MD09G1291100.v1.1

Protein ROOT PRIMORDIUM DEFECTIVE

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr09
OG0010308
Physical Location & Seq
Forward (+)
37299524 .. 37301092
1569 bp
Loading structure...
UTR
Exon/CDS
Intron
MD09G1291100.v1.1.491

Sequence Viewer

Length: 1569 bp
ATGATGGAACTTAAGCTGTTTCTTTCTTCCACTAAGTCCCCTTCTTTGCCCTTGTTTCTCTCCTCCTCCTCTTGCACCAAACCTCCTTTTCTTCTTAAACCCAAGCAGTCTCTCAAAACCCCCCATTTCTCGCTCTCCCAAAAATCCCATTTCTGGGGCAATAGTTTAGTTTTACACGAGAGAGATGCTGCTTGGGGTAACCTCGCCAAAACCACCCATGTCCCATTTGGCCCAATATGTGCTGCTGCTGCTGTCAAGAGAAGGAAGGAGCTTCCCTTTGACAACGTCATTCAAAAGGATAAGAAGCTGAAGCTGGTTCTCAAGATACGCAAGATTTTAGTCAGCCAACCTGATAGGGTTATGTCGCTTAGAGAGTTAGGTAGGTACAGGAGAGAATTGGGTCTGCAGAAAAAGCGCCGTTTCATTGCCCTTTTAAAGAAATTCCCGGCCGTGTTTGAGATTGTTGAAGAAGGGGTTTATTCCTTGCAATTTAAACTGACTCCCGAAGCCGAAAGGCTTTATTTTGAGGAGTTGAAGGTTAGGAATGAGATGGAAGACTTGCTGGTGGTCAAGTTGAGGAAATTGTTGATGATGTCGTTGGATAAGAGGATTCTGTTGGAGAAGATTGCCCATTTGAGAAATGATTTAGGGCTTCCCCAGGAGTTTCGTGACACTATTTGTCACCGGTACCCGCAGTTCTTTAAAGTAGTTGCAACTGCGAGAGGTCCGGCATTAGAATTAACTCATTGGGACCCTGAACTTGCAGTCTCAGCAGCTGAGTTGTCTGAAGAGGAAAACCGGGTTAGAGAGATTGAAGAGAAGGATCTGATTATAGATAGGCCTATCAAGTTCAATAGACTAAAGCTGCCAAAGGGCCTCAATCTTTCAAAGGGTGAGATGAGGAGGATATGCCTGTTTAGAGACATACCTTATATATCCCCTTACTCTGATTTCTCGGGACTGAGATCAGGTACTATTGAGAAAGAGAAGCATGCTTGTGCGGTTGTTCATGAGATTTTGAGTCTTACTGTGGAGAAGAGAACTCTTGTGGATCACCTTACTCATTTTCGAGAAGAGTTTAAGTTCTCTCAACAGGTGAGAGGTATGCTGATAAGGCACCCTGATTTGTTTTACGTGTCCTTGAAAGGAGATAGAGATTCAGTTTTCCTTAGGGAAGCATATCGTGATTCTCAATTGATAGACAAGGATCGTTTGTTGATCATAAAGGAGAAGCTTCGATCTATTATTTCTGTTCCTAGGTTTCCTAGACAGGGTGCTCCCAGAACTGAGGCAGATGGTGCAGAAGGAAGTGATGAGGCAAACGATGGAACTCTTGAGGAAGGAGAGGAGTGGTCTGGGGATGATGATGAGTTCAATGATGACGAAGATGATGATGAAGATGATTGGAGTGATGAAGATGATGATACACCCCCAGATTTTGACGAAGATGGGAAAACACCGACTATTGGAGTGAGCAAACCAGTCAAACAGGAGGGCAGTTCGAGAGAGAATAATGGAAAAGTGCTTGTTCCAGTGTTGCCAGATGGTCAACCAAGGGAGCGCTGGTAA

Protein Analysis

523

Amino Acids

60.23

Weight (kDa)

6.37

Isoelectric Point (pI)

