Rw3G022820

Pentatricopeptide repeat-containing protein At2g13420, mitochondrial-like

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0006370
Physical Location & Seq
Forward (+)
28212328 .. 28220373
8046 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G022820.1

Sequence Viewer

Length: 1419 bp
ATGGCACAATGTCGCTTCTCCTCCTCTCTTCTTCGTCTTCTCCGTTCAGCTTGCCGGTTCTCCTCACTCCCCAACCCAACAACAACGACCCAAAACGACGCCGAACTGGTATCAAACATCCTCCTCCACCACCACAACCCCTTCCACGCCATGGAGTCCTCTCTCCAGCTCCACGGCATCACTCTCTCCCCCGACCTCCTCCACCACACTCTCCTCCGCCTCAAGCACAATTCCAAAATCGCCCTCGCCCTCTTCCACTACGCCAAGTCCCTCCCCTCCCCCCCGCCCCTCACCTCCCACGCCTTCCACCTCCTCATCGACATCGTCGCCAAGGTCCGCCAGTACGACGTCGCTTGGCAGCTCATCCTCGAAATGGACCGCCACAACCTCACCCCCACCGCCGCCACCTTCCTCATCCTCATCCGCCGCCTCATCGCCTCTGGCCTCACCCGCCAGGCCGTCCGGGCCTTCGACGACATCGAGACCTTCGTCCTGACCCGCCCCACCACCCAAGACTTCTGCTTCTTACTCGACACCCTCTGTAAATACGGCTACGTTAAGCTCGCGGCTGAAGTTTTCAACAAAAGGAAGCATGACTATGTGGCCGATGTGAAAATGTACACTGTTCTGGTTTACGGGTGGTGTAAGATCGGCCGTTTCGATATGGCGGAGAGGTTCTTGAGGGATATGATTGAGCGTGGTATTGAGCCCAATGTGGTTACTTACAATGTGTTTCTGGATGGGATTTGTAGGAAGGCGAGTTTGCACCCTCAGGACAGGTTTGAGAGGACCATAAGAAATGCACTGAAGGTGTTCGACGAAATGTCCAGCAGAGGCATTGAGCCGGACGTGACGAGTTTTTCGATCCTTCTTCATTGTCTTTGCTCTTGCGGGAGGCTTGAGGAAGCGGAGGAGTTGCTTGGTGAGATGGTGAGGAATGGGGTTAGTCCCTCTGCGGCTACGTATAATTGTTTCTTCAAAGAGTACAGGGGGAGAAAGGACTCGGAAAGTGCTTTGAAGTTGTATAGGAAGATGAAGGAGGATAGATTGTTTGCGCCGAGTGTGCACACTTATAATATTTTGGTGGGGATGTTTTTGCAGTTGAATCGAGTGGAGACTGTGAGAGAGATATGGGATGACATGAAAGAGAGCGGGGCGGGGCCGGATTTGGATTCGTATACGATGTTGATTCATGGGTTATGTGAGAAGCAGAAGTGGAGAGAGGCGTGCCAGTTTTTTGTGGAGATGATAGAGAAGGGGCTTCTTCCTCAGAAAGTTACTTTTGAGACGCTTTACAGAGGGTTAATACAGTCTGATATGTTGAGAACTTGGAGAAGATTGAAGAAGAAGCTCGATGAAGAGTCTGTTACTTTTGGATCCGAGTTTCAAAATTATCACCTTAAGCCATACAGGAGATGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
No pathways identified.
Pfam Domains
Protein Families
PPR PPR_2 PPR_3

Protein Analysis

472

Amino Acids

54.73

Weight (kDa)

8.79

Isoelectric Point (pI)

