Rroxscaffold_4G00323710

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0004806
Physical Location & Seq
Reverse (-)
54639893 .. 54644668
4776 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00323710.1

Sequence Viewer

Length: 1710 bp
ATGCTAATCTCCAATCTCTCAAAGCTTCCCCCAATCTCTTCTCTCACCCATCTTCTTCGAACTCTCTCATCCATTGCTGTTCCATCTCACAACCACATATCACATCTTCTACTCGAACAAAAATCAGCCACCCAGGTCCTCGACACCTTCCAATGGGCCTCCAAACTTCCCAGCTTCACCCACTCCCCGTCCACTTACCGAGCCCTCATCCGCAAGCTATGCACCTTTCGCCGCTTCGACATTGCCCACCAAGTGCTCGACGAAATGCCCCACTCAATTGGCCTACCCCCAGATGACCACATTTTCGTCACACTGATTCATGGCCTCGGCCGAGCCCATTTGGTGAAGCAAGCGATCAAGGTGCTTGACTTGGTTCGCAAGTATAACCAGAAACCTTCTCTCAAGATATTCAATTCGATACTTGATGTTCTTGTGAAGGAGGATATAGATGTAGCTAGGGAGTTTTATAGGAAGAAGATGATGGCAAGTGGCGTCAAGGGTGATGATTATACTTTTGGTATCTTGATGAAAGGTCTTTGTTTGACGAATCGGATTGGTGATGGGTTTAAGCTTTTGCAAGCTATTAAGTCGAGGGGAGTTGCGCCGAATACTGTGGTTTATAACACATTGCTGCATGCACTTTGCAGGAATGGGAAAGTTGGGAGAGCCAGAAGCTTGATGAATGAGATGGAAGACCCCAATGATGTGACTTTTAATATTTTGATATCTGGTTATTGTGGAGAAGAGAATTTAGTGCAGGCGCTTGTTATGTTAGAGAAGTGCTTTGGTCTGGGGTATGTGCCTGATGTTGTCACGACAACCAAGGTGTTGGAAATTCTGTGCAATGATGGTCGGGTAATGGAGGCTGTCAAGGTTATAGAGAGAGTGGAGAGCAATGGAAGGTTGGTTGATGTTGTGGCATATAATACCTTGATTAAGGGTTACTGTCGGTTAGGGAAAGCAAAACTTGGTCTTCGCATTTTGAAGGAGATGGAGAGAAAAGGGTGTCTTCCAAATGTTGATACCTACAATGTCTTGATCTCGGGTTTTTGTGAGTCTGGGATGTTGGATAAAGCTCTTGATCTGTTTAATGATATGAAAACAGATGGCATCAATTGGAATTTTGCTACATATGATACGTTAATAAGAGGCTTGTGTTCAGGAGGAAGAACTGAAGATGGGTTAAAAATTTTGGATTTGATGAATGAGAGCAAAGATGGTTGTAGGGGTCGAATAGGTCCTTTTAATAGTGTCTTGTATGGCATGTATAAGGAAAAACGTTTGGACGAAGCACTTGAGTTTCTTGCCAATATGGGTAAACTATTTCCCAGAGCTGTTGATAGGAGCTTTAGGATTTTAGGTTTCTGTGAGGAGGGTGCCACTGAGATTGCAAAGAAGGTCTATGATCAGATGATTGTGGAAAGGGCAGTCCCATGTGTTTTGATTTATGACTATCTAATCCATAGATTTTGCCAACAAGGGTGTGTTCGTCAAGCCTTTGAGCTTATGAATGAGATGATTGCTCATTGTTACTTTCCTGTTTCATCGACTTTCAATGTTCTGATTAACGGGTTTTGTGAGCAAGGAAAAGTTGGTAGTGCGCTAAAGCTCCTCGATGAGATGATTGGTAGAGGTTGTTTACCTGATATAGAAAGTTATAGTCATTTGGTAGGTGCTTTTTGCCAGAAGGGGATTTTCAGAAAGCTTTAA

Protein Analysis

569

Amino Acids

63.9

Weight (kDa)

8.63

Isoelectric Point (pI)

