Rorug04G0396000

Pentatricopeptide repeat-containing protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000004
OG0015053
Physical Location & Seq
Forward (+)
56256420 .. 56258336
1917 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug04G0396000.1

Sequence Viewer

Length: 1620 bp
ATGAGAGAAACCCAACAACAGCTAGAAATGGCAGAAGAGCTAATGCAGCAGCTCAGATCCAAAGCCACAGAGCTCTTACTCAGAGAAGAATGGAGCGAATCCATACAAGTCTATTCTCAGTTCATCAATCTCTGCCAACAAAACATCAATGATTATGAAACCACCCCAGACAACCTCCCAAAGCTCCACAAGTCCCTCTGCCTGGCCCTATCGAACCGAGCCGAAGCGCGATCCAGACTCCGAGACTATGCACAAGCCTTGAAGGATTGTGATGAGGCACTGAAAATTGAGAGCACCCATTTCAAGACTCTCATCTGCAAAGGTAAGATTTTGCTGAATTTGAACAGGTACTCCATGGCATTGACTTGCTTCAGAACTGCTCAGCTTGATCCTCAGGCAAATGGGAGCTCGGTTGGGCTTAATGGGTACCTGCAGAAATGCAAGAAGCTCGAACTGATGTCGAAAACTGGAGCTTTCGATATGTCTGAGTGGGTGATCAATGGGTTTCGGGCTAAGCCTCCGGAGCCGGCTGAGTACATTGGAGGGGCAGTGGAGATGAGGAAGTCGGGGATTAGAGGGCGTGGTTTGTTTGCGACGAAGAATATGGAAGCTGGGAGTTTGGTGCTGATTAATAAAGCTGTTGCAACGGAGAGAGGTATTTTGCCGGGTCAAGATTTGGATGAGAATGCCCAATTAGTTATGTGGAAGACTTTTACTGAGAAAGTGATGGATTCCGTGGCCAAATGTTCGAGAACATGTGGTTTGATTAGTACTCTGTCGAGTGGTGAAGATGAGGATGGGCTTGAGGTGCCTGAGATTAATCTGTTTAAGCCTGACTCGGAGCACTTAATTGGGTACTCAAATGAGAAGAAGCTTGATGCGAGTAGGGTTTTAAGTATTTTGGATGTCAATTCTATTGTTGAGGATTCCATTTCGTCTAAGGTTTTGGGGAAGAACAGTGATTACTATGGTGTTGGGCTTTGGGTACTTGCTTCATTCATCAACCATTCATGTATTCCCAATGCAAGGCGTTTGCATGTTGGGGACTATGTGATTGTTCATGCTTCAAGAGATGTCAAGGCTGGTGAGGAGCTAACATTTGCATATTTCGATGTGCTGAATCCGTTGGAAAAGCGCAACGAAATGTCAAAGACTTGGGGGTTTAGGTGCAACTGCAGGAGGTGTAAGTTTGAGGCTGAACTATGTTCGAGGCAAGAAGGCATTGGAGAGATTGAGATGGGTTTCGAAAGAGGGATGGATTCGGGTGCTGCGGTCTATAGGCTCGAGGAAGGCATGAGAAAATGGAAGGTGAAGGAAAAGGAAAAAGGGTACTTGAGAGCTTCATTTTGGGCTGCATATGGCTCAGAGAAGTTGATGAGAAGTTGGGGAAGACGGATCCCAATGATGGAGTCCGTGGTTGATAGCATTGTGGAAGCTGTGGGAAGTGATGAGAGGGTGTTGAAGATGGTGGTGGAGAAGATAAAGAAAGGTAATGGTGGCAGTTCAGTGGTGGAAATAGAAAGAGCTTTGAAGTTGGGAAGAGGAGTTTATGGAAAAGTAATGAAGAAGCAAGCAATGAAGAGTCTTCTTGGCCTTGGCATTCTTGAACCCAGCTATTGA

Protein Analysis

539

Amino Acids

60.57

Weight (kDa)

8.26

Isoelectric Point (pI)