48.9

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 101 - 144 7.7e-06 PPR repeat family
PPR_3 PF13812 202 - 247 7.4e-06 Pentatricopeptide repeat domain
PPR_2 PF13041 203 - 251 7.7e-14 PPR repeat family
PPR_long PF17177 229 - 345 5e-08 Pentacotripeptide-repeat region of PRORP
PPR_2 PF13041 265 - 295 1e-08 PPR repeat family
PPR_3 PF13812 270 - 329 4.6e-10 Pentatricopeptide repeat domain
PPR_1 PF12854 278 - 311 3.8e-11 PPR repeat
PPR PF01535 286 - 315 1.2e-07 PPR repeat
PPR_2 PF13041 287 - 328 1.5e-10 PPR repeat family
PPR_2 PF13041 321 - 363 2.3e-07 PPR repeat family
PPR_2 PF13041 353 - 401 4.2e-12 PPR repeat family
PPR_2 PF13041 388 - 435 2.6e-10 PPR repeat family
PPR_1 PF12854 388 - 416 6.5e-07 PPR repeat
PPR PF01535 392 - 421 1e-05 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) 1074
AatII GACGTC 1 cut(s) 351
AccB7I CCANNNNNTGG 1 cut(s) 151
AccBSI CCGCTC 1 cut(s) 1152
AccI GTMKAC 1 cut(s) 1178
AccII CGCG 1 cut(s) 566
AclWI GGATC 3 cut(s) 859, 1371, 1384
AcoI YGGCCR 2 cut(s) 603, 652
AcuI CTGAAG 2 cut(s) 591, 827
AcyI GRCGYC 2 cut(s) 99, 348
AfaI GTAC 3 cut(s) 344, 620, 986
AfiI CCNNNNNNNGG 2 cut(s) 151, 373
AflII CTTAAG 1 cut(s) 1400
AgsI TTSAA 6 cut(s) 580, 979, 1018, 1105, 1342, 1388
AhdI GACNNNNNGTC 1 cut(s) 823
AjiI CACGTC 1 cut(s) 850
AjnI CCWGG 1 cut(s) 453
AluBI AGCT 5 cut(s) 50, 169, 361, 562, 1351
AluI AGCT 5 cut(s) 50, 169, 361, 562, 1351
Alw21I GWGCWC 1 cut(s) 1068
Alw26I GTCTC 3 cut(s) 476, 1109, 1280
Alw44I GTGCAC 1 cut(s) 1064
AlwI GGATC 3 cut(s) 859, 1371, 1384
AoxI GGCC 6 cut(s) 442, 456, 465, 603, 652, 1160
ApaLI GTGCAC 1 cut(s) 1064
ApeKI GCWGC 1 cut(s) 358
ArsI GACNNNNNNTTYG 2 cut(s) 844, 876
Asp700I GAANNNNTTC 1 cut(s) 812
AspLEI GCGC 1 cut(s) 1057
AspS9I GGNCC 5 cut(s) 334, 376, 465, 789, 1160
AsuC2I CCSGG 1 cut(s) 464
AsuHPI GGTGA 6 cut(s) 283, 382, 439, 935, 943, 1388
AvaII GGWCC 3 cut(s) 334, 376, 789
AxyI CCTNAGG 1 cut(s) 771
BaeGI GKGCMC 1 cut(s) 1068
BamHI GGATCC 1 cut(s) 1376
BanII GRGCYC 1 cut(s) 711
BbsI GAAGAC 1 cut(s) 29
Bbv12I GWGCWC 1 cut(s) 1068
BbvI GCAGC 1 cut(s) 370
BccI CCATC 2 cut(s) 734, 922
BceAI ACGGC 4 cut(s) 190, 443, 565, 639
BcgI CGANNNNNNTGC 2 cut(s) 1088, 1122
BciT130I CCWGG 1 cut(s) 455
BcnI CCSGG 1 cut(s) 464