27.99

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_3 PF13812 190 - 246 5.7e-07 Pentatricopeptide repeat domain
PPR_1 PF12854 198 - 231 2e-11 PPR repeat
PPR_2 PF13041 202 - 246 1.6e-14 PPR repeat family
PPR PF01535 205 - 231 2.3e-06 PPR repeat
PPR_1 PF12854 233 - 260 3.7e-06 PPR repeat
TPR_24 PF23276 234 - 330 1.8e-07 Fungal tetratrico peptide repeats
PPR_3 PF13812 292 - 349 2.1e-13 Pentatricopeptide repeat domain
PPR_1 PF12854 303 - 332 3e-07 PPR repeat
PPR_2 PF13041 304 - 351 9e-19 PPR repeat family
PPR PF01535 306 - 336 1.9e-08 PPR repeat
PPR_1 PF12854 334 - 367 9.6e-14 PPR repeat
PPR_2 PF13041 338 - 386 3.5e-17 PPR repeat family
PPR PF01535 342 - 371 4.9e-10 PPR repeat
PPR_1 PF12854 511 - 541 1.3e-09 PPR repeat
PPR_2 PF13041 515 - 562 1.9e-13 PPR repeat family
PPR PF01535 516 - 546 5.7e-08 PPR repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 621
AccB1I GGYRCC 1 cut(s) 1376
AciI CCGC 2 cut(s) 211, 232
AclI AACGTT 1 cut(s) 1279
AcoI YGGCCR 1 cut(s) 328
AcsI RAATTY 4 cut(s) 748, 834, 1120, 1188
AcuI CTGAAG 1 cut(s) 1194
AcyI GRCGYC 1 cut(s) 492
AdeI CACNNNGTG 1 cut(s) 253
AfiI CCNNNNNNNGG 1 cut(s) 153
AgsI TTSAA 3 cut(s) 412, 985, 1555
AjnI CCWGG 1 cut(s) 132
Alw21I GWGCWC 1 cut(s) 258
Ama87I CYCGRG 1 cut(s) 1042
AoxI GGCC 4 cut(s) 156, 280, 322, 328
ApeKI GCWGC 1 cut(s) 631
ApoI RAATTY 4 cut(s) 748, 834, 1120, 1188
ArsI GACNNNNNNTTYG 2 cut(s) 287, 319
AspLEI GCGC 3 cut(s) 604, 763, 1603
AspS9I GGNCC 3 cut(s) 136, 156, 1238
AsuHPI GGTGA 5 cut(s) 37, 169, 355, 512, 569
AsuII TTCGAA 1 cut(s) 58
AvaI CYCGRG 1 cut(s) 1042
AvaII GGWCC 2 cut(s) 136, 1238
BanI GGYRCC 1 cut(s) 1376
BanII GRGCYC 2 cut(s) 205, 337
BbsI GAAGAC 3 cut(s) 699, 965, 1001
Bbv12I GWGCWC 1 cut(s) 258
BbvI GCAGC 1 cut(s) 618
BcgI CGANNNNNNTGC 2 cut(s) 343, 377
BciT130I CCWGG 1 cut(s) 134
BclI TGATCA 1 cut(s) 1405
BfaI CTAG 1 cut(s) 456
BfoI RGCGCY 1 cut(s) 764
BisI GCNGC 2 cut(s) 232, 632
BlsI GCNGC 2 cut(s) 233, 633
Bme1390I CCNGG 1 cut(s) 134
Bme18I GGWCC 2 cut(s) 136, 1238
BmeT110I CYCGRG 1 cut(s) 1042
BmgT120I GGNCC 3 cut(s) 136, 156, 1238
BmiI GGNNCC 1 cut(s) 1378
BmrFI CCNGG 1 cut(s) 134
BmsI GCATC 1 cut(s) 1119
BpiI GAAGAC 3 cut(s) 699, 965, 1001
Bpu14I TTCGAA 1 cut(s) 58
BpuEI CTTGAG 2 cut(s) 386, 1316
BsaHI GRCGYC 1 cut(s) 492
