Rh3DG034600

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3D
OG0016670
Physical Location & Seq
Forward (+)
2302017 .. 2303447
1431 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3DG034600.1

Sequence Viewer

Length: 1431 bp
ATGCACCATCTGCCAAGACTCAGATCTCTCTCCCTCTTAAACCTGAAACTAAAATCCACACACCAATTGAAGCAAGCCCATGCCCAGTTGATTACCAATGGTCTCAAATCAACTTCCATATATGGCAAGCTAATCCAGCAATGCTGTGCCTTATCAGACCCAGAAAGCACCAGCCTTTATGCCCATTTAGTATTCAGACACTTTGATGAGCCTAATCTGTTCCTGTTGAACACTTTGATTAGATGTACTCAACCTAAAGACTCCATTTTTCTTTTTGCCAATTGGGTTTCTAAAGCAAGCTTGTGTTTTGATGACTTTACCTACAAGTTTGTTCTTGGAGCTTGTGCTAGATTACCTTCAATACCAACATTAGTAGTAGGTAGAGAAGTTCATGCCCGGATAGTAAAAGAGGGCATCATATCAAACATTTTAGTGCAAACTACTTTACTACATTTTTATGCTAGTAATAAGGACCTTGATTCGGCACGAAAGGTGTTCGATGAAATGACTGAGAGAAATAGTGTTACGTGGAATGCAATGATCACGGGGTACTCTTCGCAAAGAGAAAGTGCCCGGGATGCATTGCTGTTGTTTCGGGACATGTTGGATTGTGATTCTGGGGTGAAACCTACTGATACTACTATGGTTTGTGTTCTCTCCGCGGCTTCTCAGTTGGGTGTGCTGGAAACTGGTGCTTGTATACATGGTTATGTAGAGAAGGCAATGCCTGCTCCTGATGGTGATGTTTTTATGGGAACTGGTCTTGTTGATATGTACTCGAAATGTGGAAGTGTTGATAGTGCTTTAACCATTTTTAAGCGAATGAAACAGAGAAATGTCTTGACTTGGACAGCAATGGCAACAGGGCTAGCTATTCATGGTAAGGGGAGTGAAGCACTGGAGGTTTTGGATGTAATGAAAGCTCATGGAACAAACCCAAATGAAGTGACTTTCACCAGCTTGCTTTCAGCTTGCTGCCATGTCGGGCTTGTTGAAGAAGGCCTGCATTTGTTCCATATGATGAAGACCAAGTTTGGAGTCACCCCTCATATGCAGCATTACGGTTGCATAGTTGACCTGCTTAGCCGAAGTGGGCATTTGAATGAGGCCTATGACTTTATAATAGCAATGCCAGTTGAACCTGATGCTGTCTTGTGGAGGAGTTTGCTAAGTGCATGCAAAGTTCATGGGAATGTCGCAATGGGAGAGAAGGTTGGGAAGAAGCTGCTTCGCATCCAGCTGACGCAGAGTTTTGCAGATGGAACTCCAAAGAGTGAAGACTATGTAGCTTTGTCGAACATTTATGCTTATGCCGAAAAGTGGGATGCTGTGGAGATGGTGAGAGAGGAGATGAAAGTCATGGGAATTGAAAATAAAGCTGGGTCTAGTTCTGTTCAAACTACTAGCAATCATGCCTCGGATGGGTTGTAG

Protein Analysis

476

Amino Acids

52.53

Weight (kDa)

6.83

Isoelectric Point (pI)

33.9

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PPR_2 PF13041 172 - 221 1.9e-06 PPR repeat family
PPR_2 PF13041 278 - 327 2.4e-11 PPR repeat family
PPR_3 PF13812 278 - 325 4.2e-06 Pentatricopeptide repeat domain
PPR_long PF17177 297 - 396 1.2e-06 Pentacotripeptide-repeat region of PRORP
PPR PF01535 316 - 343 3.5e-06 PPR repeat
E_motif PF20431 425 - 466 1.6e-09 E motif
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: OG0016670)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G18970
fragaria_vesca FvH4_6g02930
malus_domestica MD04G1224500.v1.1 MD12G1241200.v1.1
prunus_persica Prupe.6G343200_v2.0.a1
rosa_chinensis RchiOBHm_Chr3g0451131
rosa_laevigata RLG00000025687
rosa_multiflora Rmu_sc0039775.1_g000001 Rmu_ssc0000461.1_g000009
rosa_roxburghii Rroxscaffold_6G00428600
rosa_rugosa Rorug02G0631800
rosa_samantha Rh3AG034600 Rh3DG034600
rosa_wichuraiana Rw3G002520

