From: A multilocus timescale for oomycete evolution estimated under three distinct molecular clock models
Gene | Domainsa | Referenceb |
---|---|---|
Chromatin modification | Â | Â |
Anti-silencing factor Asf1 | asf1 | PITG_17091 |
Brahma-like | HAS, SNF2 N-terminal, Helicase conserved C-terminal, Bromodomain | PITG_19037 |
Chromodomain-containing protein (A) | 2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal | PITG_15837 |
Chromodomain-containing protein (B) | [PDZ, QLQ], 2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal, PHD-finger, PHD-like (zf-HC5HC2H_2) | PITG_10083 |
Chromodomain-containing protein (C) | PHD-finger, 2x Chromo, SNF2 N-terminal, Helicase conserved C-terminal | PITG_00140 |
Chromodomain-containing protein (D) | [Chromo], Bromodomain, PHD, Chromo, [PDZ], SNF2 N-terminal, Helicase conserved C-terminal, PHD, [PHD], PHD-like (zf-HC5HC2H), PHD | PITG_03401 |
CXXC zinc finger containing protein | [SNF2 N-terminal], 2x CXXC zinc finger, [FHA] | PITG_03547 |
DNA methyltransferase 1-associated protein | [DNA methyltransferase 1-associated protein] | PITG_15785 |
ESA1-like histone acetyltransferase | Tudor-knot RNA binding, MOZ/SAS | PITG_01456 |
GCN5-like histone acetyltransferase | GNAT Acetyltransferase, Bromodomain | PITG_20197 |
HAT1-like histone acetyltransferase | HAT1 N-terminus, [GNAT Acetyltransferase] | PITG_00186 |
KAT11 domain histone acetyltransferase (A) | TAZ zinc finger, Bromodomain, [PHD], KAT11, ZZ zinc finger, TAZ zinc finger | PITG_07302 |
KAT11 domain histone acetyltransferase (B) | [TAZ, TAZ], Bromodomain, [DUF902], [PHD], KAT11, [ZZ, TAZ] | PITG_06533 |
KAT11 domain histone acetyltransferase (C) | Bromodomain, [PHD], KAT11 | PITG_18027 |
KAT11 domain histone acetyltransferase (D) | Bromodomain, KAT11 | PITG_08587 |
Histone deacetylase HDA1 | histone deacetylase | PITG_01897 |
Histone deacetylase HDA2 | [ankyrin repeats], histone deacetylase | PITG_08237 |
Histone deacetylase HDA4 | histone deacetylase | PITG_05176 |
Histone deacetylase HDA5 | histone deacetylase | PITG_15415 |
Histone deacetylase HDA6 | histone deacetylase | PITG_21309 |
Histone deacetylase HDA7 | histone deacetylase | PITG_12962 |
Histone deacetylase HDA8 | histone deacetylase | PITG_01911 |
Histone deacetylase HDA9 | histone deacetylase | PITG_04499 |
DOT1-like histone methyltransferase | DOT1 | PITG_00145 |
Histone-lysine N-methyltransferase | Bromodomain, PHD-like zinc-binding (zf-HC5HC2H), F/Y-rich N-terminus, SET | PITG_20502, PITG_04185 |
Protein methyltransferase w/bicoid | Methyltransferase, bicoid-interacting protein 3 | PITG_14915 |
SLIDE domain-containing protein (A) | DUF1898, SNF2 N-terminal, Helicase conserved C-terminal, SLIDE, [myb-like DNA-binding], HMG box | PITG_02286 |
SLIDE domain-containing protein (B) | SNF2 N-terminal, Helicase conserved C-terminal, [HAND], SLIDE | PITG_17273 |
SSRP1 subunit, FACT complex | Structure-specific recognition protein, Histone chaperone Rttp106-like | PITG_14260 |