BcoDI GTCTC 3 cut(s) 476, 1109, 1280
BfrI CTTAAG 1 cut(s) 1400
BglI GCCNNNNNGGC 1 cut(s) 464
BisI GCNGC 5 cut(s) 359, 402, 427, 567, 957
BlsI GCNGC 5 cut(s) 360, 403, 428, 568, 958
Bme1390I CCNGG 2 cut(s) 455, 464
Bme18I GGWCC 3 cut(s) 334, 376, 789
BmeRI GACNNNNNGTC 1 cut(s) 823
BmgBI CACGTC 1 cut(s) 850
BmgT120I GGNCC 5 cut(s) 334, 376, 465, 789, 1160
BmiI GGNNCC 2 cut(s) 1161, 1378
BmrFI CCNGG 2 cut(s) 455, 464
BmsI GCATC 1 cut(s) 186
BoxI GACNNNNGTC 1 cut(s) 488
BpiI GAAGAC 1 cut(s) 29
BpmI CTGGAG 1 cut(s) 149
BpuEI CTTGAG 3 cut(s) 206, 700, 920
BpuMI CCSGG 1 cut(s) 464
BsaAI YACGTR 1 cut(s) 963
BsaHI GRCGYC 2 cut(s) 99, 348
BsaI GGTCTC 1 cut(s) 476
BsaJI CCNNGG 3 cut(s) 150, 172, 330
Bsc4I CCNNNNNNNGG 2 cut(s) 151, 373
Bse118I RCCGGY 1 cut(s) 54
Bse1I ACTGG 3 cut(s) 111, 340, 1231
Bse21I CCTNAGG 1 cut(s) 771
BseBI CCWGG 1 cut(s) 455
BseDI CCNNGG 3 cut(s) 150, 172, 330
BseGI GGATG 7 cut(s) 117, 363, 414, 420, 745, 1095, 1141
BseLI CCNNNNNNNGG 2 cut(s) 151, 373
BseMII CTCAG 2 cut(s) 785, 1283
BseNI ACTGG 3 cut(s) 111, 340, 1231
BseRI GAGGAG 8 cut(s) 10, 13, 52, 113, 188, 203, 302, 926
BseSI GKGCMC 1 cut(s) 1068
BseX3I CGGCCG 1 cut(s) 652
BseXI GCAGC 1 cut(s) 370
Bsh1236I CGCG 1 cut(s) 566
Bsh1285I CGRYCG 1 cut(s) 655
BshFI GGCC 6 cut(s) 444, 458, 467, 605, 654, 1162
BsiEI CGRYCG 1 cut(s) 655
BsiHKAI GWGCWC 1 cut(s) 1068
BsiSI CCGG 4 cut(s) 55, 463, 845, 1163
BslFI GGGAC 2 cut(s) 253, 933
BslI CCNNNNNNNGG 2 cut(s) 151, 373
BsmAI GTCTC 3 cut(s) 476, 1109, 1280
BsmBI CGTCTC 1 cut(s) 1280
BsmFI GGGAC 2 cut(s) 253, 933
BsnI GGCC 6 cut(s) 444, 458, 467, 605, 654, 1162
Bso31I GGTCTC 1 cut(s) 476
Bsp1286I GDGCHC 2 cut(s) 711, 1068
Bsp1407I TGTACA 1 cut(s) 618
Bsp143I GATC 3 cut(s) 648, 864, 1376
Bsp19I CCATGG 1 cut(s) 150
BspANI GGCC 6 cut(s) 444, 458, 467, 605, 654, 1162
BspCNI CTCAG 2 cut(s) 784, 1282
BspFNI CGCG 1 cut(s) 566
BspLI GGNNCC 2 cut(s) 1161, 1378
BspPI GGATC 3 cut(s) 859, 1371, 1384
BspTI CTTAAG 1 cut(s) 1400
BspTNI GGTCTC 1 cut(s) 476
BsrBI CCGCTC 1 cut(s) 1152
BsrFI RCCGGY 1 cut(s) 54
BsrGI TGTACA 1 cut(s) 618
BsrI ACTGG 3 cut(s) 111, 340, 1231
BssAI RCCGGY 1 cut(s) 54
BssECI CCNNGG 3 cut(s) 150, 172, 330
BssMI GATC 3 cut(s) 648, 864, 1376
BssNAI GTATAC 1 cut(s) 1179
BssNI GRCGYC 2 cut(s) 99, 348
