Nuclear RNA-directed RNA polymerase complex Gene Set

Dataset COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025
Category structural or functional annotations
Type cellular component
Description A complex required for RNAi mediated heterochromatin assembly. In S. pombe this contains RNA-directed RNA polymerase, a putative helicase and a protein containing a pap25 associated domain. (Gene Ontology, GO_0031380)
External Link http://amigo.geneontology.org/amigo/term/GO:0031380
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Genes

359 proteins co-occuring with the Nuclear RNA-directed RNA polymerase complex cellular component in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.

Symbol Name Standardized Value
SLC1A5 solute carrier family 1 (neutral amino acid transporter), member 5 3.412
AGO1 argonaute RISC catalytic component 1 3.27
AGO4 argonaute RISC catalytic component 4 3.267
DICER1 dicer 1, ribonuclease type III 3.215
AGO2 argonaute RISC catalytic component 2 2.74
AGO3 argonaute RISC catalytic component 3 2.495
CD302 CD302 molecule 2.485
PIWIL4 piwi-like RNA-mediated gene silencing 4 2.464
PIWIL1 piwi-like RNA-mediated gene silencing 1 2.435
DROSHA drosha, ribonuclease type III 2.164
GOLPH3 golgi phosphoprotein 3 (coat-protein) 2.104
H3-7 H3.7 histone (putative) 2.019
H3C13 H3 clustered histone 13 2.019
H3-5 H3.5 histone 2.019
H3C7 H3 clustered histone 7 2.018
H3-4 H3.4 histone, cluster member 2.018
H3-3B H3.3 histone B 2.017
OXTR oxytocin receptor 2.016
SUV39H1 suppressor of variegation 3-9 homolog 1 (Drosophila) 1.893
SRRT serrate, RNA effector molecule 1.746
NRDE2 NRDE-2, necessary for RNA interference, domain containing 1.687
SMARCA2 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 1.667
SIRT2 sirtuin 2 1.643
POLR2G polymerase (RNA) II (DNA directed) polypeptide G 1.64
STC1 stanniocalcin 1 1.626
PAPOLB poly(A) polymerase beta (testis specific) 1.613
PAPOLA poly(A) polymerase alpha 1.604
PAPOLG poly(A) polymerase gamma 1.592
SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 1.581
MYB v-myb avian myeloblastosis viral oncogene homolog 1.522
RSU1 Ras suppressor protein 1 1.519
XRN2 5'-3' exoribonuclease 2 1.515
SDE2 SDE2 telomere maintenance homolog (S. pombe) 1.5
MMS19 MMS19 nucleotide excision repair homolog (S. cerevisiae) 1.5
AHCY adenosylhomocysteinase 1.472
NSG2 neuronal vesicle trafficking associated 2 1.448
HDAC9 histone deacetylase 9 1.439
SLC10A3 solute carrier family 10, member 3 1.426
DDX47 DEAD (Asp-Glu-Ala-Asp) box polypeptide 47 1.42
CETN1 centrin, EF-hand protein, 1 1.391
EXOSC7 exosome component 7 1.376
EXOSC9 exosome component 9 1.366
CFTR cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7) 1.344
POLR2B polymerase (RNA) II (DNA directed) polypeptide B, 140kDa 1.34
ADCY4 adenylate cyclase 4 1.333
DCP2 decapping mRNA 2 1.331
UPF1 UPF1 regulator of nonsense transcripts homolog (yeast) 1.331
WTIP Wilms tumor 1 interacting protein 1.325
MILR1 mast cell immunoglobulin-like receptor 1 1.318
SERPINB6 serpin peptidase inhibitor, clade B (ovalbumin), member 6 1.313
SETD1A SET domain containing 1A 1.311
ZFAND1 zinc finger, AN1-type domain 1 1.305
CENPA centromere protein A 1.299
MTREX Mtr4 exosome RNA helicase 1.296
AJUBA ajuba LIM protein 1.291
SKIC2 SKI2 subunit of superkiller complex 1.29
NFXL1 nuclear transcription factor, X-box binding-like 1 1.28
ERI1 exoribonuclease 1 1.278
LIMD1 LIM domains containing 1 1.276
SF3B1 splicing factor 3b, subunit 1, 155kDa 1.271
SIRT1 sirtuin 1 1.269
BCKDHA branched chain keto acid dehydrogenase E1, alpha polypeptide 1.269
