Rroxscaffold_6G00394240

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0015461
Physical Location & Seq
Reverse (-)
14600568 .. 14601764
1197 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00394240.1

Sequence Viewer

Length: 1107 bp
ATGGGAAAGATGTCCCCCTCGGTCCGTTCACTAGTCTCAACTTCCCTCGGATCCCCAAACCAATCCCCTTCTCATAAATTCCATAACTCTCGGACCCATCTCCCCGAAAAAACCCCCCTCGATCTTTGCGTCCACAACGCCCTCCTCCAATCCTATGCCGCAATCTCCACCGTCAACGACTCCATCGCTCTCTTCAACCACATGATCAAAATCCAACCCGCATTCTCGCCGGACCGGTCCACCTACCACATCTTGCTCGCCCGGTCCTGCACCGTACCCGATCGACCTTCCAATCTGTTCACCAAGTCCTTAACTTTATGCTCAACAATGGCTTCCACCCGGATAAGGTCACCACCGACATTGCAGTCCGGTCGCTGCGCTTGGCGGGACACGTGGACGAGGCGGCAAGTGATGAAGCAAATGTCGTTGAAAAACGCGGTACCGGATACTTATACTTACAATTTTCTTGTCAAGTGTCTCTGCAAGTCGAGAGTTTTGAGTATTGTTAAAGAGTTTATTGACGATATGCGAAAGTCTTTCGATTTGAAGCCGGATTTGGTTACTTATACGATTATGATTGACAATGTAGCTAATAGCAAGAATTTACATAAGGCTAGCCAATTCGTGAAGGAGTTGGATAAGGAGGGGTTTAAGCCGGATTGCTATGTTTACAATATGATTATGAAAGGTTATTGTATGCCGAGTAAGGGTAATGAGGCGGTTATGGAGGTGAAGAAGTATTTGCGGATCATGGTGGACATGGGGCATTTCCCCAACGAGGTGACTTATACTTCATTGATGAATGGATTGTGTCGGAAGGGGGATGCATTTGGTGCGGTGGCATTGTTGGAGGAGATGCAAGCGCGGGGGTGCAGCCCGAATGAGTGCACCTATAATACCTTGCTTCATGGGTTGTGTAAGGGAAGGTTGTTAGAGAAAGGGCTGGAATTGTATGGACTGATGAAAAAAGATGGGATGAAGCTTGACACGGCTTCGTATAGTACACTTGTGAGGACACTTTGTAGGGCGAGCGGGGTTGCGTACGCTTATGGAGTGTTTGATTATGCAGTTGAGAGTAAGAGCTTAACAAATGTTTCGCTTACTTGA

Protein Analysis

368

Amino Acids

41.29

Weight (kDa)

9.25

Isoelectric Point (pI)

44.05

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 148 - 197 4.1e-09 PPR repeat family
PPR_3 PF13812 180 - 231 5.5e-09 Pentatricopeptide repeat domain
PPR_2 PF13041 184 - 232 1e-10 PPR repeat family
PPR_long PF17177 194 - 343 9.7e-11 Pentacotripeptide-repeat region of PRORP
PPR_3 PF13812 251 - 303 2.5e-08 Pentatricopeptide repeat domain
PPR_1 PF12854 254 - 287 4e-11 PPR repeat
PPR_2 PF13041 258 - 307 1.5e-18 PPR repeat family
PPR PF01535 261 - 291 3.4e-08 PPR repeat
PPR_1 PF12854 289 - 321 1e-08 PPR repeat
PPR_2 PF13041 293 - 342 3.9e-13 PPR repeat family
PPR PF01535 297 - 325 4.8e-07 PPR repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0015461)

Species Orthologous Gene IDs
arabidopsis_thaliana AT2G17670 AT2G17670
fragaria_vesca FvH4_1g10671
malus_domestica MD02G1120600.v1.1
prunus_persica Prupe.7G178400_v2.0.a1
rosa_laevigata RLG00000016739
rosa_multiflora Rmu_co8429607.1_g000001 Rmu_sc0000974.1_g000027 Rmu_sc0008442.1_g000010
rosa_roxburghii Rroxscaffold_6G00394240
rosa_rugosa Rorug02G0068500
rosa_samantha Rh2AG115200 Rh2BG118100 Rh2CG119700 Rh2DG119400
rosa_wichuraiana Rw2G009000