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1121
Acc36I ACCTGC 1 cut(s) 1086
AccI GTMKAC 1 cut(s) 700
AccII CGCG 1 cut(s) 662
AciI CCGC 2 cut(s) 660, 662
AfaI GTAC 3 cut(s) 247, 551, 776
AfiI CCNNNNNNNGG 3 cut(s) 481, 1320, 1422
AflIII ACRYGT 1 cut(s) 600
AgsI TTSAA 8 cut(s) 70, 229, 360, 995, 1102, 1139, 1370, 1397
Alw26I GTCTC 1 cut(s) 107
Ama87I CYCGRG 1 cut(s) 573
AoxI GGCC 2 cut(s) 1000, 1107
ApeKI GCWGC 3 cut(s) 975, 1054, 1225
AspS9I GGNCC 1 cut(s) 472
AsuC2I CCSGG 3 cut(s) 397, 574, 575
AsuHPI GGTGA 5 cut(s) 634, 752, 946, 1033, 1351
AsuNHI GCTAGC 1 cut(s) 868
AvaI CYCGRG 1 cut(s) 573
AvaII GGWCC 1 cut(s) 472
BaeGI GKGCMC 1 cut(s) 574
BbsI GAAGAC 2 cut(s) 1031, 1284
BbvI GCAGC 3 cut(s) 962, 1066, 1212
BccI CCATC 5 cut(s) 15, 731, 1253, 1330, 1415
BclI TGATCA 1 cut(s) 540
BcnI CCSGG 3 cut(s) 397, 574, 575
BcoDI GTCTC 1 cut(s) 107
BfaI CTAG 5 cut(s) 348, 462, 869, 1386, 1404
BfuAI ACCTGC 1 cut(s) 1086
BglII AGATCT 1 cut(s) 23
BisI GCNGC 4 cut(s) 663, 976, 1055, 1226
BlpI GCTNAGC 1 cut(s) 1082
BlsI GCNGC 4 cut(s) 664, 977, 1056, 1227
Bme1390I CCNGG 3 cut(s) 397, 574, 575
Bme18I GGWCC 1 cut(s) 472
BmeT110I CYCGRG 1 cut(s) 573
BmgT120I GGNCC 1 cut(s) 472
BmrFI CCNGG 3 cut(s) 397, 574, 575
BmrI ACTGGG 1 cut(s) 79
BmsI GCATC 5 cut(s) 423, 568, 1135, 1242, 1315
BmtI GCTAGC 1 cut(s) 872
BmuI ACTGGG 1 cut(s) 79
BpiI GAAGAC 2 cut(s) 1031, 1284
BpmI CTGGAG 1 cut(s) 920
Bpu1102I GCTNAGC 1 cut(s) 1082
BpuMI CCSGG 3 cut(s) 397, 574, 575
BsaAI YACGTR 1 cut(s) 528
BsaI GGTCTC 1 cut(s) 107
BsaJI CCNNGG 3 cut(s) 573, 660, 1416
BsaXI ACNNNNNCTCC 2 cut(s) 1197, 1227
Bsc4I CCNNNNNNNGG 3 cut(s) 481, 1320, 1422
Bse1I ACTGG 5 cut(s) 85, 694, 763, 903, 1133
Bse3DI GCAATG 7 cut(s) 146, 543, 581, 729, 861, 1134, 1206
BseDI CCNNGG 3 cut(s) 573, 660, 1416
BseGI GGATG 5 cut(s) 583, 916, 1233, 1330, 1426
BseLI CCNNNNNNNGG 3 cut(s) 481, 1320, 1422
BseMI GCAATG 7 cut(s) 146, 543, 581, 729, 861, 1134, 1206
BseMII CTCAG 3 cut(s) 34, 501, 683
BseNI ACTGG 5 cut(s) 85, 694, 763, 903, 1133
BseRI GAGGAG 2 cut(s) 1174, 1361
BseSI GKGCMC 1 cut(s) 574
BseXI GCAGC 3 cut(s) 962, 1066, 1212
BseYI CCCAGC 1 cut(s) 1379
Bsh1236I CGCG 1 cut(s) 662
BshFI GGCC 2 cut(s) 1002, 1109
