Protein : Qrob_P0359360.2 Q. robur
Protein Identifier  ? Qrob_P0359360.2 Organism . Name  Quercus robur
Score  100.0 Score Type  egn
Protein Description  (M=1) PTHR23273//PTHR23273:SF3 - REPLICATION FACTOR A 1, RFA1 // SUBFAMILY NOT NAMED Gene Prediction Quality  validated
Protein length 

Sequence

Length: 535  
Kegg Orthology  K07466
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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:0003676 nucleic acid binding Interacting selectively and non-covalently with any nucleic 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: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:0006260 DNA replication The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
GO:0006310 DNA recombination Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.

35 Blast

Analysis Hit Start End Strand Length Note Hit Coverage Hit Length Hit Pident E Val Hit Description
blastp_kegg lcl|sot:102589752 1 533 + 533 Gaps:13 84.20 614 81.82 0.0 replication protein A 70 kDa DNA-binding subunit B-like
blastp_kegg lcl|sly:101255870 1 533 + 533 Gaps:13 84.20 614 81.43 0.0 replication protein A 70 kDa DNA-binding subunit-like
blastp_kegg lcl|cit:102626798 1 529 + 529 Gaps:7 83.63 623 79.85 0.0 replication protein A 70 kDa DNA-binding subunit B-like
blastp_kegg lcl|vvi:100255412 1 534 + 534 Gaps:3 85.12 625 77.63 0.0 replication protein A 70 kDa DNA-binding subunit-like
blastp_kegg lcl|cic:CICLE_v10019317mg 1 529 + 529 Gaps:7 83.63 623 79.65 0.0 hypothetical protein
blastp_kegg lcl|rcu:RCOM_1469680 1 534 + 534 Gaps:7 84.41 622 77.14 0.0 replication factor A 1 rfa1 putative
blastp_kegg lcl|mdm:103437891 6 533 + 528 Gaps:13 84.41 635 75.19 0.0 replication protein A 70 kDa DNA-binding subunit B-like
blastp_kegg lcl|tcc:TCM_014274 1 534 + 534 Gaps:9 77.99 677 76.33 0.0 Replication protein A 70 kDa DNA-binding subunit
blastp_kegg lcl|pxb:103937748 6 533 + 528 Gaps:14 84.38 634 75.33 0.0 replication protein A 70 kDa DNA-binding subunit B-like
blastp_kegg lcl|gmx:100777091 3 531 + 529 Gaps:7 84.35 620 74.57 0.0 replication protein A 70 kDa DNA-binding subunit D-like
blastp_pdb 1jmc_A 177 426 + 250 Gaps:9 97.97 246 44.81 4e-63 mol:protein length:246 PROTEIN (REPLICATION PROTEIN A (RPA))
blastp_pdb 1fgu_B 180 426 + 247 Gaps:9 94.44 252 44.96 2e-62 mol:protein length:252 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBU
blastp_pdb 1fgu_A 180 426 + 247 Gaps:9 94.44 252 44.96 2e-62 mol:protein length:252 REPLICATION PROTEIN A 70 KDA DNA-BINDING SUBU
blastp_pdb 1ynx_A 178 290 + 113 Gaps:1 98.25 114 43.75 4e-24 mol:protein length:114 Replication factor-A protein 1
blastp_uniprot_sprot sp|Q9SD82|RFA1B_ARATH 1 534 + 534 Gaps:26 84.60 604 72.02 0.0 Replication protein A 70 kDa DNA-binding subunit B OS Arabidopsis thaliana GN RPA1B PE 3 SV 1
blastp_uniprot_sprot sp|Q9FME0|RFA1D_ARATH 1 528 + 528 Gaps:6 84.10 629 69.57 0.0 Replication protein A 70 kDa DNA-binding subunit D OS Arabidopsis thaliana GN RPA1D PE 2 SV 1
blastp_uniprot_sprot sp|Q10Q08|RFA1B_ORYSJ 5 530 + 526 Gaps:8 83.65 630 64.52 0.0 Replication protein A 70 kDa DNA-binding subunit B OS Oryza sativa subsp. japonica GN RPA1B PE 1 SV 1
blastp_uniprot_sprot sp|Q9SKI4|RFA1A_ARATH 29 443 + 415 Gaps:32 68.28 640 33.41 3e-68 Replication protein A 70 kDa DNA-binding subunit A OS Arabidopsis thaliana GN RPA1A PE 1 SV 1
blastp_uniprot_sprot sp|F4JSG3|RFA1E_ARATH 29 450 + 422 Gaps:57 60.08 784 31.00 9e-64 Replication protein A 70 kDa DNA-binding subunit E OS Arabidopsis thaliana GN RPA1E PE 2 SV 1
blastp_uniprot_sprot sp|Q9FHJ6|RFA1C_ARATH 168 433 + 266 Gaps:5 31.07 853 40.38 6e-62 Replication protein A 70 kDa DNA-binding subunit C OS Arabidopsis thaliana GN RPA1C PE 3 SV 1
