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Aliases for RTF1 Gene

Aliases for RTF1 Gene

  • Rtf1, Paf1/RNA Polymerase II Complex Component, Homolog (S. Cerevisiae) 2 3
  • KIAA0252 2 3 4 6
  • RNA Polymerase-Associated Protein RTF1 Homolog 3
  • Ortholog Of Mouse Gene Trap Locus 7 3
  • GTL7 3

External Ids for RTF1 Gene

Previous Symbols for RTF1 Gene

  • KIAA0252

Summaries for RTF1 Gene

Entrez Gene Summary for RTF1 Gene

  • This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]

GeneCards Summary for RTF1 Gene

RTF1 (Rtf1, Paf1/RNA Polymerase II Complex Component, Homolog (S. Cerevisiae)) is a Protein Coding gene. GO annotations related to this gene include single-stranded DNA binding.

UniProtKB/Swiss-Prot for RTF1 Gene

  • Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and Ser-2- and Ser-5-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 Lys-4 (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of Lys-120 of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3 end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 Lys-4 (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity).

Gene Wiki entry for RTF1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTF1 Gene

Genomics for RTF1 Gene

Genomic Location for RTF1 Gene

Start:
41,408,408 bp from pter
End:
41,483,563 bp from pter
Size:
75,156 bases
Orientation:
Plus strand

Genomic View for RTF1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RTF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTF1 Gene

Regulatory Elements for RTF1 Gene

Proteins for RTF1 Gene

  • Protein details for RTF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92541-RTF1_HUMAN
    Recommended name:
    RNA polymerase-associated protein RTF1 homolog
    Protein Accession:
    Q92541
    Secondary Accessions:
    • Q96BX6

    Protein attributes for RTF1 Gene

    Size:
    710 amino acids
    Molecular mass:
    80313 Da
    Quaternary structure:
    • Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61; the association of RTF1 appears to be less stable than that of other subunits. At least in HeLa cells a N-terminal shorter form of RTF1 is also found in the complex.
    SequenceCaution:
    • Sequence=AAH15052.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA13382.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RTF1 Gene

neXtProt entry for RTF1 Gene

Proteomics data for RTF1 Gene at MOPED

Post-translational modifications for RTF1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RTF1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTF1 Gene

Domains for RTF1 Gene

Protein Domains for RTF1 Gene

InterPro:
ProtoNet:

UniProtKB/Swiss-Prot:

RTF1_HUMAN
Domain:
  • The Plus3 domain mediates single-stranded DNA-binding.:
    • Q92541
  • Contains 1 Plus3 domain.:
    • Q92541
genes like me logo Genes that share domains with RTF1: view

No data available for Gene Families for RTF1 Gene

Function for RTF1 Gene

Molecular function for RTF1 Gene

UniProtKB/Swiss-Prot Function: Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and Ser-2- and Ser-5-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 Lys-4 (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of Lys-120 of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3 end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 Lys-4 (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity).

Gene Ontology (GO) - Molecular Function for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding --
GO:0003697 single-stranded DNA binding IDA 18184592
GO:0005515 protein binding IPI 15923622
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with RTF1: view
genes like me logo Genes that share phenotypes with RTF1: view

miRNA for RTF1 Gene

miRTarBase miRNAs that target RTF1

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targeting and HOMER Transcription for RTF1 Gene

Localization for RTF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTF1 Gene

Nucleus, nucleoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RTF1 Gene COMPARTMENTS Subcellular localization image for RTF1 gene
Compartment Confidence
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus --
GO:0005730 nucleolus IEA --
GO:0016593 Cdc73/Paf1 complex IDA 20178742
genes like me logo Genes that share ontologies with RTF1: view

Pathways for RTF1 Gene

SuperPathways for RTF1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter ISS --
GO:0001711 endodermal cell fate commitment ISS --
GO:0006352 DNA-templated transcription, initiation IEA --
GO:0016055 Wnt signaling pathway IEA --
GO:0016570 histone modification --
genes like me logo Genes that share ontologies with RTF1: view