35.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
SET PF00856 193 - 369 3.7e-14 SET domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
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Orthologous Genes (Group: OG0015053)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G04370
fragaria_vesca FvH4_3g01610
malus_domestica MD10G1325500.v1.1
prunus_persica Prupe.4G016600_v2.0.a1
pyrus_communis pycom10g27520
rosa_chinensis RchiOBHm_Chr5g0002401
rosa_laevigata RLG00000031029
rosa_multiflora Rmu_co8285719.1_g000001 Rmu_sc0001717.1_g000003
rosa_roxburghii Rroxscaffold_1G00073450
rosa_rugosa Rorug04G0396000
rosa_samantha Rh5AG018800 Rh5BG021600 Rh5CG020700 Rh5DG019800
rosa_wichuraiana Rw5G001760

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 438
Acc65I GGTACC 1 cut(s) 426
AccB1I GGYRCC 2 cut(s) 426, 808
AccII CGCG 1 cut(s) 229
AccIII TCCGGA 1 cut(s) 520
AciI CCGC 1 cut(s) 1271
AclWI GGATC 5 cut(s) 51, 225, 383, 1390, 1403
AcoI YGGCCR 1 cut(s) 738
AcsI RAATTY 1 cut(s) 337
AcuI CTGAAG 1 cut(s) 355
AfaI GTAC 7 cut(s) 350, 428, 536, 772, 857, 987, 1331
AfiI CCNNNNNNNGG 3 cut(s) 202, 1026, 1405
AflIII ACRYGT 1 cut(s) 755
AgsI TTSAA 7 cut(s) 262, 304, 343, 1068, 1462, 1531, 1607
AjnI CCWGG 1 cut(s) 201
AloI GAACNNNNNNTCC 2 cut(s) 335, 367
Alw21I GWGCWC 4 cut(s) 75, 296, 410, 846
Alw26I GTCTC 1 cut(s) 237
AlwI GGATC 5 cut(s) 51, 225, 383, 1390, 1403
Ama87I CYCGRG 1 cut(s) 1283
Aor13HI TCCGGA 1 cut(s) 520
AoxI GGCC 3 cut(s) 204, 738, 1591
ApeKI GCWGC 4 cut(s) 46, 49, 1268, 1352
ApoI RAATTY 1 cut(s) 337
AseI ATTAAT 2 cut(s) 630, 819
Asp718I GGTACC 1 cut(s) 426
AspLEI GCGC 2 cut(s) 229, 1137
AspS9I GGNCC 1 cut(s) 205
AsuC2I CCSGG 1 cut(s) 666
AsuHPI GGTGA 4 cut(s) 505, 797, 1097, 1321
AsuII TTCGAA 1 cut(s) 1245
AvaI CYCGRG 1 cut(s) 1283
AxyI CCTNAGG 1 cut(s) 393
BalI TGGCCA 1 cut(s) 740
BamHI GGATCC 1 cut(s) 1395
BanI GGYRCC 2 cut(s) 426, 808
BanII GRGCYC 2 cut(s) 75, 410
BbsI GAAGAC 3 cut(s) 713, 1396, 1577
Bbv12I GWGCWC 4 cut(s) 75, 296, 410, 846
BbvI GCAGC 4 cut(s) 58, 61, 1255, 1339
BccI CCATC 6 cut(s) 721, 791, 1231, 1249, 1399, 1459
BcgI CGANNNNNNTGC 2 cut(s) 430, 464
BciT130I CCWGG 1 cut(s) 203
BclI TGATCA 1 cut(s) 495
BcnI CCSGG 1 cut(s) 666
BcoDI GTCTC 1 cut(s) 237
