Protein : Qrob_P0340830.2 Q. robur
Protein Identifier  ? Qrob_P0340830.2 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: 659  
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 1 658 + 658 Gaps:10 100.00 656 79.88 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|tcc:TCM_029914 1 658 + 658 Gaps:8 100.00 660 80.76 0.0 PAF1 complex component isoform 1
blastp_kegg lcl|gmx:100791327 1 658 + 658 Gaps:10 100.00 656 80.03 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|rcu:RCOM_0935630 1 658 + 658 Gaps:12 100.00 660 80.45 0.0 RNA polymerase-associated protein RTF1 putative
blastp_kegg lcl|cam:101496126 1 658 + 658 Gaps:6 100.00 658 77.05 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|pvu:PHAVU_002G226300g 1 658 + 658 Gaps:10 100.00 654 78.44 0.0 hypothetical protein
blastp_kegg lcl|pop:POPTR_0011s04770g 1 658 + 658 Gaps:10 100.00 664 75.45 0.0 POPTRDRAFT_771126 plus-3 domain-containing family protein
blastp_kegg lcl|pop:POPTR_0004s03960g 1 658 + 658 Gaps:6 100.00 662 75.23 0.0 POPTRDRAFT_555549 plus-3 domain-containing family protein
blastp_kegg lcl|csv:101209641 1 658 + 658 Gaps:18 100.00 660 78.79 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_kegg lcl|cmo:103494388 1 658 + 658 Gaps:6 100.00 660 78.79 0.0 RNA polymerase-associated protein RTF1 homolog
blastp_pdb 2bze_A 264 399 + 136 Gaps:5 86.93 153 31.58 1e-13 mol:protein length:153 KIAA0252 PROTEIN
blastp_pdb 3u1u_B 271 399 + 129 Gaps:4 91.24 137 31.20 3e-13 mol:protein length:137 RNA polymerase-associated protein RTF1 homolo
blastp_pdb 3u1u_A 271 399 + 129 Gaps:4 91.24 137 31.20 3e-13 mol:protein length:137 RNA polymerase-associated protein RTF1 homolo
blastp_pdb 2db9_A 271 401 + 131 Gaps:4 85.23 149 30.71 5e-13 mol:protein length:149 Paf1/RNA polymerase II complex component
blastp_uniprot_sprot sp|A2AQ19|RTF1_MOUSE 271 658 + 388 Gaps:46 49.51 715 27.12 1e-22 RNA polymerase-associated protein RTF1 homolog OS Mus musculus GN Rtf1 PE 1 SV 1
blastp_uniprot_sprot sp|Q92541|RTF1_HUMAN 271 658 + 388 Gaps:46 49.86 710 27.12 3e-22 RNA polymerase-associated protein RTF1 homolog OS Homo sapiens GN RTF1 PE 1 SV 4
blastp_uniprot_sprot sp|Q5RAD5|RTF1_PONAB 271 546 + 276 Gaps:7 41.05 665 26.01 1e-21 RNA polymerase-associated protein RTF1 homolog (Fragment) OS Pongo abelii GN RTF1 PE 2 SV 2
blastp_uniprot_sprot sp|O94667|RTF1_SCHPO 107 487 + 381 Gaps:38 63.04 560 30.59 2e-21 RNA polymerase-associated protein C651.09c OS Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN SPBC651.09c PE 1 SV 1
blastp_uniprot_sprot sp|P53064|RTF1_YEAST 107 522 + 416 Gaps:45 74.01 558 27.36 4e-18 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 267 519 + 253 Gaps:14 32.39 775 27.49 4e-18 RNA polymerase-associated protein Rtf1 OS Drosophila melanogaster GN Rtf1 PE 1 SV 1
rpsblast_cdd gnl|CDD|190531 271 377 + 107 Gaps:6 100.00 105 40.95 3e-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 267 378 + 112 Gaps:5 100.00 109 36.70 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 1 524 + 524 Gaps:67 88.87 521 25.27 3e-23 COG5296 COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription].
rpsblast_kog gnl|CDD|37613 25 609 + 585 Gaps:67 99.81 525 34.35 2e-69 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
Pfam 271 379 109 PF03126 none Plus-3 domain IPR004343
PANTHER 1 658 658 PTHR13115 none none none
ProSiteProfiles 267 402 136 PS51360 none Plus3 domain profile. IPR004343
Coils 431 471 41 Coil none none none
SUPERFAMILY 268 399 132 SSF159042 none none none
SMART 267 379 113 SM00719 none Short conserved domain in transcriptional regulators. IPR018144
PANTHER 1 658 658 PTHR13115:SF8 none none IPR031102

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_2015_nEpis_3P Qrob_Chr12 12 s_1AOES6_1466 s_1B0DDG_1094 28,97 28,55 30,1 lod 3.6 8.4
Champenoux_2015_nEpis_3P Qrob_Chr11 11 s_1DG9PM_867 s_1BZ083_1312 26,53 25,47 27,72 lod 4.4 8.9
Bourran2_2002_QTL16_peak_Bud_burst_A4 Qrob_Chr11 11 s_A9OIA_166 s_1C6WBF_114 21,23 2,83 42,83 lod 5,1 7,2
Bourran2_2015_nSeqBC_3P Qrob_Chr11 11 s_1DG9PM_867 s_1BZ083_1312 26,06 25,47 27,72 lod 3.6 7.1
Champenoux_2015_nSecLBD_3P Qrob_Chr11 11 s_1DG9PM_867 s_1BZ083_1312 25,78 25,47 27,72 lod 6.3 16.6

0 Targeting