No data available for Pathways by source for RTF1 Gene

Transcripts for RTF1 Gene

mRNA/cDNA for RTF1 Gene

Unigene Clusters for RTF1 Gene

Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for RTF1 Gene

No ASD Table

Relevant External Links for RTF1 Gene

GeneLoc Exon Structure for
RTF1
ECgene alternative splicing isoforms for
RTF1

Expression for RTF1 Gene

mRNA expression in normal human tissues for RTF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for RTF1 Gene

SOURCE GeneReport for Unigene cluster for RTF1 Gene Hs.511096

genes like me logo Genes that share expressions with RTF1: view

Orthologs for RTF1 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RTF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTF1 36
  • 99.95 (n)
  • 100 (a)
RTF1 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RTF1 36
  • 93.1 (n)
  • 98.45 (a)
RTF1 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RTF1 36
  • 94.79 (n)
  • 99.01 (a)
RTF1 37
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rtf1 36
  • 91.5 (n)
  • 98.03 (a)
Rtf1 16
Rtf1 37
  • 97 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RTF1 37
  • 97 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RTF1 37
  • 93 (a)
OneToOne
chicken
(Gallus gallus)
Aves RTF1 36
  • 82.08 (n)
  • 94.33 (a)
RTF1 37
  • 93 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RTF1 37
  • 93 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.16706 36
tropical clawed frog
(Silurana tropicalis)
Amphibia rtf1 36
  • 77.32 (n)
  • 89.4 (a)
Str.16458 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2044 36
zebrafish
(Danio rerio)
Actinopterygii Dr.15115 36
rtf1 36
  • 73.65 (n)
  • 82.93 (a)
rtf1 37
  • 81 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG12498 37
  • 26 (a)
OneToMany
CG31702 37
  • 27 (a)
OneToMany
CG31703 37
  • 27 (a)
OneToMany
Rtf1 36
  • 50.71 (n)
  • 46.73 (a)
Rtf1 37
  • 36 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F25B3.6 37
  • 33 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTF1 37
  • 24 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1372 37
  • 49 (a)
OneToOne
Species with no ortholog for RTF1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RTF1 Gene

ENSEMBL:
Gene Tree for RTF1 (if available)
TreeFam:
Gene Tree for RTF1 (if available)

Paralogs for RTF1 Gene

No data available for Paralogs for RTF1 Gene

Variants for RTF1 Gene

Sequence variations from dbSNP and Humsavar for RTF1 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type MAF
rs1942 -- 41,482,225(+) GATAA(A/G)CTGAC utr-variant-3-prime
rs167581 -- 41,474,768(+) CTGCT(A/G)TTCTC intron-variant
rs222209 -- 41,478,221(+) catgg(C/T)gaaac intron-variant
rs316604 -- 41,483,023(+) GTAGC(C/T)GCTGA utr-variant-3-prime
rs316605 -- 41,479,393(+) TACTT(A/G)CCTAG intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RTF1 Gene

Variant ID Type Subtype PubMed ID
nsv524476 CNV Loss 19592680
esv2674168 CNV Deletion 23128226
nsv1505 CNV Insertion 18451855

Relevant External Links for RTF1 Gene

HapMap Linkage Disequilibrium report
RTF1
Human Gene Mutation Database (HGMD)
RTF1

Disorders for RTF1 Gene

Relevant External Links for RTF1

Genetic Association Database (GAD)
RTF1
Human Genome Epidemiology (HuGE) Navigator
RTF1
genes like me logo Genes that share disorders with RTF1: view

No data available for UniProtKB/Swiss-Prot for RTF1 Gene

Publications for RTF1 Gene

  1. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T. … Nomura N. (DNA Res. 1996) 3 4
  2. Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones. (PMID: 12168954) Nakajima D. … Nagase T. (DNA Res. 2002) 3 4
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  4. The parafibromin tumor suppressor protein is part of a human Paf1 complex. (PMID: 15632063) Rozenblatt-Rosen O. … Meyerson M. (Mol. Cell. Biol. 2005) 2 3
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4

Products for RTF1 Gene

Sources for RTF1 Gene

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