BfaI CTAG 1 cut(s) 23
BfmI CTRYAG 3 cut(s) 431, 1174, 1276
BfuAI ACCTGC 1 cut(s) 438
BisI GCNGC 4 cut(s) 47, 50, 1269, 1353
BlpI GCTNAGC 2 cut(s) 381, 513
BlsI GCNGC 4 cut(s) 48, 51, 1270, 1354
BmcAI AGTACT 1 cut(s) 772
Bme1390I CCNGG 2 cut(s) 203, 666
BmeT110I CYCGRG 1 cut(s) 1283
BmgT120I GGNCC 1 cut(s) 205
BmiI GGNNCC 4 cut(s) 428, 525, 810, 1397
BmrFI CCNGG 2 cut(s) 203, 666
BmsI GCATC 1 cut(s) 868
BpiI GAAGAC 3 cut(s) 713, 1396, 1577
BpmI CTGGAG 1 cut(s) 489
Bpu1102I GCTNAGC 2 cut(s) 381, 513
Bpu14I TTCGAA 1 cut(s) 1245
BpuEI CTTGAG 2 cut(s) 824, 1354
BpuMI CCSGG 1 cut(s) 666
BsaJI CCNNGG 4 cut(s) 354, 735, 1413, 1594
BsaWI WCCGGW 1 cut(s) 520
BsaXI ACNNNNNCTCC 4 cut(s) 335, 365, 534, 564
Bsc4I CCNNNNNNNGG 3 cut(s) 202, 1026, 1405
Bse118I RCCGGY 1 cut(s) 526
Bse1I ACTGG 1 cut(s) 472
Bse21I CCTNAGG 1 cut(s) 393
Bse3DI GCAATG 1 cut(s) 1581
BseAI TCCGGA 1 cut(s) 520
BseBI CCWGG 1 cut(s) 203
BseDI CCNNGG 4 cut(s) 354, 735, 1413, 1594
BseGI GGATG 4 cut(s) 685, 802, 910, 1260
BseLI CCNNNNNNNGG 3 cut(s) 202, 1026, 1405
BseMI GCAATG 1 cut(s) 1581
BseNI ACTGG 1 cut(s) 472
BseRI GAGGAG 2 cut(s) 1103, 1557
BseXI GCAGC 4 cut(s) 58, 61, 1255, 1339
BseYI CCCAGC 2 cut(s) 611, 1610
Bsh1236I CGCG 1 cut(s) 229
BshFI GGCC 3 cut(s) 206, 740, 1593
BshNI GGYRCC 2 cut(s) 426, 808
BsiHKAI GWGCWC 4 cut(s) 75, 296, 410, 846
BsiHKCI CYCGRG 1 cut(s) 1283
BsiSI CCGG 3 cut(s) 521, 527, 665
BslFI GGGAC 2 cut(s) 178, 1058
BslI CCNNNNNNNGG 3 cut(s) 202, 1026, 1405
BsmAI GTCTC 1 cut(s) 237
BsmFI GGGAC 2 cut(s) 178, 1058
BsmI GAATGC 2 cut(s) 691, 1599
BsnI GGCC 3 cut(s) 206, 740, 1593
BsoBI CYCGRG 1 cut(s) 1283
Bsp119I TTCGAA 1 cut(s) 1245
Bsp1286I GDGCHC 4 cut(s) 75, 296, 410, 846
Bsp13I TCCGGA 1 cut(s) 520
Bsp143I GATC 5 cut(s) 56, 230, 388, 495, 1395
Bsp1720I GCTNAGC 2 cut(s) 381, 513
Bsp19I CCATGG 1 cut(s) 354
BspACI CCGC 1 cut(s) 1271
BspANI GGCC 3 cut(s) 206, 740, 1593
BspEI TCCGGA 1 cut(s) 520
BspFNI CGCG 1 cut(s) 229
BspLI GGNNCC 4 cut(s) 428, 525, 810, 1397
BspMAI CTGCAG 2 cut(s) 435, 1178
BspMI ACCTGC 1 cut(s) 438
BspPI GGATC 5 cut(s) 51, 225, 383, 1390, 1403
BspQI GCTCTTC 1 cut(s) 30
BspT104I TTCGAA 1 cut(s) 1245
BspT107I GGYRCC 2 cut(s) 426, 808
BsrDI GCAATG 1 cut(s) 1581
BsrFI RCCGGY 1 cut(s) 526
BsrI ACTGG 1 cut(s) 472