DHX38 DEAH (Asp-Glu-Ala-His) box polypeptide 38 1.267
PITX2 paired-like homeodomain 2 1.264
DDB1 damage-specific DNA binding protein 1, 127kDa 1.255
POLR2A polymerase (RNA) II (DNA directed) polypeptide A, 220kDa 1.25
PROK2 prokineticin 2 1.245
TUT4 terminal uridylyl transferase 4 1.244
H2BC21 H2B clustered histone 21 1.237
H2AZ1 H2A.Z variant histone 1 1.236
EXOSC10 exosome component 10 1.228
POLI polymerase (DNA directed) iota 1.218
CBX5 chromobox homolog 5 1.205
H2AC20 H2A clustered histone 20 1.203
H2AC19 H2A clustered histone 19 1.202
PDE7A phosphodiesterase 7A 1.199
XRN1 5'-3' exoribonuclease 1 1.191
ZNF398 zinc finger protein 398 1.178
PIWIL2 piwi-like RNA-mediated gene silencing 2 1.178
CENPB centromere protein B, 80kDa 1.168
ZCCHC7 zinc finger, CCHC domain containing 7 1.167
LGALS4 lectin, galactoside-binding, soluble, 4 1.158
DIS3 DIS3 exosome endoribonuclease and 3'-5' exoribonuclease 1.148
MAT2A methionine adenosyltransferase II, alpha 1.141
FBP1 fructose-1,6-bisphosphatase 1 1.14
PARP16 poly (ADP-ribose) polymerase family, member 16 1.132
SSR1 signal sequence receptor, alpha 1.124
NPR1 natriuretic peptide receptor 1 1.119
ADCY10 adenylate cyclase 10 (soluble) 1.117
RPLP1 ribosomal protein, large, P1 1.104
MYC v-myc avian myelocytomatosis viral oncogene homolog 1.102
SCARA3 scavenger receptor class A, member 3 1.096
SETD2 SET domain containing 2 1.092
HJURP Holliday junction recognition protein 1.089
PKNOX1 PBX/knotted 1 homeobox 1 1.083
EIF4E eukaryotic translation initiation factor 4E 1.076
HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 1.063
MAPK4 mitogen-activated protein kinase 4 1.043
POMGNT2 protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-) 1.035
TDRD9 tudor domain containing 9 1.03
PRDM16 PR domain containing 16 1.03
HSP90AB1 heat shock protein 90kDa alpha (cytosolic), class B member 1 1.029
DNMT1 DNA (cytosine-5-)-methyltransferase 1 1.029
ZNF346 zinc finger protein 346 1.029
TARBP2 TAR (HIV-1) RNA binding protein 2 1.027
SMNDC1 survival motor neuron domain containing 1 1.023
EEF1A1 eukaryotic translation elongation factor 1 alpha 1 1.022
EBF4 early B-cell factor 4 1.02
DNAJC22 DnaJ (Hsp40) homolog, subfamily C, member 22 1.013
UPF3A UPF3 regulator of nonsense transcripts homolog A (yeast) 1.003
NCBP1 nuclear cap binding protein subunit 1, 80kDa 0.997
LGALSL lectin, galactoside-binding-like 0.991
EIF4G1 eukaryotic translation initiation factor 4 gamma, 1 0.99
TGFBI transforming growth factor, beta-induced, 68kDa 0.989
ALYREF Aly/REF export factor 0.968
IL20RB interleukin 20 receptor beta 0.967
TNRC6A trinucleotide repeat containing 6A 0.964
SKP1 S-phase kinase-associated protein 1 0.961
SLC35C1 solute carrier family 35 (GDP-fucose transporter), member C1 0.96
RDM1 RAD52 motif containing 1 0.96
AHSA1 AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast) 0.954
HDAC7 histone deacetylase 7 0.953
TMEM37 transmembrane protein 37 0.948
PARN poly(A)-specific ribonuclease 0.948
PHGDH phosphoglycerate dehydrogenase 0.946
UPF2 UPF2 regulator of nonsense transcripts homolog (yeast) 0.936
CHD1 chromodomain helicase DNA binding protein 1 0.929
LEO1 Leo1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae) 0.929
HDAC1 histone deacetylase 1 0.928
DNMT3L DNA (cytosine-5-)-methyltransferase 3-like 0.926
ASZ1 ankyrin repeat, SAM and basic leucine zipper domain containing 1 0.924
TIPRL TOR signaling pathway regulator 0.923
ACE2 angiotensin I converting enzyme 2 0.922
WDCP WD repeat and coiled coil containing 0.919
HNMT histamine N-methyltransferase 0.914
HSPA4 heat shock 70kDa protein 4 0.914