BsaJI CCNNGG 3 cut(s) 132, 325, 822
Bsc4I CCNNNNNNNGG 1 cut(s) 153
Bse3DI GCAATG 5 cut(s) 72, 240, 626, 850, 901
BseBI CCWGG 1 cut(s) 134
BseDI CCNNGG 3 cut(s) 132, 325, 822
BseGI GGATG 3 cut(s) 68, 207, 1068
BseLI CCNNNNNNNGG 1 cut(s) 153
BseMI GCAATG 5 cut(s) 72, 240, 626, 850, 901
BseMII CTCAG 1 cut(s) 1374
BseRI GAGGAG 2 cut(s) 1385, 1601
BseX3I CGGCCG 1 cut(s) 328
BseXI GCAGC 1 cut(s) 618
BseYI CCCAGC 1 cut(s) 170
BsgI GTGCAG 1 cut(s) 776
Bsh1285I CGRYCG 1 cut(s) 331
BshFI GGCC 4 cut(s) 158, 282, 324, 330
BshNI GGYRCC 1 cut(s) 1376
BsiEI CGRYCG 1 cut(s) 331
BsiHKAI GWGCWC 1 cut(s) 258
BsiHKCI CYCGRG 1 cut(s) 1042
BslFI GGGAC 1 cut(s) 1415
BslI CCNNNNNNNGG 1 cut(s) 153
BsmFI GGGAC 1 cut(s) 1415
BsnI GGCC 4 cut(s) 158, 282, 324, 330
BsoBI CYCGRG 1 cut(s) 1042
Bsp119I TTCGAA 1 cut(s) 58
Bsp1286I GDGCHC 3 cut(s) 205, 258, 337
Bsp143I GATC 4 cut(s) 354, 1038, 1081, 1405
BspACI CCGC 2 cut(s) 211, 232
BspANI GGCC 4 cut(s) 158, 282, 324, 330
BspCNI CTCAG 1 cut(s) 1375
BspLI GGNNCC 1 cut(s) 1378
BspT104I TTCGAA 1 cut(s) 58
BspT107I GGYRCC 1 cut(s) 1376
BsrDI GCAATG 5 cut(s) 72, 240, 626, 850, 901
BssECI CCNNGG 3 cut(s) 132, 325, 822
BssMI GATC 4 cut(s) 354, 1038, 1081, 1405
BssNI GRCGYC 1 cut(s) 492
BssT1I CCWWGG 1 cut(s) 822
Bst2UI CCWGG 1 cut(s) 134
Bst4CI ACNGT 2 cut(s) 613, 947
Bst6I CTCTTC 2 cut(s) 43, 738
BstACI GRCGYC 1 cut(s) 492
BstAPI GCANNNNNTGC 1 cut(s) 219
BstBI TTCGAA 1 cut(s) 58
BstC8I GCNNGC 5 cut(s) 215, 351, 579, 636, 759
BstDEI CTNAG 1 cut(s) 1383
BstF5I GGATG 3 cut(s) 68, 207, 1068
BstH2I RGCGCY 1 cut(s) 764
BstHHI GCGC 3 cut(s) 604, 763, 1603
BstKTI GATC 4 cut(s) 357, 1041, 1084, 1408
BstMBI GATC 4 cut(s) 354, 1038, 1081, 1405
BstMCI CGRYCG 1 cut(s) 331
BstMWI GCNNNNNNNGC 2 cut(s) 219, 228
BstNI CCWGG 1 cut(s) 134
BstNSI RCATGY 2 cut(s) 638, 1267
BstSCI CCNGG 1 cut(s) 132
BstV1I GCAGC 1 cut(s) 618
BstV2I GAAGAC 3 cut(s) 699, 965, 1001
BstXI CCANNNNNNTGG 2 cut(s) 278, 829
BstZI CGGCCG 1 cut(s) 328
BsuRI GGCC 4 cut(s) 158, 282, 324, 330
BtsCI GGATG 3 cut(s) 68, 207, 1068
BtsIMutI CAGTG 2 cut(s) 311, 1380
Cac8I GCNNGC 5 cut(s) 215, 351, 579, 636, 759
CfoI GCGC 3 cut(s) 604, 763, 1603
Cfr13I GGNCC 3 cut(s) 136, 156, 1238
CseI GACGC 1 cut(s) 481
CspCI CAANNNNNGTGG 2 cut(s) 1369, 1404
CviAII CATG 4 cut(s) 320, 635, 1264, 1434