BssAI RCCGGY 1 cut(s) 526
BssECI CCNNGG 4 cut(s) 354, 735, 1413, 1594
BssMI GATC 5 cut(s) 56, 230, 388, 495, 1395
BssT1I CCWWGG 2 cut(s) 354, 1594
Bst2UI CCWGG 1 cut(s) 203
Bst4CI ACNGT 1 cut(s) 959
Bst6I CTCTTC 3 cut(s) 30, 1534, 1574
BstBI TTCGAA 1 cut(s) 1245
BstC8I GCNNGC 2 cut(s) 528, 1572
BstDSI CCRYGG 3 cut(s) 354, 735, 1413
BstF5I GGATG 4 cut(s) 685, 802, 910, 1260
BstFNI CGCG 1 cut(s) 229
BstHHI GCGC 2 cut(s) 229, 1137
BstKTI GATC 5 cut(s) 59, 233, 391, 498, 1398
BstMAI GTCTC 1 cut(s) 237
BstMBI GATC 5 cut(s) 56, 230, 388, 495, 1395
BstMWI GCNNNNNNNGC 3 cut(s) 46, 523, 808
BstNI CCWGG 1 cut(s) 203
BstNSI RCATGY 2 cut(s) 759, 1040
BstSCI CCNGG 2 cut(s) 201, 664
BstSFI CTRYAG 3 cut(s) 431, 1174, 1276
BstUI CGCG 1 cut(s) 229
BstV1I GCAGC 4 cut(s) 58, 61, 1255, 1339
BstV2I GAAGAC 3 cut(s) 713, 1396, 1577
BstX2I RGATCY 2 cut(s) 56, 1395
BstYI RGATCY 2 cut(s) 56, 1395
Bsu36I CCTNAGG 1 cut(s) 393
BsuRI GGCC 3 cut(s) 206, 740, 1593
BtgI CCRYGG 3 cut(s) 354, 735, 1413
BtsCI GGATG 4 cut(s) 685, 802, 910, 1260
BtsI GCAGTG 1 cut(s) 555
BtsIMutI CAGTG 4 cut(s) 278, 555, 964, 1512
BveI ACCTGC 1 cut(s) 438
Cac8I GCNNGC 2 cut(s) 528, 1572
CfoI GCGC 2 cut(s) 229, 1137
Cfr10I RCCGGY 1 cut(s) 526
Cfr13I GGNCC 1 cut(s) 205
Csp6I GTAC 7 cut(s) 349, 427, 535, 771, 856, 986, 1330
CviAII CATG 6 cut(s) 355, 756, 1011, 1037, 1061, 1294
CviQI GTAC 7 cut(s) 349, 427, 535, 771, 856, 986, 1330
DpnI GATC 5 cut(s) 58, 232, 390, 497, 1397
DpnII GATC 5 cut(s) 56, 230, 388, 495, 1395
EaeI YGGCCR 1 cut(s) 738
Eam1104I CTCTTC 3 cut(s) 30, 1534, 1574
EarI CTCTTC 3 cut(s) 30, 1534, 1574
Ecl136II GAGCTC 2 cut(s) 73, 408
Eco130I CCWWGG 2 cut(s) 354, 1594
Eco24I GRGCYC 2 cut(s) 75, 410
Eco53kI GAGCTC 2 cut(s) 73, 408
Eco57I CTGAAG 1 cut(s) 355
Eco81I CCTNAGG 1 cut(s) 393
Eco88I CYCGRG 1 cut(s) 1283
EcoICRI GAGCTC 2 cut(s) 73, 408
EcoRII CCWGG 1 cut(s) 201
EcoT14I CCWWGG 2 cut(s) 354, 1594
EcoT38I GRGCYC 2 cut(s) 75, 410
ErhI CCWWGG 2 cut(s) 354, 1594
FaeI CATG 6 cut(s) 358, 759, 1014, 1040, 1064, 1297
FaqI GGGAC 2 cut(s) 178, 1058
FatI CATG 6 cut(s) 354, 755, 1010, 1036, 1060, 1293
FauNDI CATATG 1 cut(s) 1357
FbaI TGATCA 1 cut(s) 495
Fnu4HI GCNGC 4 cut(s) 47, 50, 1269, 1353
FokI GGATG 4 cut(s) 692, 809, 917, 1267