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 364
Acc65I GGTACC 1 cut(s) 439
AccB1I GGYRCC 1 cut(s) 439
AccBSI CCGCTC 1 cut(s) 1032
AccII CGCG 2 cut(s) 437, 865
AclWI GGATC 3 cut(s) 45, 58, 755
AcsI RAATTY 2 cut(s) 77, 601
AcvI CACGTG 1 cut(s) 393
AfaI GTAC 4 cut(s) 276, 441, 1003, 1043
AfiI CCNNNNNNNGG 3 cut(s) 345, 707, 778
AflIII ACRYGT 1 cut(s) 390
AgeI ACCGGT 1 cut(s) 234
AgsI TTSAA 3 cut(s) 196, 430, 547
AhlI ACTAGT 1 cut(s) 31
AjuI GAANNNNNNNTTGG 2 cut(s) 539, 571
AluBI AGCT 3 cut(s) 590, 982, 1083
AluI AGCT 3 cut(s) 590, 982, 1083
Alw21I GWGCWC 1 cut(s) 890
Alw26I GTCTC 2 cut(s) 40, 482
Alw44I GTGCAC 1 cut(s) 886
AlwI GGATC 3 cut(s) 45, 58, 755
ApaLI GTGCAC 1 cut(s) 886
ApeKI GCWGC 2 cut(s) 375, 873
ApoI RAATTY 2 cut(s) 77, 601
AsiGI ACCGGT 1 cut(s) 234
Asp718I GGTACC 1 cut(s) 439
AspLEI GCGC 2 cut(s) 380, 865
AspS9I GGNCC 5 cut(s) 22, 93, 232, 237, 264
AsuC2I CCSGG 2 cut(s) 262, 340
AsuHPI GGTGA 4 cut(s) 292, 342, 742, 793
AsuNHI GCTAGC 1 cut(s) 614
AvaII GGWCC 5 cut(s) 22, 93, 232, 237, 264
BaeGI GKGCMC 1 cut(s) 890
BamHI GGATCC 1 cut(s) 50
BanI GGYRCC 1 cut(s) 439
BbrPI CACGTG 1 cut(s) 393
Bbv12I GWGCWC 1 cut(s) 890
BbvI GCAGC 2 cut(s) 362, 885
BccI CCATC 3 cut(s) 105, 191, 965
BceAI ACGGC 1 cut(s) 1005
BcgI CGANNNNNNTGC 2 cut(s) 353, 387
BciVI GTATCC 1 cut(s) 439
BclI TGATCA 1 cut(s) 204
BcnI CCSGG 2 cut(s) 262, 340
BcoDI GTCTC 2 cut(s) 40, 482
BcuI ACTAGT 1 cut(s) 31
BfaI CTAG 2 cut(s) 32, 615
BfuI GTATCC 1 cut(s) 439
BisI GCNGC 4 cut(s) 159, 376, 404, 874
BlsI GCNGC 4 cut(s) 160, 377, 405, 875
Bme1390I CCNGG 2 cut(s) 262, 340
Bme18I GGWCC 5 cut(s) 22, 93, 232, 237, 264
BmgT120I GGNCC 5 cut(s) 22, 93, 232, 237, 264
BmiI GGNNCC 3 cut(s) 52, 95, 441
BmrFI CCNGG 2 cut(s) 262, 340
BmsI GCATC 2 cut(s) 814, 846
BmtI GCTAGC 1 cut(s) 618
BpuMI CCSGG 2 cut(s) 262, 340
BsaAI YACGTR 1 cut(s) 393
BsaBI GATNNNNATC 1 cut(s) 209
BsaJI CCNNGG 2 cut(s) 18, 46
BsaWI WCCGGW 3 cut(s) 234, 368, 442
Bsc4I CCNNNNNNNGG 3 cut(s) 345, 707, 778
Bse118I RCCGGY 1 cut(s) 234
Bse3DI GCAATG 1 cut(s) 359
Bse8I GATNNNNATC 1 cut(s) 209
BseDI CCNNGG 2 cut(s) 18, 46
BseGI GGATG 2 cut(s) 829, 981
BseJI GATNNNNATC 1 cut(s) 209