DdeI CTNAG 1 cut(s) 1383
DpnI GATC 4 cut(s) 356, 1040, 1083, 1407
DpnII GATC 4 cut(s) 354, 1038, 1081, 1405
DraIII CACNNNGTG 1 cut(s) 253
EaeI YGGCCR 1 cut(s) 328
EagI CGGCCG 1 cut(s) 328
Eam1104I CTCTTC 2 cut(s) 43, 738
EarI CTCTTC 2 cut(s) 43, 738
EclXI CGGCCG 1 cut(s) 328
Eco130I CCWWGG 1 cut(s) 822
Eco24I GRGCYC 2 cut(s) 205, 337
Eco32I GATATC 1 cut(s) 726
Eco47I GGWCC 2 cut(s) 136, 1238
Eco52I CGGCCG 1 cut(s) 328
Eco57I CTGAAG 1 cut(s) 1194
Eco88I CYCGRG 1 cut(s) 1042
EcoO109I RGGNCCY 2 cut(s) 136, 1238
EcoRII CCWGG 1 cut(s) 132
EcoRV GATATC 1 cut(s) 726
EcoT14I CCWWGG 1 cut(s) 822
EcoT38I GRGCYC 2 cut(s) 205, 337
ErhI CCWWGG 1 cut(s) 822
FaeI CATG 4 cut(s) 323, 638, 1267, 1437
FalI AAGNNNNNCTT 4 cut(s) 951, 983, 993, 1025
FaqI GGGAC 1 cut(s) 1415
FatI CATG 4 cut(s) 319, 634, 1263, 1433
FauNDI CATATG 1 cut(s) 1132
FbaI TGATCA 1 cut(s) 1405
Fnu4HI GCNGC 2 cut(s) 232, 632
FokI GGATG 3 cut(s) 55, 194, 1075
FriOI GRGCYC 2 cut(s) 205, 337
Fsp4HI GCNGC 2 cut(s) 232, 632
FspBI CTAG 1 cut(s) 456
GlaI GCGC 3 cut(s) 603, 762, 1602
GluI GCNGC 2 cut(s) 232, 632
GsaI CCCAGC 1 cut(s) 174
HaeII RGCGCY 1 cut(s) 764
HaeIII GGCC 4 cut(s) 158, 282, 324, 330
HgaI GACGC 1 cut(s) 481
HhaI GCGC 3 cut(s) 604, 763, 1603
Hin1I GRCGYC 1 cut(s) 492
Hin1II CATG 4 cut(s) 323, 638, 1267, 1437
Hin6I GCGC 3 cut(s) 602, 761, 1601
HinP1I GCGC 3 cut(s) 602, 761, 1601
HindIII AAGCTT 4 cut(s) 23, 569, 673, 1703
HinfI GANTC 3 cut(s) 316, 547, 1055
HphI GGTGA 5 cut(s) 37, 169, 355, 512, 569
Hpy166II GTNNAC 3 cut(s) 192, 1319, 1640
Hpy188I TCNGA 4 cut(s) 552, 1410, 1563, 1700
Hpy188III TCNNGA 6 cut(s) 403, 523, 814, 1036, 1079, 1161
Hpy8I GTNNAC 3 cut(s) 192, 1319, 1640
Hpy99I CGWCG 1 cut(s) 263
HpyAV CCTTC 7 cut(s) 157, 405, 430, 894, 979, 1390, 1681
HpyCH4III ACNGT 2 cut(s) 613, 947
HpyCH4IV ACGT 2 cut(s) 1139, 1279
HpyCH4V TGCA 8 cut(s) 222, 577, 634, 638, 645, 757, 843, 1391
HpyF10VI GCNNNNNNNGC 2 cut(s) 219, 228
HpyF3I CTNAG 1 cut(s) 1383
HpySE526I ACGT 2 cut(s) 1139, 1279
Hsp92I GRCGYC 1 cut(s) 492
Hsp92II CATG 4 cut(s) 323, 638, 1267, 1437
HspAI GCGC 3 cut(s) 602, 761, 1601
Ksp22I TGATCA 1 cut(s) 1405
Kzo9I GATC 4 cut(s) 354, 1038, 1081, 1405
LmnI GCTCC 2 cut(s) 1344, 1614
Lsp1109I GCAGC 1 cut(s) 618
LweI GCATC 1 cut(s) 1119
MaeI CTAG 1 cut(s) 456
