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Aliases for RTF1 Gene

Aliases for RTF1 Gene

  • RTF1 Homolog, Paf1/RNA Polymerase II Complex Component 2 3 5
  • KIAA0252 2 3 4
  • Rtf1, Paf1/RNA Polymerase II Complex Component, Homolog (S. Cerevisiae) 2
  • Rtf1, Paf1/RNA Polymerase II Complex Component, Homolog 3
  • RNA Polymerase-Associated Protein RTF1 Homolog 3
  • Ortholog Of Mouse Gene Trap Locus 7 3
  • GTL7 3

External Ids for RTF1 Gene

Previous HGNC Symbols for RTF1 Gene

  • KIAA0252

Previous GeneCards Identifiers for RTF1 Gene

  • GC15P039497
  • GC15P041709
  • GC15P018557

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 Homolog, Paf1/RNA Polymerase II Complex Component) is a Protein Coding gene. Among its related pathways are Metabolism of proteins and Formation of HIV elongation complex in the absence of HIV Tat. GO annotations related to this gene include poly(A) RNA binding and 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

Regulatory Elements for RTF1 Gene

Enhancers for RTF1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15F041481 0.7 Ensembl ENCODE 26 +74.4 74398 2.8 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 NDUFAF1 RTF1 ZFYVE19 LOC105370790 RNU6-1169P
GH15F041404 0.8 Ensembl 25 -3.6 -3608 0.4 ZNF316 EMSY RTF1 NDUFAF1
GH15F041489 1 Ensembl ENCODE 24.3 +82.1 82074 1.1 KLF17 RAD21 ZNF366 RCOR1 ETV6 FOS CREM ZNF362 CEBPB JUNB NDUFAF1 RTF1 ITPKA LOC105370790
GH15F041492 1.1 FANTOM5 ENCODE 24.1 +86.4 86412 5.1 ZFP64 ARID4B DMAP1 ZNF2 YY1 SLC30A9 KLF13 ZNF263 SP3 SP5 NDUFAF1 RTF1 RAD51-AS1 RPAP1 ENSG00000260814 MAPKBP1 TYRO3 RNU6-1169P RPUSD2 ITPKA
GH15F041337 0.2 Ensembl 10.7 -70.7 -70708 0.2 GATA3 ZFHX2 ZNF362 ZNF366 GLIS1 ZBTB17 TCF7L2 RTF1 RNU6-1169P OIP5 ENSG00000259396
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RTF1 on UCSC Golden Path with GeneCards custom track

Genomic Location for RTF1 Gene

Chromosome:
15
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

Genes around RTF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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

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 & Families for RTF1 Gene

Gene Families for RTF1 Gene

Protein Domains for RTF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTF1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92541

UniProtKB/Swiss-Prot:

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

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:0001076 transcription factor activity, RNA polymerase II transcription factor binding IBA --
GO:0003677 DNA binding IEA --
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

Animal Models for RTF1 Gene

MGI Knock Outs for RTF1:
  • Rtf1 tm1a(KOMP)Wtsi

Animal Model Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RTF1

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets 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 2

Gene Ontology (GO) - Cellular Components for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IEA --
GO:0005730 nucleolus IEA --
GO:0016593 Cdc73/Paf1 complex IEA,IDA 20178742
genes like me logo Genes that share ontologies with RTF1: view

Pathways & Interactions for RTF1 Gene

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

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 IEA,ISS --
GO:0001832 blastocyst growth IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
genes like me logo Genes that share ontologies with RTF1: view

No data available for SIGNOR curated interactions for RTF1 Gene

Transcripts for RTF1 Gene

Unigene Clusters for RTF1 Gene

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

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RTF1

Flow Cytometry Products

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 from GTEx, Illumina, BioGPS, and SAGE for RTF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RTF1 Gene

This gene is overexpressed in Lung (32.3) and Peripheral blood mononuclear cells (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RTF1 Gene



Protein tissue co-expression partners for RTF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTF1 Gene:

RTF1

SOURCE GeneReport for Unigene cluster for RTF1 Gene:

Hs.511096
genes like me logo Genes that share expression patterns with RTF1: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RTF1 Gene

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 34 35
  • 99.95 (n)
oppossum
(Monodelphis domestica)
Mammalia RTF1 35
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia RTF1 34 35
  • 94.79 (n)
cow
(Bos Taurus)
Mammalia RTF1 34 35
  • 93.1 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RTF1 35
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Rtf1 34 16 35
  • 91.5 (n)
chicken
(Gallus gallus)
Aves RTF1 34 35
  • 82.08 (n)
lizard
(Anolis carolinensis)
Reptilia RTF1 35
  • 93 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rtf1 34
  • 77.32 (n)
Str.16458 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.16706 34
zebrafish
(Danio rerio)
Actinopterygii rtf1 34 35
  • 73.65 (n)
Dr.15115 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2044 34
fruit fly
(Drosophila melanogaster)
Insecta Rtf1 34 35
  • 50.71 (n)
CG31702 35
  • 27 (a)
OneToMany
CG31703 35
  • 27 (a)
OneToMany
CG12498 35
  • 26 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea F25B3.6 35
  • 33 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTF1 35
  • 24 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1372 35
  • 49 (a)
OneToOne
Species where no ortholog for RTF1 was found in the sources mined by GeneCards:
  • 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
rs10467908 -- 41,429,055(+) tttta(A/T)ttttt intron-variant
rs10593971 -- 41,481,245(+) GGGGG(-/GG)TCTAA intron-variant, utr-variant-3-prime
rs111332358 -- 41,457,296(+) TGGGA(-/G)GCCGA intron-variant
rs111371454 -- 41,468,419(+) TTCAC(A/G)CCATT intron-variant
rs111400206 -- 41,480,502(+) CAGGA(A/G)GCTGC intron-variant

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

Variant ID Type Subtype PubMed ID
dgv2580n100 CNV gain 25217958
esv2674168 CNV deletion 23128226
esv3636243 CNV loss 21293372
esv3636244 CNV loss 21293372
nsv1039283 CNV gain 25217958
nsv1505 CNV insertion 18451855
nsv524476 CNV loss 19592680
nsv569232 CNV loss 21841781

Variation tolerance for RTF1 Gene

Residual Variation Intolerance Score: 18.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.88; 18.37% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTF1 Gene

Human Gene Mutation Database (HGMD)
RTF1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTF1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTF1 Gene

Disorders for RTF1 Gene

Relevant External Links for RTF1

Genetic Association Database (GAD)
RTF1
Human Genome Epidemiology (HuGE) Navigator
RTF1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTF1

No disorders were found for RTF1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RTF1 Gene

Publications for RTF1 Gene

  1. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PMID: 21406692) Rigbolt K.T. … Blagoev B. (Sci. Signal. 2011) 3 4 64
  2. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. (PMID: 20178742) Kim J. … Roeder R.G. (Cell 2010) 3 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. A genome-scale RNAi screen for Oct4 modulators defines a role of the Paf1 complex for embryonic stem cell identity. (PMID: 19345177) Ding L. … Buchholz F. (Cell Stem Cell 2009) 3 4 64
  5. Structure and DNA binding of the human Rtf1 Plus3 domain. (PMID: 18184592) de Jong R.N. … Folkers G.E. (Structure 2008) 3 4 64

Products for RTF1 Gene

Sources for RTF1 Gene

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