blastp_uniprot_sprot sp|P27694|RFA1_HUMAN 180 449 + 270 Gaps:12 42.86 616 42.42 1e-59 Replication protein A 70 kDa DNA-binding subunit OS Homo sapiens GN RPA1 PE 1 SV 2
blastp_uniprot_sprot sp|Q65XV7|RFA1C_ORYSJ 168 433 + 266 Gaps:5 28.08 951 40.45 2e-59 Replication protein A 70 kDa DNA-binding subunit C OS Oryza sativa subsp. japonica GN RPA1C PE 1 SV 1
blastp_uniprot_sprot sp|Q5FW17|RFA1_XENTR 180 426 + 247 Gaps:9 39.08 609 45.80 3e-58 Replication protein A 70 kDa DNA-binding subunit OS Xenopus tropicalis GN rpa1 PE 2 SV 1
blastp_uniprot_sprot sp|Q01588|RFA1_XENLA 180 426 + 247 Gaps:9 39.08 609 46.64 1e-57 Replication protein A 70 kDa DNA-binding subunit OS Xenopus laevis GN rpa1 PE 1 SV 1
rpsblast_cdd gnl|CDD|161961 3 529 + 527 Gaps:21 85.36 608 41.43 1e-122 TIGR00617 rpa1 replication factor-a protein 1 (rpa1). All proteins in this family for which functions are known are part of a multiprotein complex made up of homologs of RPA1 RPA2 and RPA3 that bind ssDNA and function in the recognition of DNA damage for nucleotide excision repairThis family is based on the phylogenomic analysis of JA Eisen (1999 Ph.D. Thesis Stanford University).
rpsblast_cdd gnl|CDD|72946 183 286 + 104 none 100.00 104 56.73 3e-36 cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold the ssDNA-binding domain (DBD)-A of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication recombination and repair. RPA also mediates specific interactions of various nuclear proteins. In animals plants and fungi RPA is a heterotrimer with subunits of 70KDa (RPA1) 32kDa (RPA2) and 14 KDa (RPA3). In addition to DBD-A RPA1 contains three other OB folds: DBD-B DBD-C and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties they differ functionally. Antibodies to hRPA do not cross-react with ScRPA and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro whereas human RPA can..
rpsblast_cdd gnl|CDD|72947 316 422 + 107 Gaps:6 100.00 101 48.51 2e-27 cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold the ssDNA-binding domain (DBD)-B of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication recombination and repair. RPA also mediates specific interactions of various nuclear proteins. In animals plants and fungi RPA is a heterotrimer with subunits of 70KDa (RPA1) 32kDa (RPA2) and 14 KDa (RPA3). In addition to DBD-B RPA1 contains three other OB folds: DBD-A DBD-C and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties they differ functionally. Antibodies to hRPA do not cross-react with ScRPA and null mutations in the ScRPA subunits are not complemented by corresponding human genes. Also ScRPA cannot support Simian virus 40 (SV40) DNA replication in vitro whereas human RPA can..
rpsblast_cdd gnl|CDD|202872 5 107 + 103 Gaps:8 100.00 99 37.37 1e-20 pfam04057 Rep-A_N Replication factor-A protein 1 N-terminal domain.
rpsblast_cdd gnl|CDD|72949 9 105 + 97 Gaps:8 97.94 97 29.47 7e-12 cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication recombination and repair. RPA also mediates specific interactions of various nuclear proteins. In animals plants and fungi RPA is a heterotrimer with subunits of 70KDa (RPA1) 32kDa (RPA2) and 14 KDa (RPA3). RPA1N is known to specifically interact with the p53 tumor suppressor DNA polymerase alpha and transcription factors. In addition to RPA1N RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A DBD-B and DBD-C..
rpsblast_cdd gnl|CDD|149635 464 523 + 60 none 41.10 146 38.33 2e-11 pfam08646 Rep_fac-A_C Replication factor-A C terminal domain. This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication repair and recombination of DNA.