BsiHKCI CYCGRG 1 cut(s) 573
BsiSI CCGG 2 cut(s) 397, 574
BslFI GGGAC 1 cut(s) 611
BslI CCNNNNNNNGG 3 cut(s) 481, 1320, 1422
BsmAI GTCTC 1 cut(s) 107
BsmFI GGGAC 1 cut(s) 611
BsmI GAATGC 1 cut(s) 538
BsnI GGCC 2 cut(s) 1002, 1109
Bso31I GGTCTC 1 cut(s) 107
BsoBI CYCGRG 1 cut(s) 573
Bsp1286I GDGCHC 1 cut(s) 574
Bsp143I GATC 2 cut(s) 23, 540
Bsp1720I GCTNAGC 1 cut(s) 1082
BspACI CCGC 2 cut(s) 660, 662
BspANI GGCC 2 cut(s) 1002, 1109
BspCNI CTCAG 3 cut(s) 33, 502, 682
BspFNI CGCG 1 cut(s) 662
BspMI ACCTGC 1 cut(s) 1086
BspOI GCTAGC 1 cut(s) 872
BspTNI GGTCTC 1 cut(s) 107
BsrDI GCAATG 7 cut(s) 146, 543, 581, 729, 861, 1134, 1206
BsrI ACTGG 5 cut(s) 85, 694, 763, 903, 1133
BssECI CCNNGG 3 cut(s) 573, 660, 1416
BssMI GATC 2 cut(s) 23, 540
BssNAI GTATAC 1 cut(s) 701
Bst1107I GTATAC 1 cut(s) 701
Bst4CI ACNGT 1 cut(s) 1064
Bst6I CTCTTC 1 cut(s) 559
BstAPI GCANNNNNTGC 2 cut(s) 10, 728
BstBAI YACGTR 1 cut(s) 528
BstC8I GCNNGC 9 cut(s) 75, 128, 298, 729, 870, 962, 973, 1004, 1177
BstDEI CTNAG 5 cut(s) 20, 510, 669, 1082, 1169
BstDSI CCRYGG 1 cut(s) 660
BstF5I GGATG 5 cut(s) 583, 916, 1233, 1330, 1426
BstFNI CGCG 1 cut(s) 662
BstKTI GATC 2 cut(s) 26, 543
BstMAI GTCTC 1 cut(s) 107
BstMBI GATC 2 cut(s) 23, 540
BstMWI GCNNNNNNNGC 4 cut(s) 10, 136, 578, 728
BstNSI RCATGY 2 cut(s) 604, 1179
BstSCI CCNGG 3 cut(s) 395, 572, 573
BstSLI GKGCMC 1 cut(s) 574
BstUI CGCG 1 cut(s) 662
BstV1I GCAGC 3 cut(s) 962, 1066, 1212
BstV2I GAAGAC 2 cut(s) 1031, 1284
BstX2I RGATCY 1 cut(s) 23
BstYI RGATCY 1 cut(s) 23
BstZ17I GTATAC 1 cut(s) 701
BsuRI GGCC 2 cut(s) 1002, 1109
BtgI CCRYGG 1 cut(s) 660
BtsCI GGATG 5 cut(s) 583, 916, 1233, 1330, 1426
BtsIMutI CAGTG 1 cut(s) 896
BveI ACCTGC 1 cut(s) 1086
Cac8I GCNNGC 9 cut(s) 75, 128, 298, 729, 870, 962, 973, 1004, 1177
Cfr13I GGNCC 1 cut(s) 472
Cfr42I CCGCGG 1 cut(s) 663
Cfr9I CCCGGG 1 cut(s) 573
CseI GACGC 1 cut(s) 1252
Csp6I GTAC 3 cut(s) 246, 550, 775
CviQI GTAC 3 cut(s) 246, 550, 775
DdeI CTNAG 5 cut(s) 20, 510, 669, 1082, 1169
DpnI GATC 2 cut(s) 25, 542
DpnII GATC 2 cut(s) 23, 540
Eam1104I CTCTTC 1 cut(s) 559
EarI CTCTTC 1 cut(s) 559
Eco147I AGGCCT 2 cut(s) 1002, 1109
Eco31I GGTCTC 1 cut(s) 107
Eco47I GGWCC 1 cut(s) 472