45.83

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 89 - 416 4.3e-108 Plant organelle RNA recognition domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 687
AccB1I GGYRCC 2 cut(s) 687, 1116
AciI CCGC 2 cut(s) 692, 1001
AclWI GGATC 3 cut(s) 831, 1059, 1215
AcoI YGGCCR 1 cut(s) 447
AcsI RAATTY 1 cut(s) 440
AcuI CTGAAG 2 cut(s) 329, 807
AfaI GTAC 3 cut(s) 386, 689, 973
AfeI AGCGCT 1 cut(s) 1562
AfiI CCNNNNNNNGG 4 cut(s) 153, 154, 1271, 1466
AflII CTTAAG 1 cut(s) 11
AflIII ACRYGT 1 cut(s) 1134
AgeI ACCGGT 1 cut(s) 684
AgsI TTSAA 8 cut(s) 293, 467, 535, 815, 853, 888, 1144, 1375
AjnI CCWGG 1 cut(s) 657
AluBI AGCT 7 cut(s) 16, 271, 307, 313, 776, 865, 1234
AluI AGCT 7 cut(s) 16, 271, 307, 313, 776, 865, 1234
Alw21I GWGCWC 1 cut(s) 1279
Alw26I GTCTC 3 cut(s) 114, 772, 915
AlwI GGATC 3 cut(s) 831, 1059, 1215
AlwNI CAGNNNCTG 1 cut(s) 776
Ama87I CYCGRG 1 cut(s) 955
Aor51HI AGCGCT 1 cut(s) 1562
AoxI GGCC 4 cut(s) 229, 447, 839, 874
ApeKI GCWGC 6 cut(s) 188, 242, 245, 248, 773, 865
ApoI RAATTY 1 cut(s) 440
AsiGI ACCGGT 1 cut(s) 684
Asp718I GGTACC 1 cut(s) 687
AspA2I CCTAGG 1 cut(s) 1256
AspLEI GCGC 2 cut(s) 417, 1563
AspS9I GGNCC 4 cut(s) 230, 725, 751, 874
AsuC2I CCSGG 2 cut(s) 446, 800
AsuHPI GGTGA 4 cut(s) 674, 905, 1046, 1108
AvaI CYCGRG 1 cut(s) 955
AvaII GGWCC 2 cut(s) 725, 751
AvrII CCTAGG 1 cut(s) 1256
AxyI CCTNAGG 1 cut(s) 1169
BanI GGYRCC 2 cut(s) 687, 1116
BauI CACGAG 1 cut(s) 176
BbsI GAAGAC 1 cut(s) 561
Bbv12I GWGCWC 1 cut(s) 1279
BbvI GCAGC 6 cut(s) 175, 229, 232, 235, 785, 852
BccI CCATC 5 cut(s) 544, 1289, 1319, 1442, 1538
BceAI ACGGC 2 cut(s) 402, 434
BcgI CGANNNNNNTGC 2 cut(s) 167, 201
BciT130I CCWGG 1 cut(s) 659
BclI TGATCA 1 cut(s) 1218
BcnI CCSGG 2 cut(s) 446, 800
BcoDI GTCTC 3 cut(s) 114, 772, 915
BfaI CTAG 2 cut(s) 1257, 1266
BfmI CTRYAG 1 cut(s) 404
BfoI RGCGCY 2 cut(s) 418, 1564
BfrI CTTAAG 1 cut(s) 11
BisI GCNGC 6 cut(s) 189, 243, 246, 249, 774, 866
BlnI CCTAGG 1 cut(s) 1256
BlsI GCNGC 6 cut(s) 190, 244, 247, 250, 775, 867
Bme1390I CCNGG 3 cut(s) 446, 659, 800
Bme18I GGWCC 2 cut(s) 725, 751
BmeT110I CYCGRG 1 cut(s) 955
BmgT120I GGNCC 4 cut(s) 230, 725, 751, 874
BmiI GGNNCC 4 cut(s) 689, 752, 753, 1118
BmrFI CCNGG 3 cut(s) 446, 659, 800
BmsI GCATC 1 cut(s) 175