HIF1A hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) 0.914
DMAP1 DNA methyltransferase 1 associated protein 1 0.912
MIS18A MIS18 kinetochore protein A 0.908
STUB1 STIP1 homology and U-box containing protein 1, E3 ubiquitin protein ligase 0.907
CBX1 chromobox homolog 1 0.904
SUPT16H suppressor of Ty 16 homolog (S. cerevisiae) 0.903
MAT1A methionine adenosyltransferase I, alpha 0.902
EXOSC4 exosome component 4 0.899
GAPDH glyceraldehyde-3-phosphate dehydrogenase 0.893
SKIC8 SKI8 subunit of superkiller complex 0.893
HIVEP3 human immunodeficiency virus type I enhancer binding protein 3 0.892
POLR2J polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa 0.889
HDAC2 histone deacetylase 2 0.888
SPOCD1 SPOC domain containing 1 0.887
HBS1L HBS1-like translational GTPase 0.886
PRPF3 pre-mRNA processing factor 3 0.883
OLFM1 olfactomedin 1 0.878
EHMT2 euchromatic histone-lysine N-methyltransferase 2 0.877
HDAC8 histone deacetylase 8 0.875
AGL amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase 0.873
HIVEP2 human immunodeficiency virus type I enhancer binding protein 2 0.872
CENPC centromere protein C 0.871
SSRP1 structure specific recognition protein 1 0.869
CLRN1 clarin 1 0.863
XYLT2 xylosyltransferase II 0.862
SLC17A2 solute carrier family 17, member 2 0.862
MIS18BP1 MIS18 binding protein 1 0.861
GUSB glucuronidase, beta 0.857
PARP3 poly (ADP-ribose) polymerase family, member 3 0.857
DGCR8 DGCR8 microprocessor complex subunit 0.849
MORC1 MORC family CW-type zinc finger 1 0.849
FPGS folylpolyglutamate synthase 0.848
CALM3 calmodulin 3 (phosphorylase kinase, delta) 0.846
ZNF79 zinc finger protein 79 0.845
SUPT5H suppressor of Ty 5 homolog (S. cerevisiae) 0.844
SWI5 SWI5 recombination repair homolog (yeast) 0.843
FBXO2 F-box protein 2 0.841
TUT7 terminal uridylyl transferase 7 0.839
CSDC2 cold shock domain containing C2, RNA binding 0.838
CHORDC1 cysteine and histidine-rich domain (CHORD) containing 1 0.834
EPHB2 EPH receptor B2 0.834
PPHLN1 periphilin 1 0.834
DNMT3B DNA (cytosine-5-)-methyltransferase 3 beta 0.833
PLD6 phospholipase D family, member 6 0.827
TASOR transcription activation suppressor 0.819
RNASE3 ribonuclease, RNase A family, 3 0.817
KAT2A K(lysine) acetyltransferase 2A 0.813
MAN2B1 mannosidase, alpha, class 2B, member 1 0.812
GNL3 guanine nucleotide binding protein-like 3 (nucleolar) 0.804
SRCAP Snf2-related CREBBP activator protein 0.794
KCNH2 potassium channel, voltage gated eag related subfamily H, member 2 0.79
REG1A regenerating islet-derived 1 alpha 0.786
GTF3C1 general transcription factor IIIC, polypeptide 1, alpha 220kDa 0.786
DNMT3A DNA (cytosine-5-)-methyltransferase 3 alpha 0.785
COLEC11 collectin sub-family member 11 0.785
SETDB1 SET domain, bifurcated 1 0.785
CEBPZ CCAAT/enhancer binding protein (C/EBP), zeta 0.785
ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide 0.783
LBR lamin B receptor 0.783
P4HTM prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) 0.782
TNRC6C trinucleotide repeat containing 6C 0.774
DDX42 DEAD (Asp-Glu-Ala-Asp) box helicase 42 0.764
TFF3 trefoil factor 3 (intestinal) 0.763
NGLY1 N-glycanase 1 0.761
MTA3 metastasis associated 1 family, member 3 0.76
SAP25 Sin3A-associated protein, 25kDa 0.759
XYLT1 xylosyltransferase I 0.757
DZIP3 DAZ interacting zinc finger protein 3 0.757
ETF1 eukaryotic translation termination factor 1 0.756
ADH1A alcohol dehydrogenase 1A (class I), alpha polypeptide 0.754
SUPT4H1 suppressor of Ty 4 homolog 1 (S. cerevisiae) 0.753
MAF1 MAF1 homolog (S. cerevisiae) 0.753
PLPP6 phospholipid phosphatase 6 0.752
