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PAF1 Gene

protein-coding   GIFtS: 51

GC19M044569
Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
F23149_1 1, 2
FLJ11123 1, 2
PD2 1, 2, 3, 5
hPAF1 3
Descriptions
Paf1, RNA polymerase II associated factor, homolog 2
Paf1, RNA polymerase II associated factor, homolog (S.
cerevisiae) 2
Pancreatic differentiation protein 2 3
External Ids
HGNC: 254591
Entrez Gene: 546232
UniProtKB: Q8N7H53
Ensembl: ENSG000000067127
Search outside databases for aliases for PAF1 gene

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for PAF1:
PAF1, parafibromin (CDC73; MIM 607393), LEO1 (MIM 610507), and CTR9 (MIM 609366) form the PAF
protein complex that associates with the RNA polymerase II subunit POLR2A (MIM 180660) and with a
histone methyltransferase complex (Rozenblatt-Rosen et al., 2005 [PubMed 15632063]). The PAF
complex also has a role in histone monoubiquitination (Zhu et al., 2005 [PubMed
16307923]).[supplied by OMIM]

UniProtKB/Swiss-Prot: PAF1_HUMAN, Q8N7H5
Function: The mammalian PAF1 complex is a multifunctional complex. The PAF1 complex interacts with
RNA polymerase II and may be involved in both initiation and elongation, and in histone
methylation and RNA processing. Has oncogenic activity in vivo and in vitro

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the PAF1 gene  

Entrez Gene cytogenetic band: 19q13.1   Ensembl cytogenetic band:  19q13.2   HGNC cytogenetic band: 19q13.1

PAF1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 19         GeneLoc Exon Structure

GeneLoc location for GC19M044569:     (about GC identifiers)

Start:
44,568,109 bp from pter
End:
44,573,586 bp from pter
Size:
5,478 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000019.8  NT_011109.15  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: PAF1_HUMAN, Q8N7H5 (See protein sequence)
Recommended Name: RNA polymerase II-associated factor 1 homolog  
Size: 531 amino acids; 59976 Da
Subunit: Component of the mammalian PAF1 complex, which consists of, at least, CDC73, PAF1, LEO1
and CTR9. Interacts directly with POLR2A/RNA polymerase II and CDC73
Subcellular location: Nucleus. Note=Punctuate distribution throughout the nucleus except in
nucleoli and the perinuclear chromatin
Sequence caution: Sequence=AAC25503.1; Type=Erroneous gene model prediction; Sequence=EAW56880.1;
Type=Erroneous gene model prediction; Sequence=EAW56881.1; Type=Erroneous gene model prediction;
Secondary accessions: O75239 Q9H166 Q9NUU9
Alternative splicing: 2 isoforms:  Q8N7H5-1   Q8N7H5-2   

Post-translational modifications:

  • View phosphorylation sites using PhosphoSite2


  • REFSEQ proteins: NP_061961.2  

    ENSEMBL proteins: 
    ENSP00000221265 ENSP00000221266 


    Human Recombinant Proteins 
    Browse Drug Discovery Central at Invitrogen for human recombinant proteins
    Browse Purified and Recombinant Proteins at Millipore
    Browse Human Recombinant Proteins at Sigma-Aldrich  
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    Recombinant Proteins from Abcam (PAF1)
    Browse Abnova for Human Recombinant Proteins
                    Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

    1 Gene Ontology (GO) cellular component term (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634 nucleus IEA--
    About this table

    Antibodies for PAF1: 
    Browse Antibodies Central at Invitrogen
    Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
    Browse Antibodies at Sigma-Aldrich
    Browse R&D Systems for Antibodies
    Antibodies from Abcam (PAF1), each with their AbpromiseSM
    Monoclonal and Polyclonal Antibodies from Abnova (PAF1)
    Novus Biologicals Antibodies for PAF1

    Assays for PAF1: 
    Browse Invitrogen for biochemical assays
    Browse Kits and Assays available from Millipore
    Browse R&D Systems for biochemical assays
    Browse biochemical assays available from Enzo Life Sciences

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    1 InterPro domain/family:
     IPR007133 RNA_pol_II-assoc_Paf1


       GeneDecks  PAF1 for the domains selected above  
    About GeneDecksing

    Graphical View of Domain Structure for InterPro Entry Q8N7H5

    ProtoNet protein and cluster: Q8N7H5

    UniProtKB/Swiss-Prot: PAF1_HUMAN, Q8N7H5
    Similarity: Belongs to the PAF1 family

    (According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
    shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
    RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (PAF1)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_019088

                  Applied Biosystems Silencer® siRNAs for PAF1

                  Sigma-Aldrich siRNA for PAF1  
                         Sigma-Aldrich shRNA for PAF1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Clones:Invitrogen Clones for PAF1
    Browse Clones for the Expression of Recombinant Proteins Available from Millipore
                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_019088
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_019088
                                     untagged cDNA clone in CMV expression vector: NM_019088 

    Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
                  OriGene genome-wide validated SYBR primer pairs: NM_019088

    UniProtKB/Swiss-Prot: PAF1_HUMAN, Q8N7H5
    Function: The mammalian PAF1 complex is a multifunctional complex. The PAF1 complex interacts with
    RNA polymerase II and may be involved in both initiation and elongation, and in histone
    methylation and RNA processing. Has oncogenic activity in vivo and in vitro

    (Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
    Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
    About This Section


     Gene Network CentralTM Interacting Genes and Proteins Network for  PAF1 


    5/25 Interacting proteins for PAF1 (ENSP000002212653) via UniProtKB, MINT, and/or STRING (see all 25 )
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CDC73ENSP000003564053STRING (score=.987)
    RTF1ENSP000002603733STRING (score=.953)
    POLR2AENSP000003149493STRING (score=.85)
    TBX21ENSP000001776943STRING (score=.842)
    GATA3ENSP000003686323STRING (score=.839)
    About this table

    2 Gene Ontology (GO) biological process terms (links to tree view):

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006350 transcription IEA--
    GO:0006355 regulation of transcription, DNA-dependent IEA--
    About this table
    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
    About This Section

    Browse drugs & compounds from Enzo Life Sciences
    Browse Small Molecules at Sigma-Aldrich

    Browse Tocris compounds for PAF1

    (GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView,
    non coding RNAs according to RNAdb,
    ESTs according to GeneTide,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from Invitrogen, Millipore, and/or Abnova,
    siRNAs from Applied Biosystems, Sigma-Aldrich,
    shRNA from Sigma-Aldrich, OriGene,
    Tagged/untagged cDNA clones from OriGene,
    Expression Assays from Applied Biosystems)
    About This Section

    Inhib.
    RNA:
    Invitrogen RNAi Products for gene knock-down (PAF1)
    Browse for Gene Knock-down Tools from Millipore
    Browse Abnova for Chimera RNAi Products
                  OriGene 29mer shRNA kit in GFP-retroviral vector: NM_019088

                  Sigma-Aldrich siRNA for PAF1  
                         Sigma-Aldrich shRNA for PAF1  
                         Explore Sigma-Aldrich super-pooled esiRNAs  

    Applied Biosystems Silencer® siRNAs: 

    NM_019088  

    REFSEQ mRNAs for PAF1 gene: 

    NM_019088.2   

    Applied Biosystems TaqMan ® Gene Expression Assays: 

    NM_019088  

                  OriGene GFP tagged cDNA clone in CMV expression vector: NM_019088
                                     Myc/DDK tagged cDNA clone in CMV expression vector: NM_019088
                                     untagged cDNA clone in CMV expression vector: NM_019088 

    Additional cDNA sequence: 

    AF086555.1 AJ401156.1 AK001985.1 AK098423.1 AK294625.1 BC000017.2 BC013402.1 CR599585.1 
    CR604612.1 CR604698.1 CR616137.1 

    15 DOTS entries:

    DT.95178706  DT.455978  DT.121415717  DT.100797446  DT.100797444  DT.100797450  DT.100797438  DT.121415693 
    DT.92369367  DT.121415632  DT.92380018  DT.92453697  DT.99943256  DT.100797448  DT.91920931 

    24/381 AceView cDNA sequences (see all 381 ):

    CB152089 AJ401156 CF131270 BQ687402 CA425897 CB153315 BQ899118 CD366275 
    BU078045 AA479050 BM829176 BX377783 CR616137 BE906392 BQ690679 BQ689832 
    BU859511 BE122816 BQ669339 BQ717923 BQ228096 AL710971 CB241112 BQ049720 

    highest scoring ESTs for PAF1:

    AI879164 AI929472 AJ401156 AK001985 AK098423 AL516414 AL543738 AL546687 AL551152 AL599054 

    Unigene Cluster for PAF1:

    Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)
    Hs.466714  [show with all ESTs]
    Unigene Representative Sequence: NM_019088


    GeneLoc Exon Structure

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

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

    About this scheme

    ECgene alternative splicing isoforms for PAF1

    2 Ensembl transcripts including schematic representations:
    ENST00000221265  ENST00000221266  
    (Experimental results according to 1GeneNote and GNF BioGPS,
    probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
    Expression Assays from Applied Biosystems )
    About This Section

    PAF1 expression in normal and diseased human tissues

     Applied Biosystems TaqMan ® Gene Expression Assays for PAF1

    1 / 2 / 3

    3 probe-sets matching PAF1 gene


    Affymetrix
    probe-set
    Array  GeneAnnot data GeneNote data GeneTide data
    # genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

    31866_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 AC005239 0.20 1.00 0.72 1