BssT1I CCWWGG 2 cut(s) 150, 330
Bst1107I GTATAC 1 cut(s) 1179
Bst2UI CCWGG 1 cut(s) 455
Bst4CI ACNGT 3 cut(s) 625, 1120, 1311
Bst6I CTCTTC 3 cut(s) 33, 257, 1353
BstACI GRCGYC 2 cut(s) 99, 348
BstAFI CTTAAG 1 cut(s) 1400
BstAUI TGTACA 1 cut(s) 618
BstBAI YACGTR 1 cut(s) 963
BstC8I GCNNGC 3 cut(s) 52, 564, 1228
BstDEI CTNAG 2 cut(s) 771, 1269
BstDSI CCRYGG 2 cut(s) 150, 172
BstF5I GGATG 7 cut(s) 117, 363, 414, 420, 745, 1095, 1141
BstFNI CGCG 1 cut(s) 566
BstHHI GCGC 1 cut(s) 1057
BstKTI GATC 3 cut(s) 651, 867, 1379
BstMAI GTCTC 3 cut(s) 476, 1109, 1280
BstMBI GATC 3 cut(s) 648, 864, 1376
BstMCI CGRYCG 1 cut(s) 655
BstMWI GCNNNNNNNGC 3 cut(s) 450, 464, 1063
BstNI CCWGG 1 cut(s) 455
BstPAI GACNNNNGTC 1 cut(s) 488
BstSCI CCNGG 2 cut(s) 453, 462
BstSLI GKGCMC 1 cut(s) 1068
BstSNI TACGTA 1 cut(s) 963
BstUI CGCG 1 cut(s) 566
BstV1I GCAGC 1 cut(s) 370
BstV2I GAAGAC 1 cut(s) 29
BstX2I RGATCY 1 cut(s) 1376
BstYI RGATCY 1 cut(s) 1376
BstZ17I GTATAC 1 cut(s) 1179
BstZI CGGCCG 1 cut(s) 652
Bsu36I CCTNAGG 1 cut(s) 771
BsuRI GGCC 6 cut(s) 444, 458, 467, 605, 654, 1162
BtgI CCRYGG 2 cut(s) 150, 172
BtgZI GCGATG 1 cut(s) 418
BtrI CACGTC 1 cut(s) 850
BtsCI GGATG 7 cut(s) 117, 363, 414, 420, 745, 1095, 1141
BtsIMutI CAGTG 2 cut(s) 621, 803
Cac8I GCNNGC 3 cut(s) 52, 564, 1228
CfoI GCGC 1 cut(s) 1057
Cfr10I RCCGGY 1 cut(s) 54
Cfr13I GGNCC 5 cut(s) 334, 376, 465, 789, 1160
CseI GACGC 2 cut(s) 107, 1297
Csp6I GTAC 3 cut(s) 343, 619, 985
CviAII CATG 4 cut(s) 151, 593, 1141, 1193
CviQI GTAC 3 cut(s) 343, 619, 985
DdeI CTNAG 2 cut(s) 771, 1269
DpnI GATC 3 cut(s) 650, 866, 1378
DpnII GATC 3 cut(s) 648, 864, 1376
DriI GACNNNNNGTC 1 cut(s) 823
EaeI YGGCCR 2 cut(s) 603, 652
EagI CGGCCG 1 cut(s) 652
Eam1104I CTCTTC 3 cut(s) 33, 257, 1353
Eam1105I GACNNNNNGTC 1 cut(s) 823
EarI CTCTTC 3 cut(s) 33, 257, 1353
EciI GGCGGA 4 cut(s) 206, 326, 413, 683
EclXI CGGCCG 1 cut(s) 652
Eco105I TACGTA 1 cut(s) 963
Eco130I CCWWGG 2 cut(s) 150, 330
Eco24I GRGCYC 1 cut(s) 711
Eco31I GGTCTC 1 cut(s) 476
Eco47I GGWCC 3 cut(s) 334, 376, 789
Eco52I CGGCCG 1 cut(s) 652
Eco57I CTGAAG 2 cut(s) 591, 827
Eco81I CCTNAGG 1 cut(s) 771
EcoRII CCWGG 1 cut(s) 453
EcoT14I CCWWGG 2 cut(s) 150, 330
EcoT38I GRGCYC 1 cut(s) 711
