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] See more...

Aliases for RTF1 Gene

Aliases for RTF1 Gene

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

External Ids for RTF1 Gene

Previous HGNC Symbols for RTF1 Gene

  • KIAA0252

Previous GeneCards Identifiers for RTF1 Gene

  • GC15P039497
  • GC15P041709
  • GC15P018557
  • GC15P041409
  • GC15P041410
  • GC15P041427

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. Diseases associated with RTF1 include Immunodeficiency 47 and Hereditary Wilms' Tumor. Among its related pathways are Metabolism of proteins and Chromatin Regulation / Acetylation. Gene Ontology (GO) annotations related to this gene include single-stranded DNA binding.

UniProtKB/Swiss-Prot Summary 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 independently 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 CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RTF1 Gene

Genomics for RTF1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RTF1 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTF1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTF1

Top Transcription factor binding sites by QIAGEN in the RTF1 gene promoter:
  • E2F
  • E2F-1
  • GATA-1
  • HOXA9
  • HOXA9B
  • Meis-1
  • NF-1
  • Nkx6-1
  • p53
  • SRY

Genomic Locations for RTF1 Gene

Latest Assembly
chr15:41,408,408-41,483,563
(GRCh38/hg38)
Size:
75,156 bases
Orientation:
Plus strand

Previous Assembly
chr15:41,709,302-41,775,761
(GRCh37/hg19 by Entrez Gene)
Size:
66,460 bases
Orientation:
Plus strand

chr15:41,700,606-41,775,761
(GRCh37/hg19 by Ensembl)
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 (PubMed:20178742). The PAF1 complex interacts with PHF5A (By similarity).
    SequenceCaution:
    • Sequence=AAH15052.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAA13382.2; Type=Erroneous initiation; Note=Truncated N-terminus.; 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

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RTF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RTF1 Gene

GenScript: Design optimal peptide antigens:
  • RNA polymerase-associated protein RTF1 homolog (RTF1_HUMAN)

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.
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 independently 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).

Phenotypes From GWAS Catalog for RTF1 Gene

Gene Ontology (GO) - Molecular Function for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0003697 single-stranded DNA binding IDA 18184592
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 15923622
GO:1990269 RNA polymerase II C-terminal domain phosphoserine binding IBA 21873635
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 Rtf1<tm1a(KOMP)Wtsi>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTF1

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
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTF1 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
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

Pathways by source for RTF1 Gene

Gene Ontology (GO) - Biological Process for RTF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,ISS --
GO:0001711 endodermal cell fate commitment IEA,ISS --
GO:0001832 blastocyst growth IEA --
GO:0006366 transcription by RNA polymerase II TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS --
genes like me logo Genes that share ontologies with RTF1: view

No data available for SIGNOR curated interactions for RTF1 Gene

Drugs & Compounds for RTF1 Gene

No Compound Related Data Available

Transcripts for RTF1 Gene

mRNA/cDNA for RTF1 Gene

1 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
7 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTF1

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

No ASD Table

Relevant External Links for RTF1 Gene

GeneLoc Exon Structure 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, MaxQB, and MOPED for RTF1 Gene



Protein tissue co-expression partners for RTF1 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTF1

SOURCE GeneReport for Unigene cluster for RTF1 Gene:

Hs.511096

Evidence on tissue expression from TISSUES for RTF1 Gene

  • Nervous system(4.7)
  • Blood(2.2)
  • Skin(2.1)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with RTF1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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 30 31
  • 99.95 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia RTF1 31
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia RTF1 30 31
  • 94.79 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RTF1 30 31
  • 93.1 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RTF1 31
  • 93 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Rtf1 30 17 31
  • 91.5 (n)
OneToOne
Chicken
(Gallus gallus)
Aves RTF1 30 31
  • 82.08 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RTF1 31
  • 93 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rtf1 30
  • 77.32 (n)
Str.16458 30
African clawed frog
(Xenopus laevis)
Amphibia Xl.16706 30
Zebrafish
(Danio rerio)
Actinopterygii rtf1 30 31
  • 73.65 (n)
OneToOne
Dr.15115 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2044 30
Fruit Fly
(Drosophila melanogaster)
Insecta Rtf1 30 31
  • 50.71 (n)
OneToMany
CG31703 31
  • 27 (a)
OneToMany
CG31702 31
  • 27 (a)
OneToMany
CG12498 31
  • 26 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea F25B3.6 31
  • 33 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RTF1 31
  • 24 (a)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.1372 31
  • 49 (a)
OneToOne
Species where no ortholog for RTF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (Ciona intestinalis)
  • 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)
Aminode:
Evolutionary constrained regions (ECRs) for RTF1: view image

Paralogs for RTF1 Gene

No data available for Paralogs for RTF1 Gene

Variants for RTF1 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RTF1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for RTF1 Gene

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

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTF1 Gene

Disorders for RTF1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for RTF1 Gene - From: COP

Disorder Aliases PubMed IDs
immunodeficiency 47
  • imd47
hereditary wilms' tumor
  • hereditary wilms tumor
- elite association - COSMIC cancer census association via MalaCards
Search RTF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RTF1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RTF1: view

No data available for 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 KT … Blagoev B (Science signaling 2011) 3 4
  2. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. (PMID: 20178742) Kim J … Roeder RG (Cell 2010) 3 4
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  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
  5. Structure and DNA binding of the human Rtf1 Plus3 domain. (PMID: 18184592) de Jong RN … Folkers GE (Structure (London, England : 1993) 2008) 3 4

Products for RTF1 Gene

Sources for RTF1 Gene