BpiI GAAGAC 1 cut(s) 561
BpuEI CTTGAG 2 cut(s) 305, 1355
BpuMI CCSGG 2 cut(s) 446, 800
BsaAI YACGTR 1 cut(s) 1135
BsaJI CCNNGG 3 cut(s) 657, 1256, 1553
BsaWI WCCGGW 1 cut(s) 684
BsaXI ACNNNNNCTCC 3 cut(s) 67, 97, 1550
Bsc4I CCNNNNNNNGG 4 cut(s) 153, 154, 1271, 1466
Bse118I RCCGGY 1 cut(s) 684
Bse1I ACTGG 2 cut(s) 1481, 1532
Bse21I CCTNAGG 1 cut(s) 1169
Bse3DI GCAATG 1 cut(s) 423
BseBI CCWGG 1 cut(s) 659
BseDI CCNNGG 3 cut(s) 657, 1256, 1553
BseGI GGATG 1 cut(s) 1366
BseLI CCNNNNNNNGG 4 cut(s) 153, 154, 1271, 1466
BseMI GCAATG 1 cut(s) 423
BseMII CTCAG 4 cut(s) 768, 783, 953, 1278
BseNI ACTGG 2 cut(s) 1481, 1532
BseRI GAGGAG 6 cut(s) 52, 55, 58, 542, 916, 1361
BseX3I CGGCCG 1 cut(s) 447
BseXI GCAGC 6 cut(s) 175, 229, 232, 235, 785, 852
BsgI GTGCAG 1 cut(s) 1320
Bsh1285I CGRYCG 1 cut(s) 450
BshFI GGCC 4 cut(s) 231, 449, 841, 876
BshNI GGYRCC 2 cut(s) 687, 1116
BshTI ACCGGT 1 cut(s) 684
BsiEI CGRYCG 1 cut(s) 450
BsiHKAI GWGCWC 1 cut(s) 1279
BsiHKCI CYCGRG 1 cut(s) 955
BsiSI CCGG 4 cut(s) 446, 685, 728, 799
BslFI GGGAC 4 cut(s) 22, 206, 764, 972
BslI CCNNNNNNNGG 4 cut(s) 153, 154, 1271, 1466
BsmAI GTCTC 3 cut(s) 114, 772, 915
BsmFI GGGAC 4 cut(s) 22, 206, 764, 972
BsnI GGCC 4 cut(s) 231, 449, 841, 876
BsoBI CYCGRG 1 cut(s) 955
Bsp1286I GDGCHC 1 cut(s) 1279
Bsp143I GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
BspACI CCGC 2 cut(s) 692, 1001
BspANI GGCC 4 cut(s) 231, 449, 841, 876
BspCNI CTCAG 4 cut(s) 769, 782, 954, 1279
BspHI TCATGA 1 cut(s) 1009
BspLI GGNNCC 4 cut(s) 689, 752, 753, 1118
BspMAI CTGCAG 1 cut(s) 408
BspPI GGATC 3 cut(s) 831, 1059, 1215
BspT107I GGYRCC 2 cut(s) 687, 1116
BspTI CTTAAG 1 cut(s) 11
BsrDI GCAATG 1 cut(s) 423
BsrFI RCCGGY 1 cut(s) 684
BsrI ACTGG 2 cut(s) 1481, 1532
BssAI RCCGGY 1 cut(s) 684
BssECI CCNNGG 3 cut(s) 657, 1256, 1553
BssMI GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
BssSI CACGAG 1 cut(s) 176
BssT1I CCWWGG 2 cut(s) 1256, 1553
Bst2BI CACGAG 1 cut(s) 176
Bst2UI CCWGG 1 cut(s) 659
Bst4CI ACNGT 1 cut(s) 1030
Bst6I CTCTTC 4 cut(s) 783, 810, 1031, 1068
BstAFI CTTAAG 1 cut(s) 11
BstAPI GCANNNNNTGC 1 cut(s) 1298
BstBAI YACGTR 1 cut(s) 1135
BstC8I GCNNGC 1 cut(s) 993
BstDEI CTNAG 7 cut(s) 33, 368, 769, 777, 962, 1169, 1287
BstEII GGTNACC 1 cut(s) 197