RNA Methylation | Â | Â |
FtsJ-like rRNA Methyltransferase (A) | FtsJ-like methyltransferase | PITG_09405 |
FtsJ-like rRNA Methyltransferase (B) | FtsJ-like methyltransferase | PITG_06848 |
FtsJ-like rRNA Methyltransferase (C) | FtsJ-like methyltransferase | PITG_16337 |
Spb1-like rRNA Methyltransferase | FtsJ-like methyltransferase, DUF3381, Spb1 C-terminal domain | PITG_00663 |
Guanosine 2'O tRNA methyltransferase | CCCH zinc finger, U11-48Â K CHHC zinc finger, TRM13 methyltransferase | PITG_04858 |
N2,N2-dimethylguanosine tRNA methyltransferase | N2,N2-dimethylguanosine tRNA methyltransferase (TRM) | PITG_10166 |
MnmA-like tRNA 2'-thiouridylase | tRNA methyltransferase | PITG_08823 |
RNA Silencing | Â | Â |
Argonaute (A) | DUF1785, PAZ, Piwi | PITG_04470, PITG_04471 |
Argonaute (B) | DUF1785, PAZ, Piwi | PITG_01400, PITG_01443, PITG_01444 |
Dicer-like | [DEAD/H box helicase], dsRNA binding, 2x Rnase III domains | PITG_09292 |
Drosha-like | 2x Rnase III domains, [dsRNA binding] | Psojae_300435 |
dsRNA-binding protein | dsRNA binding | PITG_12183 |
dsRNA-binding protein w/ Bin3 | [methyltransferase], dsRNA binding, Bicoid-interacting 3 | PITG_03262 |
RnaseIII domain protein | Rnase III domain, [dsRNA binding] | PITG_08831 |
RNA-dependant RNA polymerase | DEAD/H box helicase, Helicase conserved C-terminal, RdRP domain, [NTP transferase] | PITG_10457 |
Transcription factors | Â | Â |
Histone-like CBF/NF-Y | CBF/NF-Y [CENP-S associated centromere protein X] | PITG_00914 |
Histone-like CBF/NF-Y w/HMG | HMG, CBF/NF-Y | PITG_19530 |
Med17 subunit of Mediator complex | Med17 | PITG_03899 |
p15 transcriptional coactivator | 2x PC4 | PITG_07058 |
TFIIB | TFIIB zinc-binding, 2x TFIIB | PITG_14596 |
TFIID, TATA-binding protein (A) | 2x TBP | PITG_07312 |
TFIID, TATA-binding protein (B) | 2x TBP, [DUF3378] | PITG_12304 |
TFIID, TATA-binding protein (C) | TBP, [2x DUF3378], TBP | PITG_06201 |
TFIID, TAF1 subunit | DUF3591, Bromodomain | PITG_02547 |
TFIID, TAF2 subunit | Peptidase M1, [HEAT repeat] | PITG_18882, PITG_14044 |
TFIID, TAF5 subunit | TFIID 90Â kDa, 5x WD domain | PITG_16023 |
TFIID, TAF6 subunit | TAF, DUF1546, [HEAT repeat] | PITG_03978 |
TFIID, TAF8 subunit | Bromodomain (histone-like fold), TAF8 C-terminal | PITG_18355 |
TFIID, TAF9 subunit | TFIID 31Â kDa | PITG_04860 |
TFIID, TAF10 subunit | TFIID 23–30 kDa | PITG_07637, PITG_14668 |
TFIID, TAF12 subunit | TFIID 20Â kDa | PITG_00683 |
TFIID, TAF14 subunit | YEATS | PITG_01229 |
TFIIE, alpha subunit | TFIIEalpha | PITG_08403 |
TFIIF, alpha subunit | TFIIFalpha | PITG_02327 |
TFIIF, beta subunit | TFIIFbeta | PITG_10081 |
TFIIH, Rad3 subunit | DEAD 2, DUF1227, Helicase C-terminal | PITG_15696 |
TFIIH, Ssl1 subunit | Ssl1-like, TFIIH c1-like | Psojae_345458 |
TFIIH, Tfb1 subunit | [TFIIH p62 N-terminal], BSD | PITG_03523 |
TFIIH, Tfb2 subunit | Tfb2 | PITG_15486 |
TFIIH, Tfb4 subunit | Tfb4 | PITG_00220 |
TFIIIB, Brf1-like subunit | TFIIB zinc-binding, 2x TFIIB, Brf1-like TBP-binding | PITG_16669 |