NCBP2L nuclear cap binding protein subunit 2-like 0.747
MEI4 meiosis-specific 4 homolog (S. cerevisiae) 0.744
GLRX glutaredoxin (thioltransferase) 0.742
TAF10 TAF10 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 30kDa 0.741
RMDN2 regulator of microtubule dynamics 2 0.74
FOLH1 folate hydrolase (prostate-specific membrane antigen) 1 0.737
NBR1 neighbor of BRCA1 gene 1 0.737
OIP5 Opa interacting protein 5 0.737
PTBP3 polypyrimidine tract binding protein 3 0.736
TGIF1 TGFB-induced factor homeobox 1 0.735
H4C7 H4 clustered histone 7 0.734
PYDC1 PYD (pyrin domain) containing 1 0.729
MAGEB2 melanoma antigen family B2 0.726
TEX15 testis expressed 15 0.724
RBP7 retinol binding protein 7, cellular 0.724
CENPN centromere protein N 0.723
EPPIN epididymal peptidase inhibitor 0.723
STK24 serine/threonine kinase 24 0.723
EXOSC1 exosome component 1 0.722
PDCL2 phosducin-like 2 0.718
PID1 phosphotyrosine interaction domain containing 1 0.718
CTTNBP2 cortactin binding protein 2 0.717
H4C15 H4 clustered histone 15 0.716
MARCHF6 membrane associated ring-CH-type finger 6 0.716
RBPJ recombination signal binding protein for immunoglobulin kappa J region 0.714
TOM1 target of myb1 (chicken) 0.714
EEF1A2 eukaryotic translation elongation factor 1 alpha 2 0.713
CBX3 chromobox homolog 3 0.712
CYP51A1 cytochrome P450, family 51, subfamily A, polypeptide 1 0.709
MED31 mediator complex subunit 31 0.708
DNAJC2 DnaJ (Hsp40) homolog, subfamily C, member 2 0.704
CDC40 cell division cycle 40 0.703
MAPKAP1 mitogen-activated protein kinase associated protein 1 0.702
POLR2D polymerase (RNA) II (DNA directed) polypeptide D 0.702
SLC28A1 solute carrier family 28 (concentrative nucleoside transporter), member 1 0.7
GZMM granzyme M (lymphocyte met-ase 1) 0.698
DZIP1 DAZ interacting zinc finger protein 1 0.697
TERT telomerase reverse transcriptase 0.693
EXOSC6 exosome component 6 0.693
SLCO6A1 solute carrier organic anion transporter family, member 6A1 0.691
CDC20 cell division cycle 20 0.69
FURIN furin (paired basic amino acid cleaving enzyme) 0.69
GTF3A general transcription factor IIIA 0.689
ST6GALNAC1 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 0.689
SUPT6H suppressor of Ty 6 homolog (S. cerevisiae) 0.684
TADA3 transcriptional adaptor 3 0.682
RTL5 retrotransposon Gag like 5 0.677
LSG1 large 60S subunit nuclear export GTPase 1 0.676
WRN Werner syndrome, RecQ helicase-like 0.675
CUL4A cullin 4A 0.675
CUL1 cullin 1 0.674
PTGDR prostaglandin D2 receptor (DP) 0.671
ZBTB43 zinc finger and BTB domain containing 43 0.668
CALML6 calmodulin-like 6 0.667
MAG myelin associated glycoprotein 0.667
RBX1 ring-box 1, E3 ubiquitin protein ligase 0.666
CALML4 calmodulin-like 4 0.666
CALML5 calmodulin-like 5 0.665
CALML3 calmodulin-like 3 0.665
CDC5L cell division cycle 5-like 0.662
HDAC3 histone deacetylase 3 0.662
POLR2C polymerase (RNA) II (DNA directed) polypeptide C, 33kDa 0.661
NISCH nischarin 0.661
IPO8 importin 8 0.659
CREB1 cAMP responsive element binding protein 1 0.651
PSMD5 proteasome (prosome, macropain) 26S subunit, non-ATPase, 5 0.649
CWC15 CWC15 spliceosome-associated protein 0.649
KCNQ1 potassium channel, voltage gated KQT-like subfamily Q, member 1 0.647
MORC2 MORC family CW-type zinc finger 2 0.646
ZKSCAN7 zinc finger with KRAB and SCAN domains 7 0.639
GABARAPL2 GABA(A) receptor-associated protein-like 2 0.636
RBM8A RNA binding motif protein 8A 0.636
MPHOSPH8 M-phase phosphoprotein 8 0.635
SFRP4 secreted frizzled-related protein 4 0.635
PGLYRP2 peptidoglycan recognition protein 2 0.635
SUGT1 SGT1, suppressor of G2 allele of SKP1 (S. cerevisiae) 0.634
