtKB/Swiss-Prot
    A2AQ19, Q08EC5
    Related
    ENSMUSP00000028767.9, ENSMUST00000028767.9
    Conserved Domains (2) summary
    COG5296
    Location:194 → 628
    COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
    pfam03126
    Location:364 → 462
    Plus-3; Plus-3 domain

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_000068.8 Reference GRCm39 C57BL/6J

    Range
    119505549..119565888
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_036162668.1 → XP_036018561.1  RNA polymerase-associated protein RTF1 homolog isoform X3

    Conserved Domains (2) summary
    COG5296
    Location:148 → 413
    COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
    pfam03126
    Location:149 → 249
    Plus-3; Plus-3 domain

  2. XM_036162666.1 → XP_036018559.1  RNA polymerase-associated protein RTF1 homolog isoform X1

    Conserved Domains (2) summary
    COG5296
    Location:154 → 588
    COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
    pfam03126
    Location:324 → 424
    Plus-3; Plus-3 domain

  3. XM_036162667.1 → XP_036018560.1  RNA polymerase-associated protein RTF1 homolog isoform X2

    Conserved Domains (2) summary
    COG5296
    Location:3 → 437
    COG5296; Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
    pfam03126
    Location:173 → 273
    Plus-3; Plus-3 domain
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
A2AQ19.1 GenPept UniProtKB/Swiss-Prot:A2AQ19

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