BseLI CCNNNNNNNGG 3 cut(s) 345, 707, 778
BseMI GCAATG 1 cut(s) 359
BseRI GAGGAG 2 cut(s) 134, 866
BseSI GKGCMC 1 cut(s) 890
BseXI GCAGC 2 cut(s) 362, 885
BsgI GTGCAG 2 cut(s) 253, 892
Bsh1236I CGCG 2 cut(s) 437, 865
Bsh1285I CGRYCG 2 cut(s) 283, 373
BshNI GGYRCC 1 cut(s) 439
BshTI ACCGGT 1 cut(s) 234
BsiEI CGRYCG 2 cut(s) 283, 373
BsiHKAI GWGCWC 1 cut(s) 890
BsiSI CCGG 8 cut(s) 230, 235, 262, 340, 369, 443, 551, 656
BsiWI CGTACG 1 cut(s) 1041
BslFI GGGAC 1 cut(s) 401
BslI CCNNNNNNNGG 3 cut(s) 345, 707, 778
BsmAI GTCTC 2 cut(s) 40, 482
BsmFI GGGAC 1 cut(s) 401
BsmI GAATGC 1 cut(s) 221
Bsp1286I GDGCHC 1 cut(s) 890
Bsp143I GATC 5 cut(s) 50, 121, 204, 280, 747
BspFNI CGCG 2 cut(s) 437, 865
BspLI GGNNCC 3 cut(s) 52, 95, 441
BspOI GCTAGC 1 cut(s) 618
BspPI GGATC 3 cut(s) 45, 58, 755
BspT107I GGYRCC 1 cut(s) 439
BsrBI CCGCTC 1 cut(s) 1032
BsrDI GCAATG 1 cut(s) 359
BsrFI RCCGGY 1 cut(s) 234
BssAI RCCGGY 1 cut(s) 234
BssECI CCNNGG 2 cut(s) 18, 46
BssMI GATC 5 cut(s) 50, 121, 204, 280, 747
Bst4CI ACNGT 2 cut(s) 172, 274
Bst6I CTCTTC 1 cut(s) 197
BstAPI GCANNNNNTGC 1 cut(s) 833
BstBAI YACGTR 1 cut(s) 393
BstC8I GCNNGC 4 cut(s) 258, 616, 861, 1030
BstEII GGTNACC 1 cut(s) 348
BstF5I GGATG 2 cut(s) 829, 981
BstFNI CGCG 2 cut(s) 437, 865
BstHHI GCGC 2 cut(s) 380, 865
BstKTI GATC 5 cut(s) 53, 124, 207, 283, 750
BstMAI GTCTC 2 cut(s) 40, 482
BstMBI GATC 5 cut(s) 50, 121, 204, 280, 747
BstMCI CGRYCG 2 cut(s) 283, 373
BstMWI GCNNNNNNNGC 1 cut(s) 833
BstPI GGTNACC 1 cut(s) 348
BstSCI CCNGG 2 cut(s) 260, 338
BstSLI GKGCMC 1 cut(s) 890
BstUI CGCG 2 cut(s) 437, 865
BstV1I GCAGC 2 cut(s) 362, 885
BstX2I RGATCY 1 cut(s) 50
BstYI RGATCY 1 cut(s) 50
BsuI GTATCC 1 cut(s) 439
BtgZI GCGATG 1 cut(s) 169
BtsCI GGATG 2 cut(s) 829, 981
Cac8I GCNNGC 4 cut(s) 258, 616, 861, 1030
CfoI GCGC 2 cut(s) 380, 865
Cfr10I RCCGGY 1 cut(s) 234
Cfr13I GGNCC 5 cut(s) 22, 93, 232, 237, 264
CpoI CGGWCCG 2 cut(s) 22, 232
CseI GACGC 1 cut(s) 118
Csp6I GTAC 4 cut(s) 275, 440, 1002, 1042
CspAI ACCGGT 1 cut(s) 234
CspCI CAANNNNNGTGG 2 cut(s) 342, 377
CspI CGGWCCG 2 cut(s) 22, 232
CviAII CATG 4 cut(s) 202, 751, 760, 908
CviQI GTAC 4 cut(s) 275, 440, 1002, 1042
