Protein : Qrob_P0355700.2 Q. robur
Protein Identifier  ? Qrob_P0355700.2 Organism . Name  Quercus robur
Score  93.1 Score Type  egn
Protein Description  (M=1) K03142 - transcription initiation factor TFIIH subunit 2 Gene Prediction Quality  validated
Protein length 

Sequence

Length: 424  
Kegg Orthology  K03142
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0 Synonyms

6 GO Terms

Identifier Name Description
GO:0008270 zinc ion binding Interacting selectively and non-covalently with zinc (Zn) ions.
GO:0046872 metal ion binding Interacting selectively and non-covalently with any metal ion.
GO:0006289 nucleotide-excision repair A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
GO:0006281 DNA repair The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
GO:0006351 transcription, DNA-templated The cellular synthesis of RNA on a template of DNA.
GO:0000439 core TFIIH complex The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.

29 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|vvi:100253554 2 423 + 422 Gaps:2 97.92 433 86.56 0.0 general transcription factor IIH subunit 2-like
blastp_kegg lcl|tcc:TCM_041075 1 417 + 417 none 99.29 420 84.65 0.0 General transcription factor II H2 isoform 1
blastp_kegg lcl|pmum:103324920 1 422 + 422 Gaps:5 99.76 420 85.44 0.0 general transcription factor IIH subunit 2
blastp_kegg lcl|pxb:103930639 1 422 + 422 Gaps:5 99.76 420 85.20 0.0 general transcription factor IIH subunit 2
blastp_kegg lcl|pper:PRUPE_ppa006259mg 1 422 + 422 Gaps:5 99.76 420 85.20 0.0 hypothetical protein
blastp_kegg lcl|csv:101212151 1 422 + 422 Gaps:3 100.00 423 82.74 0.0 general transcription factor IIH subunit 2-like
blastp_kegg lcl|cmo:103504674 1 416 + 416 Gaps:3 98.58 423 83.93 0.0 general transcription factor IIH subunit 2
blastp_kegg lcl|mdm:103422116 1 422 + 422 Gaps:5 99.76 420 84.96 0.0 general transcription factor IIH subunit 2
blastp_kegg lcl|fve:101309025 1 422 + 422 Gaps:4 99.52 420 84.93 0.0 TFIIH basal transcription factor complex p47 subunit-like
blastp_kegg lcl|cit:102608574 1 422 + 422 Gaps:2 99.76 425 79.95 0.0 general transcription factor IIH subunit 2-like
blastp_pdb 1z60_A 362 409 + 48 Gaps:5 72.88 59 51.16 4e-07 mol:protein length:59 TFIIH basal transcription factor complex p44
blastp_uniprot_sprot sp|O74995|TFH47_SCHPO 5 410 + 406 Gaps:35 94.30 421 44.58 1e-109 TFIIH basal transcription factor complex p47 subunit OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN tfh47 PE 1 SV 1
blastp_uniprot_sprot sp|Q86KZ2|TF2H2_DICDI 2 411 + 410 Gaps:25 88.29 461 41.77 6e-107 General transcription factor IIH subunit 2 OS Dictyostelium discoideum GN gtf2h2 PE 3 SV 2
blastp_uniprot_sprot sp|Q2TBV5|TF2H2_BOVIN 29 409 + 381 Gaps:32 94.94 395 45.60 1e-106 General transcription factor IIH subunit 2 OS Bos taurus GN GTF2H2 PE 2 SV 1
blastp_uniprot_sprot sp|A0JN27|TF2H2_RAT 29 409 + 381 Gaps:33 94.95 396 44.95 2e-105 General transcription factor IIH subunit 2 OS Rattus norvegicus GN Gtf2h2 PE 1 SV 1
blastp_uniprot_sprot sp|Q13888|TF2H2_HUMAN 29 409 + 381 Gaps:32 94.94 395 45.87 1e-102 General transcription factor IIH subunit 2 OS Homo sapiens GN GTF2H2 PE 1 SV 1
blastp_uniprot_sprot sp|Q6P1K8|T2H2L_HUMAN 29 409 + 381 Gaps:32 94.94 395 45.87 2e-102 General transcription factor IIH subunit 2-like protein OS Homo sapiens GN GTF2H2C PE 1 SV 1
blastp_uniprot_sprot sp|Q9JIB4|TF2H2_MOUSE 29 409 + 381 Gaps:33 94.95 396 44.95 3e-101 General transcription factor IIH subunit 2 OS Mus musculus GN Gtf2h2 PE 1 SV 1
blastp_uniprot_sprot sp|Q04673|SSL1_YEAST 20 411 + 392 Gaps:27 84.38 461 43.44 2e-98 Suppressor of stem-loop protein 1 OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN SSL1 PE 1 SV 1
blastp_uniprot_sprot sp|P34567|TF2H2_CAEEL 15 409 + 395 Gaps:31 99.47 376 40.91 3e-81 General transcription factor IIH subunit 2 OS Caenorhabditis elegans GN T16H12.4 PE 3 SV 3
rpsblast_cdd gnl|CDD|34752 5 411 + 407 Gaps:29 94.54 421 42.96 6e-98 COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH subunit SSL1 [Transcription / DNA replication recombination and repair].
rpsblast_cdd gnl|CDD|190848 90 280 + 191 Gaps:2 100.00 193 60.62 5e-87 pfam04056 Ssl1 Ssl1-like. Ssl1-like proteins are 40kDa subunits of the Transcription factor II H complex.
rpsblast_cdd gnl|CDD|29226 82 264 + 183 none 100.00 183 58.47 1e-74 cd01453 vWA_transcription_factor_IIH_type Transcription factors IIH type: TFIIH is a multiprotein complex that is one of the five general transcription factors that binds RNA polymerase II holoenzyme. Orthologues of these genes are found in all completed eukaryotic genomes and all these proteins contain a VWA domain. The p44 subunit of TFIIH functions as a DNA helicase in RNA polymerase II transcription initiation and DNA repair and its transcriptional activity is dependent on its C-terminal Zn-binding domains. The function of the vWA domain is unclear but may be involved in complex assembly. The MIDAS motif is not conserved in this sub-group..
rpsblast_cdd gnl|CDD|129709 302 411 + 110 Gaps:11 99.11 112 55.86 7e-35 TIGR00622 ssl1 transcription factor ssl1. All proteins in this family for which functions are known are components of the TFIIH complex which is involved in the initiaiton of transcription and nucleotide excision repair.This family is based on the phylogenomic analysis of JA Eisen (1999 Ph.D. Thesis Stanford University).
rpsblast_cdd gnl|CDD|116585 363 410 + 48 none 100.00 48 68.75 1e-19 pfam07975 C1_4 TFIIH C1-like domain. The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif whereas the second is characterized by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C (pfam00130).
rpsblast_cdd gnl|CDD|198115 364 410 + 47 Gaps:2 100.00 49 63.27 5e-16 smart01047 C1_4 TFIIH C1-like domain. The carboxyl-terminal region of TFIIH is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C.
rpsblast_cdd gnl|CDD|197656 87 256 + 170 Gaps:17 97.71 175 23.39 4e-14 smart00327 VWA von Willebrand factor (vWF) type A domain. VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
rpsblast_cdd gnl|CDD|205697 87 243 + 157 Gaps:15 89.53 172 25.97 2e-08 pfam13519 VWA_2 von Willebrand factor type A domain.
rpsblast_kog gnl|CDD|38018 15 411 + 397 Gaps:22 99.21 378 58.40 1e-144 KOG2807 KOG2807 KOG2807 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH subunit SSL1 [Transcription Replication recombination and repair].