Eco88I CYCGRG 1 cut(s) 573
EcoO109I RGGNCCY 1 cut(s) 472
EcoT22I ATGCAT 1 cut(s) 583
FaqI GGGAC 1 cut(s) 611
FauNDI CATATG 2 cut(s) 1017, 1050
FbaI TGATCA 1 cut(s) 540
FblI GTMKAC 1 cut(s) 700
Fnu4HI GCNGC 4 cut(s) 663, 976, 1055, 1226
FokI GGATG 4 cut(s) 590, 923, 1220, 1337
Fsp4HI GCNGC 4 cut(s) 663, 976, 1055, 1226
FspBI CTAG 5 cut(s) 348, 462, 869, 1386, 1404
GluI GCNGC 4 cut(s) 663, 976, 1055, 1226
GsaI CCCAGC 1 cut(s) 1383
GsuI CTGGAG 1 cut(s) 920
HaeIII GGCC 2 cut(s) 1002, 1109
HapII CCGG 2 cut(s) 397, 574
HgaI GACGC 1 cut(s) 1252
HincII GTYRAC 1 cut(s) 1075
HindII GTYRAC 1 cut(s) 1075
HindIII AAGCTT 1 cut(s) 298
HinfI GANTC 5 cut(s) 18, 260, 479, 614, 1038
HpaII CCGG 2 cut(s) 397, 574
HphI GGTGA 5 cut(s) 634, 752, 946, 1033, 1351
Hpy166II GTNNAC 2 cut(s) 701, 1075
Hpy188I TCNGA 4 cut(s) 23, 157, 197, 1420
Hpy188III TCNNGA 3 cut(s) 596, 734, 841
Hpy8I GTNNAC 2 cut(s) 701, 1075
HpyAV CCTTC 4 cut(s) 366, 712, 992, 1204
HpyCH4III ACNGT 1 cut(s) 1064
HpyCH4IV ACGT 1 cut(s) 527
HpyF10VI GCNNNNNNNGC 4 cut(s) 10, 136, 578, 728
HpyF3I CTNAG 5 cut(s) 20, 510, 669, 1082, 1169
HpySE526I ACGT 1 cut(s) 527
Ksp22I TGATCA 1 cut(s) 540
KspI CCGCGG 1 cut(s) 663
Kzo9I GATC 2 cut(s) 23, 540
LmnI GCTCC 2 cut(s) 338, 736
Lsp1109I GCAGC 3 cut(s) 962, 1066, 1212
LweI GCATC 5 cut(s) 423, 568, 1135, 1242, 1315
MaeI CTAG 5 cut(s) 348, 462, 869, 1386, 1404
MaeII ACGT 1 cut(s) 527
MaeIII GTNAC 3 cut(s) 523, 946, 1039
MalI GATC 2 cut(s) 25, 542
MboI GATC 2 cut(s) 23, 540
MboII GAAGA 5 cut(s) 546, 1007, 1036, 1231, 1289
MfeI CAATTG 2 cut(s) 65, 280
MflI RGATCY 1 cut(s) 23
MhlI GDGCHC 1 cut(s) 574
MluCI AATT 3 cut(s) 65, 280, 1365
MlyI GAGTC 3 cut(s) 12, 254, 1047
MmeI TCCRAC 1 cut(s) 585
MnlI CCTC 8 cut(s) 44, 403, 895, 1056, 1099, 1152, 1339, 1426
Mph1103I ATGCAT 1 cut(s) 583
MseI TTAA 3 cut(s) 38, 806, 816
MslI CAYNNNNRTG 6 cut(s) 204, 431, 456, 708, 1101, 1191
MspA1I CMGCKG 2 cut(s) 662, 1240
MspI CCGG 2 cut(s) 397, 574
MspR9I CCNGG 3 cut(s) 397, 574, 575
MunI CAATTG 2 cut(s) 65, 280
Mva1269I GAATGC 1 cut(s) 538
MvnI CGCG 1 cut(s) 662
MwoI GCNNNNNNNGC 4 cut(s) 10, 136, 578, 728
NciI CCSGG 3 cut(s) 397, 574, 575
NdeI CATATG 2 cut(s) 1017, 1050
NdeII GATC 2 cut(s) 23, 540