FriOI GRGCYC 2 cut(s) 75, 410
Fsp4HI GCNGC 4 cut(s) 47, 50, 1269, 1353
FspBI CTAG 1 cut(s) 23
GlaI GCGC 2 cut(s) 228, 1136
GluI GCNGC 4 cut(s) 47, 50, 1269, 1353
GsaI CCCAGC 2 cut(s) 615, 1614
GsuI CTGGAG 1 cut(s) 489
HaeIII GGCC 3 cut(s) 206, 740, 1593
HapII CCGG 3 cut(s) 521, 527, 665
HhaI GCGC 2 cut(s) 229, 1137
Hin1II CATG 6 cut(s) 358, 759, 1014, 1040, 1064, 1297
Hin6I GCGC 2 cut(s) 227, 1135
HinP1I GCGC 2 cut(s) 227, 1135
HindIII AAGCTT 1 cut(s) 872
HpaII CCGG 3 cut(s) 521, 527, 665
HphI GGTGA 4 cut(s) 505, 797, 1097, 1321
Hpy188I TCNGA 7 cut(s) 56, 83, 242, 374, 487, 841, 1366
Hpy188III TCNNGA 7 cut(s) 234, 304, 521, 671, 750, 1068, 1604
Hpy99I CGWCG 1 cut(s) 598
HpyAV CCTTC 5 cut(s) 256, 1211, 1283, 1300, 1306
HpyCH4III ACNGT 1 cut(s) 959
HpyF10VI GCNNNNNNNGC 3 cut(s) 46, 523, 808
Hsp92II CATG 6 cut(s) 358, 759, 1014, 1040, 1064, 1297
HspAI GCGC 2 cut(s) 227, 1135
Kpn2I TCCGGA 1 cut(s) 520
KpnI GGTACC 1 cut(s) 430
KroI GCCGGC 1 cut(s) 526
KroNI GCCGGC 1 cut(s) 528
Ksp22I TGATCA 1 cut(s) 495
Kzo9I GATC 5 cut(s) 56, 230, 388, 495, 1395
LguI GCTCTTC 1 cut(s) 30
LmnI GCTCC 7 cut(s) 93, 189, 405, 470, 523, 841, 1090
Lsp1109I GCAGC 4 cut(s) 58, 61, 1255, 1339
LweI GCATC 1 cut(s) 868
MaeI CTAG 1 cut(s) 23
MalI GATC 5 cut(s) 58, 232, 390, 497, 1397
MboI GATC 5 cut(s) 56, 230, 388, 495, 1395
MflI RGATCY 2 cut(s) 56, 1395
MhlI GDGCHC 4 cut(s) 75, 296, 410, 846
MlsI TGGCCA 1 cut(s) 740
MluCI AATT 5 cut(s) 285, 337, 692, 849, 910
MluNI TGGCCA 1 cut(s) 740
MlyI GAGTC 5 cut(s) 231, 301, 830, 1418, 1591
MmeI TCCRAC 1 cut(s) 1107
Mox20I TGGCCA 1 cut(s) 740
MroI TCCGGA 1 cut(s) 520
MroNI GCCGGC 1 cut(s) 526
MscI TGGCCA 1 cut(s) 740
MseI TTAA 6 cut(s) 420, 630, 819, 828, 848, 893
Msp20I TGGCCA 1 cut(s) 740
MspI CCGG 3 cut(s) 521, 527, 665
MspR9I CCNGG 2 cut(s) 203, 666
Mva1269I GAATGC 2 cut(s) 691, 1599
MvaI CCWGG 1 cut(s) 203
MvnI CGCG 1 cut(s) 229
MwoI GCNNNNNNNGC 3 cut(s) 46, 523, 808
NaeI GCCGGC 1 cut(s) 528
NciI CCSGG 1 cut(s) 666
NcoI CCATGG 1 cut(s) 354
NdeI CATATG 1 cut(s) 1357
NdeII GATC 5 cut(s) 56, 230, 388, 495, 1395
NgoMIV GCCGGC 1 cut(s) 526
NlaIII CATG 6 cut(s) 358, 759, 1014, 1040, 1064, 1297
NlaIV GGNNCC 4 cut(s) 428, 525, 810, 1397
NspI RCATGY 2 cut(s) 759, 1040
NspV TTCGAA 1 cut(s) 1245
