Protein : Qrob_P0287430.2 Q. robur
Protein Identifier  ? Qrob_P0287430.2 Organism . Name  Quercus robur
Score  100.0 Score Type  egn
Protein Description  (M=2) K15178 - RNA polymerase-associated protein RTF1 Gene Prediction Quality  validated
Protein length 

Sequence

Length: 663  
Kegg Orthology  K15178
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0 Synonyms

6 GO Terms

Identifier Name Description
GO:0003677 DNA binding Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0005634 nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GO:0006352 DNA-templated transcription, initiation Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
GO:0006368 transcription elongation from RNA polymerase II promoter The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
GO:0016570 histone modification The covalent alteration of one or more amino acid residues within a histone protein.
GO:0016593 Cdc73/Paf1 complex A multiprotein complex that associates with RNA polymerase II and general RNA polymerase II transcription factor complexes and may be involved in both transcriptional initiation and elongation. In Saccharomyces the complex contains Paf1p, Cdc73p, Ctr9p, Rtf1p, and Leo1p.

24 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|gmx:100818650 1 656 + 656 Gaps:6 100.00 656 70.27 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|gmx:100791327 1 656 + 656 Gaps:6 100.00 656 69.51 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|tcc:TCM_029914 1 656 + 656 Gaps:4 100.00 660 69.70 0.0 PAF1 complex component isoform 1
blastp_kegg lcl|pmum:103344404 1 656 + 656 Gaps:43 99.84 616 68.78 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|rcu:RCOM_0935630 1 656 + 656 Gaps:6 100.00 660 67.73 0.0 RNA polymerase-associated protein RTF1 putative
blastp_kegg lcl|pvu:PHAVU_002G226300g 1 656 + 656 Gaps:16 100.00 654 68.35 0.0 hypothetical protein
blastp_kegg lcl|cam:101496126 1 656 + 656 Gaps:14 100.00 658 67.78 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|pop:POPTR_0004s03960g 1 656 + 656 Gaps:10 100.00 662 67.22 0.0 POPTRDRAFT_555549 plus-3 domain-containing family protein
blastp_kegg lcl|pop:POPTR_0011s04770g 1 656 + 656 Gaps:10 100.00 664 67.32 0.0 POPTRDRAFT_771126 plus-3 domain-containing family protein
blastp_kegg lcl|csv:101209641 1 656 + 656 Gaps:8 100.00 660 68.94 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_pdb 2db9_A 274 400 + 127 Gaps:4 82.55 149 34.15 1e-13 mol:protein length:149 Paf1/RNA polymerase II complex component
blastp_pdb 3u1u_B 274 400 + 127 Gaps:4 89.78 137 34.15 2e-13 mol:protein length:137 RNA polymerase-associated protein RTF1 homolo
blastp_pdb 3u1u_A 274 400 + 127 Gaps:4 89.78 137 34.15 2e-13 mol:protein length:137 RNA polymerase-associated protein RTF1 homolo
blastp_pdb 2bze_A 274 400 + 127 Gaps:4 80.39 153 34.15 3e-13 mol:protein length:153 KIAA0252 PROTEIN
blastp_uniprot_sprot sp|O94667|RTF1_SCHPO 108 490 + 383 Gaps:48 63.04 560 29.18 2e-24 RNA polymerase-associated protein C651.09c OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN SPBC651.09c PE 1 SV 1
blastp_uniprot_sprot sp|A2AQ19|RTF1_MOUSE 274 656 + 383 Gaps:37 49.51 715 28.81 6e-24 RNA polymerase-associated protein RTF1 homolog OS Mus musculus GN Rtf1 PE 1 SV 1
blastp_uniprot_sprot sp|Q92541|RTF1_HUMAN 274 656 + 383 Gaps:33 49.86 710 28.53 6e-24 RNA polymerase-associated protein RTF1 homolog OS Homo sapiens GN RTF1 PE 1 SV 4
blastp_uniprot_sprot sp|Q5RAD5|RTF1_PONAB 274 601 + 328 Gaps:18 47.22 665 27.71 2e-21 RNA polymerase-associated protein RTF1 homolog (Fragment) OS Pongo abelii GN RTF1 PE 2 SV 2
blastp_uniprot_sprot sp|P53064|RTF1_YEAST 108 533 + 426 Gaps:39 75.45 558 25.18 4e-19 RNA polymerase-associated protein RTF1 OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN RTF1 PE 1 SV 2
blastp_uniprot_sprot sp|Q9W261|RTF1_DROME 270 656 + 387 Gaps:47 44.90 775 27.87 8e-19 RNA polymerase-associated protein Rtf1 OS Drosophila melanogaster GN Rtf1 PE 1 SV 1
rpsblast_cdd gnl|CDD|190531 274 380 + 107 Gaps:6 100.00 105 40.00 7e-27 pfam03126 Plus-3 Plus-3 domain. This domain is about 90 residues in length and is often found associated with the pfam02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.
rpsblast_cdd gnl|CDD|197843 270 381 + 112 Gaps:5 100.00 109 33.94 2e-25 smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein which interacts with Spt6p and in parsley CIP which interacts with the bZIP protein CPRF1.
rpsblast_cdd gnl|CDD|34887 1 533 + 533 Gaps:76 90.02 521 23.24 5e-25 COG5296 COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription].
rpsblast_kog gnl|CDD|37613 26 607 + 582 Gaps:62 99.81 525 33.02 2e-63 KOG2402 KOG2402 KOG2402 Paf1/RNA polymerase II complex RTF1 component (involved in regulation of TATA box-binding protein) [Transcription].

7 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
PANTHER 1 656 656 PTHR13115 none none none
SMART 270 382 113 SM00719 none Short conserved domain in transcriptional regulators. IPR018144
ProSiteProfiles 270 405 136 PS51360 none Plus3 domain profile. IPR004343
PANTHER 1 656 656 PTHR13115:SF8 none none IPR031102
Pfam 274 382 109 PF03126 none Plus-3 domain IPR004343
Coils 434 467 34 Coil none none none
SUPERFAMILY 271 400 130 SSF159042 none none none

0 Localization

7 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_nLBD*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 34,91 16,12 53,62 lod 2,4961 5,2
Bourran2_2014_rEpiBC*_A4 Qrob_Chr08 8 v_12498_318 v_12364_308 35,77 14,11 55,31 lod 2,9413 6,2
Bourran_2000_2002_QTL6_Delta.F Qrob_Chr03 3 s_2HYXJ2_207 s_1AUAXK_317 29.12 6,3 45,37 lod 3.1666 0.026
Bourran2_2014_nLBD_3P Qrob_Chr03 3 s_1ET7H8_604 s_1BYNB5_834 23,73 0 46,72 lod 1,7573 3,8
PM_1999_QTL14_peak_Bud_burst_3P Qrob_Chr03 3 s_2F0SI1_756 v_6056_735 11,78 3,78 50,78 lod 2,5 4,5
Bourran2_2014_nPriLBD*_3P Qrob_Chr11 11 v_12066_307 s_1B15GJ_447 3,37 0,57 16,17 lod 3,4299 6,9
Bourran2_2014_rEpiBC*_3P Qrob_Chr03 3 s_1A3B3X_1163 s_1DKGMO_450 23,04 4,92 41,12 lod 2,5668 7

0 Targeting