NheI GCTAGC 1 cut(s) 868
NmuCI GTSAC 2 cut(s) 946, 1039
NsiI ATGCAT 1 cut(s) 583
NspI RCATGY 2 cut(s) 604, 1179
PaeI GCATGC 1 cut(s) 1179
PceI AGGCCT 2 cut(s) 1002, 1109
PciI ACATGT 1 cut(s) 600
PctI GAATGC 1 cut(s) 538
PfeI GAWTC 2 cut(s) 479, 614
PkrI GCNGC 4 cut(s) 664, 977, 1056, 1227
PleI GAGTC 3 cut(s) 12, 254, 1046
PpsI GAGTC 3 cut(s) 12, 254, 1046
Ppu21I YACGTR 1 cut(s) 528
PpuMI RGGWCCY 1 cut(s) 472
PscI ACATGT 1 cut(s) 600
PsiI TTATAA 1 cut(s) 1121
Psp5II RGGWCCY 1 cut(s) 472
PspFI CCCAGC 1 cut(s) 1379
PspPI GGNCC 1 cut(s) 472
PspPPI RGGWCCY 1 cut(s) 472
PsuI RGATCY 1 cut(s) 23
PvuII CAGCTG 1 cut(s) 1240
RsaI GTAC 3 cut(s) 247, 551, 776
RsaNI GTAC 3 cut(s) 246, 550, 775
RseI CAYNNNNRTG 6 cut(s) 204, 431, 456, 708, 1101, 1191
SacII CCGCGG 1 cut(s) 663
SaqAI TTAA 3 cut(s) 38, 806, 816
SatI GCNGC 4 cut(s) 663, 976, 1055, 1226
Sau3AI GATC 2 cut(s) 23, 540
Sau96I GGNCC 1 cut(s) 472
SchI GAGTC 3 cut(s) 12, 254, 1047
ScrFI CCNGG 3 cut(s) 397, 574, 575
SduI GDGCHC 1 cut(s) 574
SfaNI GCATC 5 cut(s) 423, 568, 1135, 1242, 1315
Sfr303I CCGCGG 1 cut(s) 663
SgrBI CCGCGG 1 cut(s) 663
SinI GGWCC 1 cut(s) 472
SmaI CCCGGG 1 cut(s) 575
SmiMI CAYNNNNRTG 6 cut(s) 204, 431, 456, 708, 1101, 1191
SphI GCATGC 1 cut(s) 1179
Sse9I AATT 3 cut(s) 65, 280, 1365
SseBI AGGCCT 2 cut(s) 1002, 1109
SsiI CCGC 2 cut(s) 660, 662
SspMI CTAG 5 cut(s) 348, 462, 869, 1386, 1404
StuI AGGCCT 2 cut(s) 1002, 1109
StyD4I CCNGG 3 cut(s) 395, 572, 573
TaaI ACNGT 1 cut(s) 1064
TaiI ACGT 1 cut(s) 530
TaqI TCGA 3 cut(s) 498, 779, 1295
TasI AATT 3 cut(s) 65, 280, 1365
TatI WGTACW 2 cut(s) 245, 774
TauI GCSGC 1 cut(s) 665
TfiI GAWTC 2 cut(s) 479, 614
Tru1I TTAA 3 cut(s) 38, 806, 816
Tru9I TTAA 3 cut(s) 38, 806, 816
TscAI CASTG 1 cut(s) 903
TseFI GTSAC 2 cut(s) 946, 1039
TseI GCWGC 3 cut(s) 975, 1054, 1225
Tsp45I GTSAC 2 cut(s) 946, 1039
TspDTI ATGAA 9 cut(s) 380, 516, 839, 866, 932, 957, 1037, 1175, 1367
TspMI CCCGGG 1 cut(s) 573
TspRI CASTG 1 cut(s) 903
VpaK11BI GGWCC 1 cut(s) 472
XceI RCATGY 2 cut(s) 604, 1179
XmaI CCCGGG 1 cut(s) 573
XmiI GTMKAC 1 cut(s) 700
XspI CTAG 5 cut(s) 348, 462, 869, 1386, 1404
Zsp2I ATGCAT 1 cut(s) 583
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.