This gene encodes a subunit of the polymerase associated factor (PAF1) complex. The PAF1 complex interacts with RNA polymerase II and plays a role in transcription elongation as well as histone modifications including ubiquitylation and methylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 20... See more...

Aliases for PAF1 Gene

Aliases for PAF1 Gene

  • PAF1 Homolog, Paf1/RNA Polymerase II Complex Component 2 3 5
  • RNA Polymerase II-Associated Factor 1 Homolog 3 4
  • Pancreatic Differentiation Protein 2 3 4
  • PD2 3 4
  • Paf1, RNA Polymerase II Associated Factor, Homolog (S. Cerevisiae) 2
  • Paf1, RNA Polymerase II Associated Factor, Homolog 3
  • F23149_1 3
  • HPAF1 4

External Ids for PAF1 Gene

Previous GeneCards Identifiers for PAF1 Gene

  • GC19M044569
  • GC19M039876
  • GC19M036322

Summaries for PAF1 Gene

Entrez Gene Summary for PAF1 Gene

  • This gene encodes a subunit of the polymerase associated factor (PAF1) complex. The PAF1 complex interacts with RNA polymerase II and plays a role in transcription elongation as well as histone modifications including ubiquitylation and methylation. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

GeneCards Summary for PAF1 Gene

PAF1 (PAF1 Homolog, Paf1/RNA Polymerase II Complex Component) is a Protein Coding gene. Diseases associated with PAF1 include Vulvitis. Among its related pathways are Protein ubiquitination and Tat-mediated elongation of the HIV-1 transcript. Gene Ontology (GO) annotations related to this gene include chromatin binding and RNA polymerase II complex binding.

UniProtKB/Swiss-Prot Summary for PAF1 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. Connects PAF1C with the RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors. Has oncogenic activity in vivo and in vitro.

Additional gene information for PAF1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PAF1 Gene

Genomics for PAF1 Gene

GeneHancer (GH) Regulatory Elements for PAF1 Gene

Promoters and enhancers for PAF1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH19J039397 Promoter/Enhancer 3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 754.7 -15.9 -15880 20 PPP1R10 E2F8 GTF3C2 ZNF785 SIN3A ZNF24 SP1 ZBTB40 CTCF SREBF1 ZFP36 PAF1 5EW4_A-031 MG828566 HNRNPL FBL ENSG00000269688 SUPT5H RPS16 PLEKHG2
GH19J039389 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 750.6 +0.3 343 3.5 PPP1R10 ZNF785 SIN3A SP1 ZBTB40 CTCF SREBF1 SIX5 ZBTB6 RBPJ MED29 PAF1 lnc-RPS16-2 lnc-RPS16-5 HNRNPL PSMC4 FBL SUPT5H RPS16 EID2B
GH19J039393 Promoter/Enhancer 0.7 Ensembl dbSUPER 750.6 -1.9 -1905 0.2 ZNF362 ZNF121 MED29 PAF1 lnc-RPS16-2 RPS16 SUPT5H EID2B PAK4 lnc-PAF1-3
GH19J039479 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 39 -89.7 -89692 3 SIN3A ZNF24 SP1 SREBF1 SIX5 ZBTB6 MLX RBPJ SMARCE1 POLR2A TIMM50 HSALNG0126016 piR-49423-125 HNRNPL PAF1 RPS16 FBL PLEKHG2 SUPT5H EID2B
GH19J039427 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 31.6 -41.2 -41221 10 ZNF785 SIN3A SP1 ZBTB40 ZBTB6 FOXA1 MLX SMARCE1 RBPJ POLR2A RPS16 HNRNPL SUPT5H ZNF780B AKT2 PAF1 PLEKHG2 FBL EID2B ZNF780A
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PAF1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PAF1 gene promoter:
  • AP-1
  • ATF-2
  • c-Fos
  • c-Jun
  • p300
  • Pbx1a
  • Sp1

Genomic Locations for PAF1 Gene

Genomic Locations for PAF1 Gene
chr19:39,385,629-39,391,195
(GRCh38/hg38)
Size:
5,567 bases
Orientation:
Minus strand
chr19:39,876,269-39,881,835
(GRCh37/hg19)
Size:
5,567 bases
Orientation:
Minus strand

Genomic View for PAF1 Gene

Genes around PAF1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PAF1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PAF1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PAF1 Gene