BstF5I GGATG 1 cut(s) 1366
BstH2I RGCGCY 2 cut(s) 418, 1564
BstHHI GCGC 2 cut(s) 417, 1563
BstKTI GATC 6 cut(s) 826, 968, 1054, 1210, 1221, 1241
BstMAI GTCTC 3 cut(s) 114, 772, 915
BstMBI GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
BstMCI CGRYCG 1 cut(s) 450
BstMWI GCNNNNNNNGC 5 cut(s) 248, 412, 770, 1114, 1298
BstNI CCWGG 1 cut(s) 659
BstNSI RCATGY 1 cut(s) 995
BstPI GGTNACC 1 cut(s) 197
BstSCI CCNGG 3 cut(s) 444, 657, 798
BstSFI CTRYAG 1 cut(s) 404
BstV1I GCAGC 6 cut(s) 175, 229, 232, 235, 785, 852
BstV2I GAAGAC 1 cut(s) 561
BstX2I RGATCY 1 cut(s) 823
BstYI RGATCY 1 cut(s) 823
BstZI CGGCCG 1 cut(s) 447
Bsu36I CCTNAGG 1 cut(s) 1169
BsuRI GGCC 4 cut(s) 231, 449, 841, 876
BtsCI GGATG 1 cut(s) 1366
BtsIMutI CAGTG 1 cut(s) 1539
Cac8I GCNNGC 1 cut(s) 993
CaiI CAGNNNCTG 1 cut(s) 776
CciI TCATGA 1 cut(s) 1009
CfoI GCGC 2 cut(s) 417, 1563
Cfr10I RCCGGY 1 cut(s) 684
Cfr13I GGNCC 4 cut(s) 230, 725, 751, 874
Csp6I GTAC 3 cut(s) 385, 688, 972
CspAI ACCGGT 1 cut(s) 684
CviAII CATG 3 cut(s) 218, 992, 1010
CviQI GTAC 3 cut(s) 385, 688, 972
DdeI CTNAG 7 cut(s) 33, 368, 769, 777, 962, 1169, 1287
DpnI GATC 6 cut(s) 825, 967, 1053, 1209, 1220, 1240
DpnII GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
DraI TTTAAA 3 cut(s) 435, 493, 703
EaeI YGGCCR 1 cut(s) 447
EagI CGGCCG 1 cut(s) 447
Eam1104I CTCTTC 4 cut(s) 783, 810, 1031, 1068
EarI CTCTTC 4 cut(s) 783, 810, 1031, 1068
EclXI CGGCCG 1 cut(s) 447
Eco130I CCWWGG 2 cut(s) 1256, 1553
Eco147I AGGCCT 1 cut(s) 841
Eco47I GGWCC 2 cut(s) 725, 751
Eco47III AGCGCT 1 cut(s) 1562
Eco52I CGGCCG 1 cut(s) 447
Eco57I CTGAAG 2 cut(s) 329, 807
Eco81I CCTNAGG 1 cut(s) 1169
Eco88I CYCGRG 1 cut(s) 955
Eco91I GGTNACC 1 cut(s) 197
EcoO109I RGGNCCY 2 cut(s) 751, 874
EcoO65I GGTNACC 1 cut(s) 197
EcoRII CCWGG 1 cut(s) 657
EcoT14I CCWWGG 2 cut(s) 1256, 1553
ErhI CCWWGG 2 cut(s) 1256, 1553
FaeI CATG 3 cut(s) 221, 995, 1013
FaqI GGGAC 4 cut(s) 22, 206, 764, 972
FatI CATG 3 cut(s) 217, 991, 1009
FauI CCCGC 1 cut(s) 699
FbaI TGATCA 1 cut(s) 1218
Fnu4HI GCNGC 6 cut(s) 189, 243, 246, 249, 774, 866
FokI GGATG 1 cut(s) 1373
Fsp4HI GCNGC 6 cut(s) 189, 243, 246, 249, 774, 866
FspBI CTAG 2 cut(s) 1257, 1266
GlaI GCGC 2 cut(s) 416, 1562
GluI GCNGC 6 cut(s) 189, 243, 246, 249, 774, 866