DpnI GATC 5 cut(s) 52, 123, 206, 282, 749
DpnII GATC 5 cut(s) 50, 121, 204, 280, 747
DrdI GACNNNNNNGTC 1 cut(s) 364
DseDI GACNNNNNNGTC 1 cut(s) 364
Eam1104I CTCTTC 1 cut(s) 197
EarI CTCTTC 1 cut(s) 197
Eco47I GGWCC 5 cut(s) 22, 93, 232, 237, 264
Eco72I CACGTG 1 cut(s) 393
Eco91I GGTNACC 1 cut(s) 348
EcoO65I GGTNACC 1 cut(s) 348
EcoT22I ATGCAT 1 cut(s) 829
FaeI CATG 4 cut(s) 205, 754, 763, 911
FaqI GGGAC 1 cut(s) 401
FatI CATG 4 cut(s) 201, 750, 759, 907
FauI CCCGC 4 cut(s) 226, 378, 858, 1025
FbaI TGATCA 1 cut(s) 204
Fnu4HI GCNGC 4 cut(s) 159, 376, 404, 874
FokI GGATG 2 cut(s) 836, 988
Fsp4HI GCNGC 4 cut(s) 159, 376, 404, 874
FspBI CTAG 2 cut(s) 32, 615
GlaI GCGC 2 cut(s) 379, 864
GluI GCNGC 4 cut(s) 159, 376, 404, 874
HapII CCGG 8 cut(s) 230, 235, 262, 340, 369, 443, 551, 656
HgaI GACGC 1 cut(s) 118
HhaI GCGC 2 cut(s) 380, 865
Hin1II CATG 4 cut(s) 205, 754, 763, 911
Hin6I GCGC 2 cut(s) 378, 863
HinP1I GCGC 2 cut(s) 378, 863
HincII GTYRAC 1 cut(s) 175
HindII GTYRAC 1 cut(s) 175
HindIII AAGCTT 1 cut(s) 980
HinfI GANTC 1 cut(s) 179
HpaII CCGG 8 cut(s) 230, 235, 262, 340, 369, 443, 551, 656
HphI GGTGA 4 cut(s) 292, 342, 742, 793
Hpy188I TCNGA 3 cut(s) 50, 93, 816
Hpy188III TCNNGA 2 cut(s) 489, 625
HpyAV CCTTC 5 cut(s) 78, 297, 622, 811, 918
HpyCH4III ACNGT 2 cut(s) 172, 274
HpyCH4IV ACGT 1 cut(s) 392
HpyCH4V TGCA 8 cut(s) 270, 364, 483, 827, 859, 873, 888, 1067
HpyF10VI GCNNNNNNNGC 1 cut(s) 833
HpySE526I ACGT 1 cut(s) 392
Hsp92II CATG 4 cut(s) 205, 754, 763, 911
HspAI GCGC 2 cut(s) 378, 863
KpnI GGTACC 1 cut(s) 443
Ksp22I TGATCA 1 cut(s) 204
Kzo9I GATC 5 cut(s) 50, 121, 204, 280, 747
Lsp1109I GCAGC 2 cut(s) 362, 885
LweI GCATC 2 cut(s) 814, 846
MaeI CTAG 2 cut(s) 32, 615
MaeII ACGT 1 cut(s) 392
MaeIII GTNAC 3 cut(s) 348, 559, 781
MalI GATC 5 cut(s) 52, 123, 206, 282, 749
MbiI CCGCTC 1 cut(s) 1032
MboI GATC 5 cut(s) 50, 121, 204, 280, 747
MboII GAAGA 2 cut(s) 184, 745
MflI RGATCY 1 cut(s) 50
MhlI GDGCHC 1 cut(s) 890
MluCI AATT 5 cut(s) 77, 460, 601, 620, 947
MlyI GAGTC 1 cut(s) 173
MmeI TCCRAC 4 cut(s) 238, 615, 794, 828
Mph1103I ATGCAT 1 cut(s) 829
MseI TTAA 4 cut(s) 311, 507, 651, 1085
MspI CCGG 8 cut(s) 230, 235, 262, 340, 369, 443, 551, 656