PaeR7I CTCGAG 1 cut(s) 1283
PciI ACATGT 1 cut(s) 755
PciSI GCTCTTC 1 cut(s) 30
PctI GAATGC 2 cut(s) 691, 1599
PdiI GCCGGC 1 cut(s) 528
PfeI GAWTC 5 cut(s) 98, 731, 926, 1120, 1259
PkrI GCNGC 4 cut(s) 48, 51, 1270, 1354
PleI GAGTC 5 cut(s) 231, 301, 830, 1417, 1590
PpsI GAGTC 5 cut(s) 231, 301, 830, 1417, 1590
PscI ACATGT 1 cut(s) 755
PshBI ATTAAT 2 cut(s) 630, 819
Psp124BI GAGCTC 2 cut(s) 75, 410
Psp6I CCWGG 1 cut(s) 201
PspFI CCCAGC 2 cut(s) 611, 1610
PspGI CCWGG 1 cut(s) 201
PspN4I GGNNCC 4 cut(s) 428, 525, 810, 1397
PspPI GGNCC 1 cut(s) 205
PspXI VCTCGAGB 1 cut(s) 1283
PsrI GAACNNNNNNTAC 2 cut(s) 947, 979
PstI CTGCAG 2 cut(s) 435, 1178
PsuI RGATCY 2 cut(s) 56, 1395
RsaI GTAC 7 cut(s) 350, 428, 536, 772, 857, 987, 1331
RsaNI GTAC 7 cut(s) 349, 427, 535, 771, 856, 986, 1330
SacI GAGCTC 2 cut(s) 75, 410
SapI GCTCTTC 1 cut(s) 30
SaqAI TTAA 6 cut(s) 420, 630, 819, 828, 848, 893
SatI GCNGC 4 cut(s) 47, 50, 1269, 1353
Sau3AI GATC 5 cut(s) 56, 230, 388, 495, 1395
Sau96I GGNCC 1 cut(s) 205
ScaI AGTACT 1 cut(s) 772
SchI GAGTC 5 cut(s) 231, 301, 830, 1418, 1591
ScrFI CCNGG 2 cut(s) 203, 666
SduI GDGCHC 4 cut(s) 75, 296, 410, 846
SfaNI GCATC 1 cut(s) 868
SfcI CTRYAG 3 cut(s) 431, 1174, 1276
Sfr274I CTCGAG 1 cut(s) 1283
SfuI TTCGAA 1 cut(s) 1245
SlaI CTCGAG 1 cut(s) 1283
SmlI CTYRAG 3 cut(s) 803, 1283, 1333
SmoI CTYRAG 3 cut(s) 803, 1283, 1333
Sse9I AATT 5 cut(s) 285, 337, 692, 849, 910
SsiI CCGC 1 cut(s) 1271
SspMI CTAG 1 cut(s) 23
SstI GAGCTC 2 cut(s) 75, 410
StyD4I CCNGG 2 cut(s) 201, 664
StyI CCWWGG 2 cut(s) 354, 1594
TaaI ACNGT 1 cut(s) 959
TasI AATT 5 cut(s) 285, 337, 692, 849, 910
TatI WGTACW 2 cut(s) 534, 770
TfiI GAWTC 5 cut(s) 98, 731, 926, 1120, 1259
Tru1I TTAA 6 cut(s) 420, 630, 819, 828, 848, 893
Tru9I TTAA 6 cut(s) 420, 630, 819, 828, 848, 893
TscAI CASTG 4 cut(s) 285, 555, 964, 1512
TseI GCWGC 4 cut(s) 46, 49, 1268, 1352
TspDTI ATGAA 9 cut(s) 112, 171, 984, 988, 999, 1049, 1332, 1577, 1592
TspGWI ACGGA 5 cut(s) 662, 724, 1113, 1402, 1408
TspRI CASTG 4 cut(s) 285, 555, 964, 1512
VspI ATTAAT 2 cut(s) 630, 819
XapI RAATTY 1 cut(s) 337
XceI RCATGY 2 cut(s) 759, 1040
XhoI CTCGAG 1 cut(s) 1283
XspI CTAG 1 cut(s) 23
ZrmI AGTACT 1 cut(s) 772
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.