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Protein

RNA polymerase II-associated factor 1 homolog

Gene

PAF1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.7 Publications

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • RNA polymerase II core binding Source: UniProtKB

GO - Biological processi

  • cellular response to lipopolysaccharide Source: UniProtKB
  • endodermal cell fate commitment Source: UniProtKB
  • histone H2B ubiquitination Source: UniProtKB
  • histone monoubiquitination Source: UniProtKB
  • mRNA polyadenylation Source: UniProtKB
  • negative regulation of myeloid cell differentiation Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • nucleosome positioning Source: CACAO
  • positive regulation of histone methylation Source: CACAO
  • positive regulation of mRNA 3'-end processing Source: UniProtKB
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: UniProtKB
  • positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  • protein localization to nucleus Source: CACAO
  • stem cell population maintenance Source: Ensembl
  • transcription elongation from RNA polymerase II promoter Source: InterPro
  • Wnt signaling pathway Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Transcription, Transcription regulation, Wnt signaling pathway

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II-associated factor 1 homolog
Short name:
hPAF1
Alternative name(s):
Pancreatic differentiation protein 2
Gene namesi
Name:PAF1
Synonyms:PD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 19

Organism-specific databases

HGNCiHGNC:25459. PAF1.

Subcellular locationi

GO - Cellular componenti

  • Cdc73/Paf1 complex Source: UniProtKB
  • cell junction Source: HPA
  • cytoplasm Source: CACAO
  • membrane Source: CACAO
  • nucleoplasm Source: HPA
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Keywords - Diseasei

Tumor suppressor

Organism-specific databases

MalaCardsiPAF1.
PharmGKBiPA142671206.

Polymorphism and mutation databases

BioMutaiPAF1.
DMDMi182670295.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 531531RNA polymerase II-associated factor 1 homologPRO_0000326400Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei117 – 1171PhosphoserineCombined sources
Modified residuei456 – 4561PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8N7H5.
MaxQBiQ8N7H5.
PaxDbiQ8N7H5.
PeptideAtlasiQ8N7H5.
PRIDEiQ8N7H5.

PTM databases

iPTMnetiQ8N7H5.
PhosphoSiteiQ8N7H5.

Expressioni

Gene expression databases

BgeeiENSG00000006712.
CleanExiHS_PAF1.
ExpressionAtlasiQ8N7H5. baseline and differential.
GenevisibleiQ8N7H5. HS.

Organism-specific databases

HPAiHPA041875.
HPA043637.

Interactioni

Subunit structurei

Component of the PAF1 complex, which consists of CDC73, PAF1, LEO1, CTR9, RTF1 and WDR61. Interacts with POLR2A, TCEA1, TTC37, KMT2A/MLL1, SUPT5H, RNF20 and RNF40. Interacts with UBE2E1. Interacts with influenza A strain H3N2 NS1 protein; the interaction interferes with host cell gene transcription, specifically with that of antiviral genes.9 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q6P1J926EBI-2607770,EBI-930143
CTR9Q6PD6223EBI-2607770,EBI-1019583
FXR2P511164EBI-2607770,EBI-740459
HSPB1P047922EBI-2607770,EBI-352682
KMT2AQ031644EBI-2607770,EBI-591370
LEO1Q8WVC021EBI-2607770,EBI-932432
NS1B2BUF16EBI-2607770,EBI-4291940From a different organism.
POLR2AP249285EBI-2607770,EBI-295301
RTF1Q9254116EBI-2607770,EBI-1055239
TCEA1P231934EBI-2607770,EBI-2608271
TTC37Q6PGP72EBI-2607770,EBI-6083436
UBE2E1P519652EBI-2607770,EBI-348546

GO - Molecular functioni

  • RNA polymerase II core binding Source: UniProtKB

Protein-protein interaction databases

BioGridi120081. 62 interactions.
DIPiDIP-48673N.
IntActiQ8N7H5. 26 interactions.
STRINGi9606.ENSP00000221265.