    202093_s_at2, 3 U133-A 2 1.00 0.95 -- -- NM_019088 0.60 1.00 0.82 1

    202093_s_at2 U133Plus2 2 1.00 0.95 -- -- -- -- -- -- --
    About this table
    Data from (Publications) and GNF BioGPS
        About these images
    About these images

    CGAP SAGE TAG: AATGAGAAGG

    SOURCE GeneReport for Unigene cluster: Hs.466714
    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
    About This Section


    Orthologs for PAF1 gene from 5/13 species (see all 13 )
    Organism Gene Locus Description Human
    Similarity
    NCBI accessions
    dog
    (Canis familiaris)
    PAF11   -- Paf1, RNA polymerase II associated factor, homolog more 91.92(n)
    99.24(a)
    476464  XM_533675.2  XP_533675.2 
    cow
    (Bos taurus)
    PAF11   -- Paf1, RNA polymerase II associated factor, homolog more 91.7(n)
    98.87(a)
    528744  NM_001046293.1  NP_001039758.1 
    rat
    (Rattus norvegicus)
    Paf11   -- Paf1, RNA polymerase II associated factor, homolog more 90.33(n)
    98.49(a)
    361531  NM_001024898.1  NP_001020069.1 
    mouse
    (Mus musculus)
    Paf11, 5 75
    Paf1, RNA polymerase II associated factor, homolog more1, 5 90.27(n)1
    98.87(a)1
    546241  NM_019458.31  NP_062331.21 
     AA6750455  AB0416155  (see all 16)
    zebrafish
    (Danio rerio)
    paf1l1   -- paf1, RNA polymerase II associated factor, homolog more 75.15(n)
    79.56(a)
    553020  NM_001024453.1  NP_001019624.1 
    About this table        Species with no ortholog for PAF1

    ENSEMBL Gene Tree for PAF1
    (Paralogs according to 1HomoloGene
    and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
    About This Section

      --
    (According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
    About This Section


    10/14 NCBI SNPs in PAF1 are shown (see all 14 )
    (Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 32)
    ABGenomic DataTranscription DataAllele Frequencies
    SNP IDValidChr 19 posSequenceRecsAA
    Chg
    TypeMoreRecsAllele
    freq
    PopTotal
    sample
    More
    ------------
    rs129726521,2
    H44569027(+) CGTGGT/GTTTCT 1 T/N mis1 ese34Minor allele frequency- G:0.00EU EA WA 406
    rs404411,2
    A,C,F,H,O44569846(-) TGACAC/TATAca 1 -- int18Minor allele frequency- N:0.00EU EA WA NA 632
    rs403531,2
    A,C,F,H,O44571503(-) TTTGTT/CCCACC 1 -- int117Minor allele frequency- C:0.24EA NA MN EU WA 1386
    rs20671021,2
    C,F,H44570984(+) TCTTCC/TCTATC 1 -- int1 trp35Minor allele frequency- T:0.09EA EU WA 1906
    --
    rs677830531,2
    --44568169(+) CAAAC-/AAAAAA 1 -- ut310--------
    rs355051621,2
    --44569246(+) TGAACC/TCCAGC 1 G/G syn11Minor allele frequency- T:0.01NA 78
    rs340050921,2
    --44568747(+) TCCTCG/ACTGCT 1 S/S syn11Minor allele frequency- A:0.01NA 68
    --
    rs562223211,2
    --44568819(+) CTCTCA/GCTGCC 1 S/S syn10--------
    --
    rs578504301,2
    --44569576(+) AGATAC/TACATC 1 -- int10--------
    --
    rs356571591,2
    --44570177(+) AACAT-/GGGGTT 1 -- int10--------
    About this table

    HapMap Linkage Disequilibrium images for PAF1 (up to first 250kb)

    (in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
    About This Section

    OMIM: 610506

    (Possibly Related Articles in Doctor's Guide)
    About This Section

      --

    (in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
    About This Section

    10/11 PubMed articles for PAF1 gene (see all 11 ):
    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section

     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)
    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
    About This Section

    Entrez Gene: 54623 HGNC: 25459 AceView: PD2 Ensembl:ENSG00000006712 euGenes: HUgn54623
    ECgene: PAF1 H-InvDB: PAF1
    (According to HUGE)
    About This Section

      --
    (According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section

    NameDescription
    ATLAS Chromosomes in Cancer entry for PAF1 Genetics and Cytogenetics in Oncology and Haematology
    (Available from WIS Yeda, Salk, Tufts)
    About This Section

      --
    (Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
    Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
    Enzo Life Sciences, and/or Tocris Bioscience)
    About This Section



    Products for PAF1:
     TaqMan ® Gene Expression Assays
     TaqMan ® Genotyping Assays
      Free SNP selection tool



      Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
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     Predesigned and custom siRNAs for PAF1 Browse antibodies at Sigma-Aldrich
     Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
     Lentivirus-delivered shRNAs for PAF1 Browse small molecules at Sigma-Aldrich
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     Antibodies for PAF1

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