MaeII ACGT 2 cut(s) 1139, 1279
MaeIII GTNAC 5 cut(s) 307, 706, 811, 941, 1529
MalI GATC 4 cut(s) 356, 1040, 1083, 1407
MboI GATC 4 cut(s) 354, 1038, 1081, 1405
MfeI CAATTG 2 cut(s) 276, 1114
MhlI GDGCHC 3 cut(s) 205, 258, 337
MluCI AATT 7 cut(s) 276, 412, 748, 834, 1114, 1120, 1188
MlyI GAGTC 1 cut(s) 1064
MmeI TCCRAC 2 cut(s) 810, 1047
MspR9I CCNGG 1 cut(s) 134
MunI CAATTG 2 cut(s) 276, 1114
MvaI CCWGG 1 cut(s) 134
MwoI GCNNNNNNNGC 2 cut(s) 219, 228
NdeI CATATG 1 cut(s) 1132
NdeII GATC 4 cut(s) 354, 1038, 1081, 1405
NlaIII CATG 4 cut(s) 323, 638, 1267, 1437
NlaIV GGNNCC 1 cut(s) 1378
NmeAIII GCCGAG 2 cut(s) 306, 356
NmuCI GTSAC 3 cut(s) 307, 706, 811
NspI RCATGY 2 cut(s) 638, 1267
NspV TTCGAA 1 cut(s) 58
PaeI GCATGC 1 cut(s) 638
PfeI GAWTC 2 cut(s) 316, 547
PkrI GCNGC 2 cut(s) 233, 633
PleI GAGTC 1 cut(s) 1063
PpsI GAGTC 1 cut(s) 1063
PpuMI RGGWCCY 2 cut(s) 136, 1238
PsiI TTATAA 1 cut(s) 621
Psp1406I AACGTT 1 cut(s) 1279
Psp5II RGGWCCY 2 cut(s) 136, 1238
Psp6I CCWGG 1 cut(s) 132
PspFI CCCAGC 1 cut(s) 170
PspGI CCWGG 1 cut(s) 132
PspN4I GGNNCC 1 cut(s) 1378
PspPI GGNCC 3 cut(s) 136, 156, 1238
PspPPI RGGWCCY 2 cut(s) 136, 1238
SatI GCNGC 2 cut(s) 232, 632
Sau3AI GATC 4 cut(s) 354, 1038, 1081, 1405
Sau96I GGNCC 3 cut(s) 136, 156, 1238
SchI GAGTC 1 cut(s) 1064
ScrFI CCNGG 1 cut(s) 134
SduI GDGCHC 3 cut(s) 205, 258, 337
SfaNI GCATC 1 cut(s) 1119
SfuI TTCGAA 1 cut(s) 58
SinI GGWCC 2 cut(s) 136, 1238
SmlI CTYRAG 2 cut(s) 401, 1295
SmoI CTYRAG 2 cut(s) 401, 1295
SphI GCATGC 1 cut(s) 638
Sse9I AATT 7 cut(s) 276, 412, 748, 834, 1114, 1120, 1188
SsiI CCGC 2 cut(s) 211, 232
SspI AATATT 1 cut(s) 718
SspMI CTAG 1 cut(s) 456
StyD4I CCNGG 1 cut(s) 132
StyI CCWWGG 1 cut(s) 822
TaaI ACNGT 2 cut(s) 613, 947
TaiI ACGT 2 cut(s) 1142, 1282
TasI AATT 7 cut(s) 276, 412, 748, 834, 1114, 1120, 1188
TauI GCSGC 1 cut(s) 234
TfiI GAWTC 2 cut(s) 316, 547
TscAI CASTG 2 cut(s) 318, 1387
TseFI GTSAC 3 cut(s) 307, 706, 811
TseI GCWGC 1 cut(s) 631
Tsp45I GTSAC 3 cut(s) 307, 706, 811
TspDTI ATGAA 7 cut(s) 308, 542, 695, 1112, 1217, 1523, 1533
TspRI CASTG 2 cut(s) 318, 1387
VpaK11BI GGWCC 2 cut(s) 136, 1238
XapI RAATTY 4 cut(s) 748, 834, 1120, 1188
XceI RCATGY 2 cut(s) 638, 1267
XspI CTAG 1 cut(s) 456
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.