ErhI CCWWGG 2 cut(s) 150, 330
Esp3I CGTCTC 1 cut(s) 1280
FaeI CATG 4 cut(s) 154, 596, 1144, 1196
FaqI GGGAC 2 cut(s) 253, 933
FatI CATG 4 cut(s) 150, 592, 1140, 1192
FauI CCCGC 6 cut(s) 291, 458, 506, 884, 1145, 1150
FblI GTMKAC 1 cut(s) 1178
Fnu4HI GCNGC 5 cut(s) 359, 402, 427, 567, 957
FokI GGATG 7 cut(s) 104, 350, 401, 407, 752, 1102, 1148
FriOI GRGCYC 1 cut(s) 711
Fsp4HI GCNGC 5 cut(s) 359, 402, 427, 567, 957
GlaI GCGC 1 cut(s) 1056
GluI GCNGC 5 cut(s) 359, 402, 427, 567, 957
GsuI CTGGAG 1 cut(s) 149
HaeIII GGCC 6 cut(s) 444, 458, 467, 605, 654, 1162
HapII CCGG 4 cut(s) 55, 463, 845, 1163
HgaI GACGC 2 cut(s) 107, 1297
HhaI GCGC 1 cut(s) 1057
Hin1I GRCGYC 2 cut(s) 99, 348
Hin1II CATG 4 cut(s) 154, 596, 1144, 1196
Hin6I GCGC 1 cut(s) 1055
HinP1I GCGC 1 cut(s) 1055
HinfI GANTC 6 cut(s) 155, 1001, 1105, 1172, 1189, 1361
HpaII CCGG 4 cut(s) 55, 463, 845, 1163
HphI GGTGA 6 cut(s) 283, 382, 439, 935, 943, 1388
Hpy166II GTNNAC 4 cut(s) 621, 634, 1066, 1179
Hpy188I TCNGA 4 cut(s) 1006, 1272, 1315, 1381
Hpy188III TCNNGA 5 cut(s) 481, 493, 679, 737, 773
Hpy8I GTNNAC 4 cut(s) 621, 634, 1066, 1179
Hpy99I CGWCG 6 cut(s) 101, 329, 350, 353, 476, 821
HpyCH4III ACNGT 3 cut(s) 625, 1120, 1311
HpyCH4IV ACGT 4 cut(s) 348, 555, 849, 962
HpyCH4V TGCA 4 cut(s) 766, 803, 1066, 1099
HpyF10VI GCNNNNNNNGC 3 cut(s) 450, 464, 1063
HpyF3I CTNAG 2 cut(s) 771, 1269
HpySE526I ACGT 4 cut(s) 348, 555, 849, 962
Hsp92I GRCGYC 2 cut(s) 99, 348
Hsp92II CATG 4 cut(s) 154, 596, 1144, 1196
HspAI GCGC 1 cut(s) 1055
Kzo9I GATC 3 cut(s) 648, 864, 1376
LmnI GCTCC 1 cut(s) 174
Lsp1109I GCAGC 1 cut(s) 370
LweI GCATC 1 cut(s) 186
MaeII ACGT 4 cut(s) 348, 555, 849, 962
MaeIII GTNAC 4 cut(s) 718, 850, 1276, 1366
MalI GATC 3 cut(s) 650, 866, 1378
MbiI CCGCTC 1 cut(s) 1152
MboI GATC 3 cut(s) 648, 864, 1376
MflI RGATCY 1 cut(s) 1376
MhlI GDGCHC 2 cut(s) 711, 1068
MluCI AATT 3 cut(s) 229, 967, 1390
MlyI GAGTC 3 cut(s) 164, 995, 1370
MroXI GAANNNNTTC 1 cut(s) 812
MseI TTAA 3 cut(s) 558, 1304, 1401
MslI CAYNNNNRTG 1 cut(s) 597
MspCI CTTAAG 1 cut(s) 1400
MspI CCGG 4 cut(s) 55, 463, 845, 1163
MspR9I CCNGG 2 cut(s) 455, 464
MvaI CCWGG 1 cut(s) 455
MvnI CGCG 1 cut(s) 566
MwoI GCNNNNNNNGC 3 cut(s) 450, 464, 1063
NciI CCSGG 1 cut(s) 464
NcoI CCATGG 1 cut(s) 150