MspR9I CCNGG 2 cut(s) 262, 340
Mva1269I GAATGC 1 cut(s) 221
MvnI CGCG 2 cut(s) 437, 865
MwoI GCNNNNNNNGC 1 cut(s) 833
NciI CCSGG 2 cut(s) 262, 340
NdeII GATC 5 cut(s) 50, 121, 204, 280, 747
NheI GCTAGC 1 cut(s) 614
NlaIII CATG 4 cut(s) 205, 754, 763, 911
NlaIV GGNNCC 3 cut(s) 52, 95, 441
NmeAIII GCCGAG 1 cut(s) 726
NmuCI GTSAC 2 cut(s) 348, 781
NsiI ATGCAT 1 cut(s) 829
PcsI WCGNNNNNNNCGW 1 cut(s) 126
PctI GAATGC 1 cut(s) 221
Pfl23II CGTACG 1 cut(s) 1041
PinAI ACCGGT 1 cut(s) 234
PkrI GCNGC 4 cut(s) 160, 377, 405, 875
Ple19I CGATCG 1 cut(s) 283
PleI GAGTC 1 cut(s) 173
PmaCI CACGTG 1 cut(s) 393
PmlI CACGTG 1 cut(s) 393
PpsI GAGTC 1 cut(s) 173
Ppu21I YACGTR 1 cut(s) 393
PspCI CACGTG 1 cut(s) 393
PspEI GGTNACC 1 cut(s) 348
PspLI CGTACG 1 cut(s) 1041
PspN4I GGNNCC 3 cut(s) 52, 95, 441
PspPI GGNCC 5 cut(s) 22, 93, 232, 237, 264
PsuI RGATCY 1 cut(s) 50
PvuI CGATCG 1 cut(s) 283
RsaI GTAC 4 cut(s) 276, 441, 1003, 1043
RsaNI GTAC 4 cut(s) 275, 440, 1002, 1042
Rsr2I CGGWCCG 2 cut(s) 22, 232
RsrII CGGWCCG 2 cut(s) 22, 232
SaqAI TTAA 4 cut(s) 311, 507, 651, 1085
SatI GCNGC 4 cut(s) 159, 376, 404, 874
Sau3AI GATC 5 cut(s) 50, 121, 204, 280, 747
Sau96I GGNCC 5 cut(s) 22, 93, 232, 237, 264
SchI GAGTC 1 cut(s) 173
ScrFI CCNGG 2 cut(s) 262, 340
SduI GDGCHC 1 cut(s) 890
SfaNI GCATC 2 cut(s) 814, 846
SinI GGWCC 5 cut(s) 22, 93, 232, 237, 264
SpeI ACTAGT 1 cut(s) 31
Sse9I AATT 5 cut(s) 77, 460, 601, 620, 947
SspMI CTAG 2 cut(s) 32, 615
StyD4I CCNGG 2 cut(s) 260, 338
TaaI ACNGT 2 cut(s) 172, 274
TaiI ACGT 1 cut(s) 395
TaqI TCGA 4 cut(s) 120, 283, 488, 540
TaqII GACCGA 1 cut(s) 10
TasI AATT 5 cut(s) 77, 460, 601, 620, 947
TatI WGTACW 1 cut(s) 1001
TauI GCSGC 2 cut(s) 161, 406
Tru1I TTAA 4 cut(s) 311, 507, 651, 1085
Tru9I TTAA 4 cut(s) 311, 507, 651, 1085
TseFI GTSAC 2 cut(s) 348, 781
TseI GCWGC 2 cut(s) 375, 873
Tsp45I GTSAC 2 cut(s) 348, 781
TspDTI ATGAA 7 cut(s) 428, 698, 783, 815, 896, 977, 992
TspGWI ACGGA 1 cut(s) 14
VneI GTGCAC 1 cut(s) 886
VpaK11BI GGWCC 5 cut(s) 22, 93, 232, 237, 264
XapI RAATTY 2 cut(s) 77, 601
XspI CTAG 2 cut(s) 32, 615
Zsp2I ATGCAT 1 cut(s) 829
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.