Structurei

Secondary structure

1
531
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi172 – 18716Combined sources
Beta strandi201 – 2066Combined sources
Beta strandi211 – 2155Combined sources
Beta strandi231 – 2344Combined sources
Beta strandi238 – 2414Combined sources
Helixi246 – 2494Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4M6TX-ray2.50A170-250[»]
ProteinModelPortaliQ8N7H5.
SMRiQ8N7H5. Positions 170-257.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili352 – 40049Sequence analysisAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi358 – 45295Glu-richAdd
BLAST

Sequence similaritiesi

Belongs to the PAF1 family.Curated

Keywords - Domaini

Coiled coil

Phylogenomic databases

eggNOGiKOG2478. Eukaryota.
ENOG410YZXE. LUCA.
GeneTreeiENSGT00390000001474.
HOGENOMiHOG000115425.
HOVERGENiHBG053131.
InParanoidiQ8N7H5.
KOiK15174.
OMAiADKRPQR.
OrthoDBiEOG091G0C3Y.
PhylomeDBiQ8N7H5.
TreeFamiTF313642.

Family and domain databases

InterProiIPR007133. RNA_pol_II-assoc_Paf1.
[Graphical view]
PfamiPF03985. Paf1. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8N7H5-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAPTIQTQAQ REDGHRPNSH RTLPERSGVV CRVKYCNSLP DIPFDPKFIT
60 70 80 90 100
YPFDQNRFVQ YKATSLEKQH KHDLLTEPDL GVTIDLINPD TYRIDPNVLL
110 120 130 140 150
DPADEKLLEE EIQAPTSSKR SQQHAKVVPW MRKTEYISTE FNRYGISNEK
160 170 180 190 200
PEVKIGVSVK QQFTEEEIYK DRDSQITAIE KTFEDAQKSI SQHYSKPRVT
210 220 230 240 250
PVEVMPVFPD FKMWINPCAQ VIFDSDPAPK DTSGAAALEM MSQAMIRGMM
260 270 280 290 300
DEEGNQFVAY FLPVEETLKK RKRDQEEEMD YAPDDVYDYK IAREYNWNVK
310 320 330 340 350
NKASKGYEEN YFFIFREGDG VYYNELETRV RLSKRRAKAG VQSGTNALLV
360 370 380 390 400
VKHRDMNEKE LEAQEARKAQ LENHEPEEEE EEEMETEEKE AGGSDEEQEK
410 420 430 440 450
GSSSEKEGSE DEHSGSESER EEGDRDEASD KSGSGEDESS EDEARAARDK
460 470 480 490 500
EEIFGSDADS EDDADSDDED RGQAQGGSDN DSDSGSNGGG QRSRSHSRSA
510 520 530
SPFPSGSEHS AQEDGSEAAA SDSSEADSDS D
Length:531
Mass (Da):59,976
Last modified:April 8, 2008 - v2
Checksum:i756F800AA64255D6
GO
Isoform 2 (identifier: Q8N7H5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     17-26: Missing.
     190-212: Missing.
     395-508: DEEQEKGSSS...SASPFPSGSE → VMLILRTMPT...QQSTFLVVCL

Note: No experimental confirmation available.
Show »
Length:485
Mass (Da):55,039
Checksum:i619FCF62CF34627D
GO
Isoform 3 (identifier: Q8N7H5-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     17-26: Missing.
     395-495: DEEQEKGSSS...SNGGGQRSRS → VMLILRTMPT...QQSTFLVVCL
     496-531: Missing.

Show »
Length:485
Mass (Da):55,473
Checksum:iE92BFB28CB9D655E
GO

Sequence cautioni

The sequence AAC25503 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence EAW56880 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence EAW56881 differs from that shown. Reason: Erroneous gene model prediction. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti58 – 581F → I in BAA92020 (PubMed:15057824).Curated
Sequence conflicti68 – 681K → R in BAC05305 (PubMed:15057824).Curated
Sequence conflicti152 – 1521E → G in BAA92020 (PubMed:15057824).Curated
Sequence conflicti378 – 3781E → G in BAA92020 (PubMed:15057824).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei17 – 2610Missing in isoform 2 and isoform 3. 1 PublicationVSP_032650
Alternative sequencei190 – 21223Missing in isoform 2. CuratedVSP_032651Add
BLAST
Alternative sequencei395 – 508114DEEQE…PSGSE → VMLILRTMPTLMMRTEDRPK VAVTMIQTAAAMGVASGAGA TAAAPVPSPVAASTRPRRMA VKLQLLIPVKLIVTVTESQG IQGWFRHHYCEQQSTFLVVC L in isoform 2. CuratedVSP_032652Add
BLAST
Alternative sequencei395 – 495101DEEQE…QRSRS → VMLILRTMPTLMMRTEDRPK VAVTMIQTAAAMGVASGAGA TAAAPVPSPVAASTRPRRMA VKLQLLIPVKLIVTVTESQG IQGWFRHHYCEQQSTFLVVC L in isoform 3. 1 PublicationVSP_055740Add
BLAST
Alternative sequencei496 – 53136Missing in isoform 3. 1 PublicationVSP_055741Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ401156 mRNA. Translation: CAC20564.1.
AK001985 mRNA. Translation: BAA92020.1.
AK098423 mRNA. Translation: BAC05305.1.
AC005239 Genomic DNA. Translation: AAC25503.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56880.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56881.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56883.1.
BC000017 mRNA. Translation: AAH00017.1.
BC013402 mRNA. Translation: AAH13402.1.
CCDSiCCDS12533.1. [Q8N7H5-1]
CCDS59387.1. [Q8N7H5-3]
RefSeqiNP_001243755.1. NM_001256826.1. [Q8N7H5-3]
NP_061961.2. NM_019088.3. [Q8N7H5-1]
UniGeneiHs.466714.