NdeII GATC 3 cut(s) 648, 864, 1376
NlaIII CATG 4 cut(s) 154, 596, 1144, 1196
NlaIV GGNNCC 2 cut(s) 1161, 1378
NmeAIII GCCGAG 1 cut(s) 1083
NmuCI GTSAC 1 cut(s) 850
PcsI WCGNNNNNNNCGW 5 cut(s) 40, 477, 486, 657, 860
PdmI GAANNNNTTC 1 cut(s) 812
PfeI GAWTC 3 cut(s) 1105, 1172, 1189
PflFI GACNNNGTC 1 cut(s) 323
PflMI CCANNNNNTGG 1 cut(s) 151
PkrI GCNGC 5 cut(s) 360, 403, 428, 568, 958
PleI GAGTC 3 cut(s) 163, 995, 1369
PpsI GAGTC 3 cut(s) 163, 995, 1369
Ppu21I YACGTR 1 cut(s) 963
PshAI GACNNNNGTC 1 cut(s) 488
PsiI TTATAA 1 cut(s) 1074
Psp6I CCWGG 1 cut(s) 453
PspGI CCWGG 1 cut(s) 453
PspN4I GGNNCC 2 cut(s) 1161, 1378
PspPI GGNCC 5 cut(s) 334, 376, 465, 789, 1160
PsuI RGATCY 1 cut(s) 1376
PsyI GACNNNGTC 1 cut(s) 323
RsaI GTAC 3 cut(s) 344, 620, 986
RsaNI GTAC 3 cut(s) 343, 619, 985
RseI CAYNNNNRTG 1 cut(s) 597
SaqAI TTAA 3 cut(s) 558, 1304, 1401
SatI GCNGC 5 cut(s) 359, 402, 427, 567, 957
Sau3AI GATC 3 cut(s) 648, 864, 1376
Sau96I GGNCC 5 cut(s) 334, 376, 465, 789, 1160
SchI GAGTC 3 cut(s) 164, 995, 1370
ScrFI CCNGG 2 cut(s) 455, 464
SduI GDGCHC 2 cut(s) 711, 1068
SfaNI GCATC 1 cut(s) 186
SfiI GGCCNNNNNGGCC 1 cut(s) 464
SinI GGWCC 3 cut(s) 334, 376, 789
SmiMI CAYNNNNRTG 1 cut(s) 597
SmlI CTYRAG 4 cut(s) 221, 679, 899, 1400
SmoI CTYRAG 4 cut(s) 221, 679, 899, 1400
SnaBI TACGTA 1 cut(s) 963
Sse9I AATT 3 cut(s) 229, 967, 1390
SspI AATATT 1 cut(s) 1078
StyD4I CCNGG 2 cut(s) 453, 462
StyI CCWWGG 2 cut(s) 150, 330
TaaI ACNGT 3 cut(s) 625, 1120, 1311
TaiI ACGT 4 cut(s) 351, 558, 852, 965
TasI AATT 3 cut(s) 229, 967, 1390
TatI WGTACW 2 cut(s) 618, 984
TauI GCSGC 4 cut(s) 404, 429, 569, 959
TfiI GAWTC 3 cut(s) 1105, 1172, 1189
Tru1I TTAA 3 cut(s) 558, 1304, 1401
Tru9I TTAA 3 cut(s) 558, 1304, 1401
TscAI CASTG 2 cut(s) 628, 810
TseFI GTSAC 1 cut(s) 850
TseI GCWGC 1 cut(s) 358
Tsp45I GTSAC 1 cut(s) 850
TspDTI ATGAA 5 cut(s) 863, 1049, 1157, 1181, 1371
TspGWI ACGGA 1 cut(s) 32
TspRI CASTG 2 cut(s) 628, 810
Tth111I GACNNNGTC 1 cut(s) 323
Van91I CCANNNNNTGG 1 cut(s) 151
Vha464I CTTAAG 1 cut(s) 1400
VneI GTGCAC 1 cut(s) 1064
VpaK11BI GGWCC 3 cut(s) 334, 376, 789
XmiI GTMKAC 1 cut(s) 1178
XmnI GAANNNNTTC 1 cut(s) 812
ZraI GACGTC 1 cut(s) 349
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.