HaeII RGCGCY 2 cut(s) 418, 1564
HaeIII GGCC 4 cut(s) 231, 449, 841, 876
HapII CCGG 4 cut(s) 446, 685, 728, 799
HhaI GCGC 2 cut(s) 417, 1563
Hin1II CATG 3 cut(s) 221, 995, 1013
Hin6I GCGC 2 cut(s) 415, 1561
HinP1I GCGC 2 cut(s) 415, 1561
HincII GTYRAC 1 cut(s) 1550
HindII GTYRAC 1 cut(s) 1550
HindIII AAGCTT 1 cut(s) 1232
HinfI GANTC 5 cut(s) 499, 610, 1021, 1157, 1187
HpaII CCGG 4 cut(s) 446, 685, 728, 799
HphI GGTGA 4 cut(s) 674, 905, 1046, 1108
Hpy166II GTNNAC 1 cut(s) 1550
Hpy188I TCNGA 3 cut(s) 787, 828, 949
Hpy8I GTNNAC 1 cut(s) 1550
HpyAV CCTTC 8 cut(s) 51, 255, 259, 464, 529, 814, 1298, 1334
HpyCH4III ACNGT 1 cut(s) 1030
HpyCH4IV ACGT 2 cut(s) 285, 1134
HpyCH4V TGCA 6 cut(s) 75, 406, 487, 713, 764, 1301
HpyF10VI GCNNNNNNNGC 5 cut(s) 248, 412, 770, 1114, 1298
HpyF3I CTNAG 7 cut(s) 33, 368, 769, 777, 962, 1169, 1287
HpySE526I ACGT 2 cut(s) 285, 1134
Hsp92II CATG 3 cut(s) 221, 995, 1013
HspAI GCGC 2 cut(s) 415, 1561
KflI GGGWCCC 1 cut(s) 751
KpnI GGTACC 1 cut(s) 691
Ksp22I TGATCA 1 cut(s) 1218
Kzo9I GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
LmnI GCTCC 3 cut(s) 268, 1282, 1558
Lsp1109I GCAGC 6 cut(s) 175, 229, 232, 235, 785, 852
LweI GCATC 1 cut(s) 175
MaeI CTAG 2 cut(s) 1257, 1266
MaeII ACGT 2 cut(s) 285, 1134
MaeIII GTNAC 3 cut(s) 197, 668, 680
MalI GATC 6 cut(s) 825, 967, 1053, 1209, 1220, 1240
MboI GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
MfeI CAATTG 1 cut(s) 1193
MflI RGATCY 1 cut(s) 823
MhlI GDGCHC 1 cut(s) 1279
MluCI AATT 6 cut(s) 395, 440, 488, 581, 737, 1193
MlyI GAGTC 2 cut(s) 493, 1030
MmeI TCCRAC 2 cut(s) 579, 597
MseI TTAA 7 cut(s) 12, 96, 434, 492, 702, 740, 1080
MslI CAYNNNNRTG 1 cut(s) 996
MspA1I CMGCKG 1 cut(s) 776
MspCI CTTAAG 1 cut(s) 11
MspI CCGG 4 cut(s) 446, 685, 728, 799
MspR9I CCNGG 3 cut(s) 446, 659, 800
MunI CAATTG 1 cut(s) 1193
MvaI CCWGG 1 cut(s) 659
MwoI GCNNNNNNNGC 5 cut(s) 248, 412, 770, 1114, 1298
NciI CCSGG 2 cut(s) 446, 800
NdeII GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
NlaIII CATG 3 cut(s) 221, 995, 1013
NlaIV GGNNCC 4 cut(s) 689, 752, 753, 1118
NmuCI GTSAC 2 cut(s) 668, 680
NspI RCATGY 1 cut(s) 995
PaeI GCATGC 1 cut(s) 995
PagI TCATGA 1 cut(s) 1009
PceI AGGCCT 1 cut(s) 841