Genome annotation databases

EnsembliENST00000221265; ENSP00000221265; ENSG00000006712. [Q8N7H5-1]
ENST00000595564; ENSP00000468874; ENSG00000006712. [Q8N7H5-3]
GeneIDi54623.
KEGGihsa:54623.
UCSCiuc002old.5. human. [Q8N7H5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Web resourcesi

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ401156 mRNA. Translation: CAC20564.1.
AK001985 mRNA. Translation: BAA92020.1.
AK098423 mRNA. Translation: BAC05305.1.
AC005239 Genomic DNA. Translation: AAC25503.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56880.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56881.1. Sequence problems.
CH471126 Genomic DNA. Translation: EAW56883.1.
BC000017 mRNA. Translation: AAH00017.1.
BC013402 mRNA. Translation: AAH13402.1.
CCDSiCCDS12533.1. [Q8N7H5-1]
CCDS59387.1. [Q8N7H5-3]
RefSeqiNP_001243755.1. NM_001256826.1. [Q8N7H5-3]
NP_061961.2. NM_019088.3. [Q8N7H5-1]
UniGeneiHs.466714.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4M6TX-ray2.50A170-250[»]
ProteinModelPortaliQ8N7H5.
SMRiQ8N7H5. Positions 170-257.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120081. 62 interactions.
DIPiDIP-48673N.
IntActiQ8N7H5. 26 interactions.
STRINGi9606.ENSP00000221265.

PTM databases

iPTMnetiQ8N7H5.
PhosphoSiteiQ8N7H5.

Polymorphism and mutation databases

BioMutaiPAF1.
DMDMi182670295.

Proteomic databases

EPDiQ8N7H5.
MaxQBiQ8N7H5.
PaxDbiQ8N7H5.
PeptideAtlasiQ8N7H5.
PRIDEiQ8N7H5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000221265; ENSP00000221265; ENSG00000006712. [Q8N7H5-1]
ENST00000595564; ENSP00000468874; ENSG00000006712. [Q8N7H5-3]
GeneIDi54623.
KEGGihsa:54623.
UCSCiuc002old.5. human. [Q8N7H5-1]

Organism-specific databases

CTDi54623.
GeneCardsiPAF1.
HGNCiHGNC:25459. PAF1.
HPAiHPA041875.
HPA043637.
MalaCardsiPAF1.
MIMi610506. gene.
neXtProtiNX_Q8N7H5.
PharmGKBiPA142671206.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2478. Eukaryota.
ENOG410YZXE. LUCA.
GeneTreeiENSGT00390000001474.
HOGENOMiHOG000115425.
HOVERGENiHBG053131.
InParanoidiQ8N7H5.
KOiK15174.
OMAiADKRPQR.
OrthoDBiEOG091G0C3Y.
PhylomeDBiQ8N7H5.
TreeFamiTF313642.

Miscellaneous databases

ChiTaRSiPAF1. human.
GenomeRNAii54623.
PROiQ8N7H5.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000006712.
CleanExiHS_PAF1.
ExpressionAtlasiQ8N7H5. baseline and differential.
GenevisibleiQ8N7H5. HS.

Family and domain databases

InterProiIPR007133. RNA_pol_II-assoc_Paf1.
[Graphical view]
PfamiPF03985. Paf1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPAF1_HUMAN
AccessioniPrimary (citable) accession number: Q8N7H5
Secondary accession number(s): M0QX35
, O75239, Q9H166, Q9NUU9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 8, 2008
Last sequence update: April 8, 2008
Last modified: September 7, 2016
This is version 104 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.