EXOSC5 exosome component 5 0.634
ARRB2 arrestin, beta 2 0.632
OCA2 oculocutaneous albinism II 0.631
LSM1 LSM1, U6 small nuclear RNA associated 0.63
BUB1 BUB1 mitotic checkpoint serine/threonine kinase 0.63
MMP10 matrix metallopeptidase 10 0.629
PNLDC1 poly(A)-specific ribonuclease (PARN)-like domain containing 1 0.625
GABARAPL1 GABA(A) receptor-associated protein like 1 0.625
POLR3D polymerase (RNA) III (DNA directed) polypeptide D, 44kDa 0.625
ZNF12 zinc finger protein 12 0.624
CUL4B cullin 4B 0.623
NCBP2 nuclear cap binding protein subunit 2, 20kDa 0.621
CHML choroideremia-like (Rab escort protein 2) 0.619
PHEX phosphate regulating endopeptidase homolog, X-linked 0.615
ALDH4A1 aldehyde dehydrogenase 4 family, member A1 0.614
NEDD8 neural precursor cell expressed, developmentally down-regulated 8 0.613
CENPT centromere protein T 0.613
CTDSP2 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2 0.613
CHIC1 cysteine-rich hydrophobic domain 1 0.611
ADCY8 adenylate cyclase 8 (brain) 0.61
PRRG1 proline rich Gla (G-carboxyglutamic acid) 1 0.61
CANX calnexin 0.608
SKIC3 SKI3 subunit of superkiller complex 0.608
FOXRED2 FAD-dependent oxidoreductase domain containing 2 0.603
RHNO1 RAD9-HUS1-RAD1 interacting nuclear orphan 1 0.602
MTR 5-methyltetrahydrofolate-homocysteine methyltransferase 0.601
ADARB1 adenosine deaminase, RNA-specific, B1 0.6
MAP3K19 mitogen-activated protein kinase kinase kinase 19 0.598
EIF4E1B eukaryotic translation initiation factor 4E family member 1B 0.598
LY6D lymphocyte antigen 6 complex, locus D 0.596
ZNF146 zinc finger protein 146 0.594
MAEL maelstrom spermatogenic transposon silencer 0.593
INO80C INO80 complex subunit C 0.59
TBL1X transducin (beta)-like 1X-linked 0.585
WT1 Wilms tumor 1 0.583
PEPD peptidase D 0.583
HPGDS hematopoietic prostaglandin D synthase 0.58
RNF5 ring finger protein 5, E3 ubiquitin protein ligase 0.58
KAT2B K(lysine) acetyltransferase 2B 0.579
RAD21 RAD21 homolog (S. pombe) 0.578
AVPR2 arginine vasopressin receptor 2 0.576
EXOSC8 exosome component 8 0.575
ELL elongation factor RNA polymerase II 0.566
RTL1 retrotransposon-like 1 0.564
FKBP2 FK506 binding protein 2, 13kDa 0.562
AATF apoptosis antagonizing transcription factor 0.557
PSAT1 phosphoserine aminotransferase 1 0.553
MT4 metallothionein 4 0.551
RFX1 regulatory factor X, 1 (influences HLA class II expression) 0.551
IER3 immediate early response 3 0.548
DNAJA1 DnaJ (Hsp40) homolog, subfamily A, member 1 0.546
RIGI RNA sensor RIG-I 0.546
RAB3IL1 RAB3A interacting protein (rabin3)-like 1 0.536
EMSY EMSY transcriptional repressor, BRCA2 interacting 0.533
SSU72 SSU72 RNA polymerase II CTD phosphatase homolog (S. cerevisiae) 0.53
NR2F1 nuclear receptor subfamily 2, group F, member 1 0.53
COPS8 COP9 signalosome subunit 8 0.53
RBBP5 retinoblastoma binding protein 5 0.528
ITM2C integral membrane protein 2C 0.526
PSMD13 proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 0.524
INCENP inner centromere protein antigens 135/155kDa 0.518
P3H3 prolyl 3-hydroxylase 3 0.516
STIP1 stress-induced phosphoprotein 1 0.512
DENND2B DENN domain containing 2B 0.51
DRD1 dopamine receptor D1 0.508
DEDD death effector domain containing 0.508
RBM5 RNA binding motif protein 5 0.508
MLEC malectin 0.507
CTDP1 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1 0.506
PSORS1C2 psoriasis susceptibility 1 candidate 2 0.505
TCEA1 transcription elongation factor A (SII), 1 0.504
PRPF39 pre-mRNA processing factor 39 0.503
SMG7 SMG7 nonsense mediated mRNA decay factor 0.502
SLC9A3R1 solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 1 0.501