PfeI GAWTC 3 cut(s) 610, 1157, 1187
PflFI GACNNNGTC 1 cut(s) 284
PinAI ACCGGT 1 cut(s) 684
PkrI GCNGC 6 cut(s) 190, 244, 247, 250, 775, 867
PleI GAGTC 2 cut(s) 493, 1029
PpsI GAGTC 2 cut(s) 493, 1029
Ppu21I YACGTR 1 cut(s) 1135
PpuMI RGGWCCY 1 cut(s) 751
Psp5II RGGWCCY 1 cut(s) 751
Psp6I CCWGG 1 cut(s) 657
PspEI GGTNACC 1 cut(s) 197
PspGI CCWGG 1 cut(s) 657
PspN4I GGNNCC 4 cut(s) 689, 752, 753, 1118
PspPI GGNCC 4 cut(s) 230, 725, 751, 874
PspPPI RGGWCCY 1 cut(s) 751
PsrI GAACNNNNNNTAC 2 cut(s) 680, 712
PstI CTGCAG 1 cut(s) 408
PstNI CAGNNNCTG 1 cut(s) 776
PsuI RGATCY 1 cut(s) 823
PsyI GACNNNGTC 1 cut(s) 284
PvuII CAGCTG 1 cut(s) 776
RsaI GTAC 3 cut(s) 386, 689, 973
RsaNI GTAC 3 cut(s) 385, 688, 972
RseI CAYNNNNRTG 1 cut(s) 996
SaqAI TTAA 7 cut(s) 12, 96, 434, 492, 702, 740, 1080
SatI GCNGC 6 cut(s) 189, 243, 246, 249, 774, 866
Sau3AI GATC 6 cut(s) 823, 965, 1051, 1207, 1218, 1238
Sau96I GGNCC 4 cut(s) 230, 725, 751, 874
SchI GAGTC 2 cut(s) 493, 1030
ScrFI CCNGG 3 cut(s) 446, 659, 800
SduI GDGCHC 1 cut(s) 1279
SfaNI GCATC 1 cut(s) 175
SfcI CTRYAG 1 cut(s) 404
SinI GGWCC 2 cut(s) 725, 751
SmiMI CAYNNNNRTG 1 cut(s) 996
SmlI CTYRAG 3 cut(s) 11, 320, 1334
SmoI CTYRAG 3 cut(s) 11, 320, 1334
SphI GCATGC 1 cut(s) 995
Sse9I AATT 6 cut(s) 395, 440, 488, 581, 737, 1193
SseBI AGGCCT 1 cut(s) 841
SsiI CCGC 2 cut(s) 692, 1001
SspMI CTAG 2 cut(s) 1257, 1266
StuI AGGCCT 1 cut(s) 841
StyD4I CCNGG 3 cut(s) 444, 657, 798
StyI CCWWGG 2 cut(s) 1256, 1553
TaaI ACNGT 1 cut(s) 1030
TaiI ACGT 2 cut(s) 288, 1137
TaqI TCGA 3 cut(s) 1069, 1237, 1502
TasI AATT 6 cut(s) 395, 440, 488, 581, 737, 1193
TfiI GAWTC 3 cut(s) 610, 1157, 1187
Tru1I TTAA 7 cut(s) 12, 96, 434, 492, 702, 740, 1080
Tru9I TTAA 7 cut(s) 12, 96, 434, 492, 702, 740, 1080
TscAI CASTG 1 cut(s) 1539
TseFI GTSAC 2 cut(s) 668, 680
TseI GCWGC 6 cut(s) 188, 242, 245, 248, 773, 865
Tsp45I GTSAC 2 cut(s) 668, 680
TspDTI ATGAA 4 cut(s) 412, 998, 1410, 1428
TspRI CASTG 1 cut(s) 1539
Tth111I GACNNNGTC 1 cut(s) 284
Vha464I CTTAAG 1 cut(s) 11
VpaK11BI GGWCC 2 cut(s) 725, 751
XapI RAATTY 1 cut(s) 440
XceI RCATGY 1 cut(s) 995
XcmI CCANNNNNNNNNTGG 2 cut(s) 224, 1560
XmaJI CCTAGG 1 cut(s) 1256
XspI CTAG 2 cut(s) 1257, 1266
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.