Proteins for PAF1 Gene

  • Protein details for PAF1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8N7H5-PAF1_HUMAN
    Recommended name:
    RNA polymerase II-associated factor 1 homolog
    Protein Accession:
    Q8N7H5
    Secondary Accessions:
    • M0QX35
    • O75239
    • Q9H166
    • Q9NUU9

    Protein attributes for PAF1 Gene

    Size:
    531 amino acids
    Molecular mass:
    59976 Da
    Quaternary structure:
    • Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61 (PubMed:19952111, PubMed:20178742). The PAF1 complex interacts with PHF5A (By similarity). Interacts with POLR2A, TCEA1, TTC37, KMT2A/MLL1, SUPT5H, RNF20 and RNF40 (PubMed:15923622, PubMed:16024656, PubMed:19952111, PubMed:20178742, PubMed:20541477, PubMed:16491129, PubMed:19410543). Interacts with UBE2E1 (PubMed:16307923). Interacts with influenza A strain H3N2 NS1 protein; the interaction interferes with host cell gene transcription, specifically with that of antiviral genes (PubMed:22419161).
    SequenceCaution:
    • Sequence=AAC25503.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAW56880.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=EAW56881.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PAF1 Gene

    Alternative splice isoforms for PAF1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PAF1 Gene

Post-translational modifications for PAF1 Gene

  • Ubiquitination at Lys290 and Lys305
  • Modification sites at PhosphoSitePlus

Other Protein References for PAF1 Gene

No data available for DME Specific Peptides for PAF1 Gene

Domains & Families for PAF1 Gene

Gene Families for PAF1 Gene

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

Protein Domains for PAF1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PAF1 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ52855, highly similar to Rattus norvegicus Paf1, RNA polymerase II associated factor, mRNA (B4DGJ5_HUMAN)
  • Pancreatic differentiation protein 2 (PAF1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8N7H5

UniProtKB/Swiss-Prot:

PAF1_HUMAN :
  • Belongs to the PAF1 family.
Family:
  • Belongs to the PAF1 family.
genes like me logo Genes that share domains with PAF1: view

Function for PAF1 Gene

Molecular function for PAF1 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. Connects PAF1C with the RNF20/40 E3 ubiquitin-protein ligase complex. Involved in polyadenylation of mRNA precursors. Has oncogenic activity in vivo and in vitro.

Phenotypes From GWAS Catalog for PAF1 Gene

Gene Ontology (GO) - Molecular Function for PAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000993 RNA polymerase II complex binding IDA,IBA 15923622
GO:0003682 chromatin binding IBA 21873635
GO:0005515 protein binding IPI 15923622
genes like me logo Genes that share ontologies with PAF1: view
genes like me logo Genes that share phenotypes with PAF1: view

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids for PAF1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PAF1 Gene

Localization for PAF1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PAF1 Gene

Nucleus. Note=Punctuate distribution throughout the nucleus except in nucleoli and the perinuclear chromatin.

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 PAF1 gene
Compartment Confidence
nucleus 5
mitochondrion 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IDA 22046413
GO:0016020 membrane IDA 22046413
GO:0016593 Cdc73/Paf1 complex IEA,IDA 16307923
genes like me logo Genes that share ontologies with PAF1: view

Pathways & Interactions for PAF1 Gene

genes like me logo Genes that share pathways with PAF1: view

Pathways by source for PAF1 Gene

Gene Ontology (GO) - Biological Process for PAF1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II ISS --
GO:0001711 endodermal cell fate commitment ISS --
GO:0006366 transcription by RNA polymerase II TAS --
GO:0006368 transcription elongation from RNA polymerase II promoter TAS,IEA --
GO:0006378 mRNA polyadenylation IMP 21329879
genes like me logo Genes that share ontologies with PAF1: view

No data available for SIGNOR curated interactions for PAF1 Gene

Drugs & Compounds for PAF1 Gene

No Compound Related Data Available

Transcripts for PAF1 Gene

mRNA/cDNA for PAF1 Gene

CRISPR Products

Clone Products

  • Addgene plasmids for PAF1

Alternative Splicing Database (ASD) splice patterns (SP) for PAF1 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: - - -
SP2: - -
SP3: - - -
SP4: -
SP5:

Relevant External Links for PAF1 Gene

GeneLoc Exon Structure for
PAF1
ECgene alternative splicing isoforms for
PAF1

Expression for PAF1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PAF1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PAF1 Gene