12 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
SMART 84 260 177 SM00327 none von Willebrand factor (vWF) type A domain IPR002035
TIGRFAM 302 411 110 TIGR00622 none ssl1: transcription factor ssl1 IPR012170
SUPERFAMILY 337 410 74 SSF57889 none none none
Pfam 363 411 49 PF07975 none TFIIH C1-like domain IPR004595
Pfam 90 280 191 PF04056 none Ssl1-like IPR007198
PANTHER 1 419 419 PTHR12695:SF2 none none IPR012170
PIRSF 2 412 411 PIRSF015919 none none IPR012170
ProSitePatterns 384 404 21 PS00028 none Zinc finger C2H2 type domain signature. IPR007087
SUPERFAMILY 82 249 168 SSF53300 none none IPR002035
SMART 363 411 49 SM01047 none TFIIH C1-like domain IPR004595
PANTHER 1 419 419 PTHR12695 none none none
Gene3D 358 410 53 G3DSA:3.10.370.10 none none none

0 Localization

5 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran2_2014_nEpiBC_3P Qrob_Chr01 1 v_1588_550 s_1AZJRA_1600 30,48 9,48 43,98 lod 2,3642 6,3
Bourran2_2014_nLBD*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 34,91 16,12 53,62 lod 2,4961 5,2
Bourran2_2014_nSecLBD_3P Qrob_Chr08 8 s_1BN2OD_551 s_1B5AYF_599 17,17 0 43,51 lod 1,9229 4,4
Bourran2_2014_rEpiBC*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 35,77 14,11 55,31 lod 2,9413 6,2
Bourran2_2015_nEpiBC_3P Qrob_Chr12 12 s_1B73S5_217 v_7050_211 28,31 26,37 28,45 lod 4.5 11.6

0 Targeting