14 Domain Motifs

Analysis Begin End Length Domain Identifier Cross Ref Description Inter Pro
TIGRFAM 3 468 466 TIGR00617 none rpa1: replication factor-a protein 1 (rpa1) IPR004591
PANTHER 1 532 532 PTHR23273 none none none
SUPERFAMILY 299 426 128 SSF50249 none none IPR012340
SUPERFAMILY 182 291 110 SSF50249 none none IPR012340
Pfam 194 280 87 PF01336 none OB-fold nucleic acid binding domain IPR004365
Pfam 5 106 102 PF04057 none Replication factor-A protein 1, N-terminal domain IPR007199
Gene3D 182 286 105 G3DSA:2.40.50.140 none none IPR012340
Pfam 463 523 61 PF08646 none Replication factor-A C terminal domain IPR013955
SUPERFAMILY 1 111 111 SSF50249 none none IPR012340
Gene3D 463 530 68 G3DSA:2.40.50.140 none none IPR012340
Gene3D 298 427 130 G3DSA:2.40.50.140 none none IPR012340
Gene3D 2 108 107 G3DSA:2.40.50.140 none none IPR012340
SUPERFAMILY 463 530 68 SSF50249 none none IPR012340
PANTHER 1 532 532 PTHR23273:SF3 none none none

0 Localization

16 Qtllist

Qtl Name Chromosome Name Linkage Group Prox Marker Dist Marker Position QTL Pos One Pos Two Test Type Test Value R 2
Bourran1_2003_QTL2_peak_Bud_burst_A4 Qrob_Chr02 2 s_1B0H8U_259 s_1CB1VL_554 17 0 87 lod 3,3 8,7
NancyGreenhouseCO2_2001_ambient_elevated_leaf_cellulose_QTL2_d13Cf Qrob_Chr02 2 s_1AQA4Z_1644 s_1AK5QX_947 53.67 14,01 79,68 lod 5.6594 0.03
Bourran1_2004_QTL2_peak_Bud_burst_3P Qrob_Chr02 2 s_1AW12F_382 s_1A77MR_223 42 6 64 lod 3,6 9,6
Bourran2_2002_QTL9_peak_Bud_burst_A4 Qrob_Chr02 2 s_1BFNDA_375 s_1A3VA1_2139 32,5 17 62 lod 3,1 4,2
Bourran2_2003_QTL8_peak_Bud_burst_3P Qrob_Chr02 2 s_1ANG6_1446 v_11270_161 40 0 72 lod 4,4 9,9
Bourran2_2014_nP_A4 Qrob_Chr11 11 s_1B58GB_1413 s_1A5BYY_1671 11,15 0 42,38 lod 1,8913 4,5
Bourran2_2015_nP_A4 Qrob_Chr02 2 s_1A0FUE_1868 s_1A1UAI_500 20,64 20,47 21,36 lod 5.8 10.9
Bourran2_2015_nPriLBD_A4 Qrob_Chr02 2 s_1CP5DI_1183 s_1A63ZX_1277 24,87 24,63 26,18 lod 3.8 7
Bourran2_2015_nEpis_A4 Qrob_Chr09 9 v_15847_485 v_8329_369 34,94 34,88 37,45 lod 3.1 7
Bourran1_2003_QTL1_peak_Bud_burst_3P Qrob_Chr02 2 s_1AR8KI_1183 s_1B0QB1_473 22 6 41 lod 4,2 11,5
Bourran1_2004_QTL3_peak_Bud_burst_A4 Qrob_Chr02 2 s_1B0H8U_259 s_1CB1VL_554 17 0 46 lod 2,9 6,4
Bourran2_2015_nEpiBC_A4 Qrob_Chr07 7 s_1DP9TW_798 v_8128_173 22,61 22,14 22,73 lod 3.1 8.5
Champenoux_2015_nEpis_A4 Qrob_Chr02 2 s_1BAGIZ_823 s_1BN4CB_644 23,06 23,06 23,06 lod 4.9 11
Champenoux_2015_nP_A4 Qrob_Chr02 2 s_1BN4CB_644 v_508_128 23,76 23,06 24,51 lod 2.8 6.2
Champenoux_2015_nPriLBD_A4 Qrob_Chr02 2 s_1CP5DI_1183 s_1A63ZX_1277 25,35 24,63 26,18 lod 4.0 8.7
Champenoux_2015_nSecLBD_A4 Qrob_Chr02 2 s_1AN4ZM_1665 v_8587_238 18,52 18,89 18,27 lod 3.2 7.4

0 Targeting