This gene is overexpressed in Lung (27.4), CD8 Tcells (7.1), and Peripheral blood mononuclear cells (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PAF1 Gene



Protein tissue co-expression partners for PAF1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PAF1 Gene:

PAF1

SOURCE GeneReport for Unigene cluster for PAF1 Gene:

Hs.466714

Evidence on tissue expression from TISSUES for PAF1 Gene

  • Pancreas(4.7)
  • Muscle(4.5)
  • Nervous system(4.3)
  • Kidney(2.5)
  • Heart(2.3)
  • Liver(2.1)
  • Blood(2)
genes like me logo Genes that share expression patterns with PAF1: view

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 PAF1 Gene

Orthologs for PAF1 Gene

This gene was present in the common ancestor of animals.

Orthologs for PAF1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PAF1 33
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Paf1 17 33 32
  • 90.29 (n)
rat
(Rattus norvegicus)
Mammalia Paf1 32
  • 90.1 (n)
dog
(Canis familiaris)
Mammalia PAF1 33 32
  • 89.71 (n)
OneToOne
cow
(Bos Taurus)
Mammalia PAF1 33 32
  • 89.39 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia -- 33
  • 88 (a)
OneToMany
-- 33
  • 86 (a)
OneToMany
platypus
(Ornithorhynchus anatinus)
Mammalia PAF1 33
  • 67 (a)
OneToOne
chicken
(Gallus gallus)
Aves PAF1 33 32
  • 80.65 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PAF1 33
  • 72 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia paf1 32
  • 75.5 (n)
MGC76249 32
African clawed frog
(Xenopus laevis)
Amphibia Xl.29705 32
zebrafish
(Danio rerio)
Actinopterygii paf1 33 32
  • 77.33 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001302 32
  • 63.21 (n)
fruit fly
(Drosophila melanogaster)
Insecta atms 33 32
  • 62.58 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea CELE_C55A6.9 32
  • 47.97 (n)
C55A6.9 33
  • 34 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 57 (a)
OneToOne
Cin.283 32
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.283 32
Species where no ortholog for PAF1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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 PAF1 Gene

ENSEMBL:
Gene Tree for PAF1 (if available)
TreeFam:
Gene Tree for PAF1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PAF1: view image

Paralogs for PAF1 Gene

No data available for Paralogs for PAF1 Gene

Variants for PAF1 Gene

Sequence variations from dbSNP and Humsavar for PAF1 Gene

SNP ID Clin Chr 19 pos Variation AA Info Type
rs1396158186 uncertain-significance, not provided 39,390,837(-) G/A coding_sequence_variant, non_coding_transcript_variant, stop_gained
rs1000004715 -- 39,387,518(-) C/T intron_variant
rs1000536828 -- 39,387,972(-) TAT/T intron_variant
rs1001215456 -- 39,392,816(-) A/G upstream_transcript_variant
rs1001838590 -- 39,391,398(-) A/C/G upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PAF1 Gene

Variant ID Type Subtype PubMed ID
esv25791 CNV gain 19812545

Variation tolerance for PAF1 Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.30; 25.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PAF1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PAF1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PAF1 Gene

Disorders for PAF1 Gene

MalaCards: The human disease database

(1) MalaCards diseases for PAF1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
vulvitis
- elite association - COSMIC cancer census association via MalaCards
Search PAF1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PAF1

genes like me logo Genes that share disorders with PAF1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PAF1 Gene

Publications for PAF1 Gene

  1. The human homologue of the RNA polymerase II-associated factor 1 (hPaf1), localized on the 19q13 amplicon, is associated with tumorigenesis. (PMID: 16491129) Moniaux N … Batra SK (Oncogene 2006) 3 4 23 56
  2. Structural insights into Paf1 complex assembly and histone binding. (PMID: 24038468) Chu X … Long J (Nucleic acids research 2013) 2 3 56
  3. Suppression of the antiviral response by an influenza histone mimic. (PMID: 22419161) Marazzi I … Tarakhovsky A (Nature 2012) 3 4 56
  4. Transcriptional activators enhance polyadenylation of mRNA precursors. (PMID: 21329879) Nagaike T … Manley JL (Molecular cell 2011) 3 4 56
  5. The PAF complex synergizes with MLL fusion proteins at HOX loci to promote leukemogenesis. (PMID: 20541477) Muntean AG … Hess JL (Cancer cell 2010) 3 4 56

Products for PAF1 Gene

Sources for PAF1 Gene