MD04G1034200.v1.1

Protein ROOT PRIMORDIUM DEFECTIVE 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
malus_domestica
Chr04
OG0011284
Physical Location & Seq
Reverse (-)
3828279 .. 3832285
4007 bp
Loading structure...
UTR
Exon/CDS
Intron
MD04G1034200.v1.1.491

Sequence Viewer

Length: 1278 bp
ATGGCCCAGTGTCTTGTGATTGTTAAGGTAGGCGGGTTTGGTTTCCTCCGTGGATGTCTGCAAGAATTTAACCATCAGCAAACGCGTGGTCTTGTGAATGTGAAGTTGAAATGGGTGAAAGATAGGGCATTGGATTTTGTTGTGGCTTCTGAGAGGGATCTCAAGGCTGCCAGCATTCTCGTTTCCGTTATTTCTTCCTCACCTCAGTGCAGCCTCCCTGTATACCGGCTCACTTGTCATCGGGGACAACTCGGTCTTCCTCACGATCTGAAGCTTGCTACTTTTATTAGGAGGTACCCATCTGTTTTTGTTGAGTCCTATGATTTTTGGGGCGGAGGCGCTCGTGTCCCATGCTTTGGCTTGACTCCTGAAGCCCTACAACTACACCAAGAGGAACTCAATGTTCTTGAGCAGAATCGAATGGATTTCATTAATAGGCTTCGAAAACTGCTCATGCTCACCCAGGCTTGGGCCCTTCCCTTACAAACCCTTGACCAACTGAAATGGGACCTGGGTTTGCCATATGATTACGTTCATTCTGTGATTCCATATCACTGCGACCTGTTCTCTTTTGTACACCTCCCTGATGACCGTGTTGGCTTGAAGCTCTTATCCTGGGATAAGGACCTTGCTGTCTCCCAATTGCAAAGGAACTCTGCCCGACAACAGAAGGAAGAAGACGTAAGAAGTGGCTGTTTAGCTTTTCCAGTTGGATTTACAAGGGGTTTTGGATTGAAGAGGAAATGCATGGAATGGTTGAAAGAGTGGCAGACCCTCCCTTATACCTCTCCGTACTCCGATGCCTCCCATTTAGATCCTCGTACAGATGTATCCGAGAAGAGGATTGTAGGGGTCTTTCACGAGCTTCTTCATCTAACTATAAACAAGAAAACTGAACGTAAGAATGTGAGCAACCTTCGCAAACCTTTGGCCCTACCTCAGAAGTTCACTAAAGTTTTTGAGCGCCATCCAGGTATTTTCTACATTTCAAATAAATGTGCCACTCAAACTGTCATTCTAAGGGAAGCCTATGACCGTCAAAAACTATTGCAAAAACACCCTACGGTCGAATTGAGGGAAAACTTTGCAAAGCTGTTGAGAAAAGGGTTCCTAGATAGGAGCAAAGGTTTGTACAAGAAAAATAAAGGTGATGGAATAGATGTGGATCCATATGCTGATGGTATTGGTAATAACCAATTCAGTTCTGAAGAAGAGTCAGATAATTTGTTTTATGAGTATGACTCAGATGAGCAACATGAACCTAGGATTCATTTGTGA
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
PORR

Protein Analysis

426

Amino Acids

49.06

Weight (kDa)

8.88

Isoelectric Point (pI)

42.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 39 - 369 9.9e-119 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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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 2 cut(s) 252, 632
Acc65I GGTACC 1 cut(s) 294
AccB1I GGYRCC 1 cut(s) 294
AccB7I CCANNNNNTGG 1 cut(s) 356
AccI GTMKAC 1 cut(s) 222
AccII CGCG 1 cut(s) 85
AciI CCGC 2 cut(s) 33, 333
AclWI GGATC 4 cut(s) 165, 809, 1160, 1173
AcsI RAATTY 1 cut(s) 65
AcuI CTGAAG 3 cut(s) 290, 390, 1227
AfaI GTAC 5 cut(s) 296, 576, 794, 823, 1133
AfiI CCNNNNNNNGG 4 cut(s) 356, 468, 469, 840
AflIII ACRYGT 1 cut(s) 83
AgsI TTSAA 5 cut(s) 109, 604, 736, 760, 990
AjnI CCWGG 4 cut(s) 462, 510, 614, 970
AleI CACNNNNGTG 1 cut(s) 205
AluBI AGCT 5 cut(s) 274, 607, 701, 865, 1093
AluI AGCT 5 cut(s) 274, 607, 701, 865, 1093
Alw26I GTCTC 1 cut(s) 640
AlwI GGATC 4 cut(s) 165, 809, 1160, 1173
AoxI GGCC 3 cut(s) 3, 471, 930
ApaI GGGCCC 1 cut(s) 475
ApeKI GCWGC 2 cut(s) 167, 210
ApoI RAATTY 1 cut(s) 65
ArsI GACNNNNNNTTYG 2 cut(s) 73, 105
AseI ATTAAT 1 cut(s) 432
Asp718I GGTACC 1 cut(s) 294
AspA2I CCTAGG 1 cut(s) 1262
AspLEI GCGC 2 cut(s) 341, 966
AspS9I GGNCC 6 cut(s) 4, 471, 472, 508, 625, 931
AsuHPI GGTGA 4 cut(s) 127, 192, 451, 1160
AsuII TTCGAA 1 cut(s) 442
AvaII GGWCC 2 cut(s) 508, 625
AvrII CCTAGG 1 cut(s) 1262
BaeGI GKGCMC 1 cut(s) 475
BaeI ACNNNNGTAYC 2 cut(s) 813, 846
BamHI GGATCC 1 cut(s) 1165
BanI GGYRCC 1 cut(s) 294
BanII GRGCYC 1 cut(s) 475
BauI CACGAG 2 cut(s) 342, 860
BbsI GAAGAC 2 cut(s) 248, 684
BbvI GCAGC 2 cut(s) 154, 222
BccI CCATC 5 cut(s) 81, 307, 975, 1145, 1172
BciT130I CCWGG 4 cut(s) 464, 512, 616, 972
BciVI GTATCC 1 cut(s) 841
BcoDI GTCTC 1 cut(s) 640
BfaI CTAG 2 cut(s) 1112, 1263
BfoI RGCGCY 2 cut(s) 342, 967
BfuI GTATCC 1 cut(s) 841
BisI GCNGC 2 cut(s) 168, 211
BlnI CCTAGG 1 cut(s) 1262
BlsI GCNGC 2 cut(s) 169, 212
Bme1390I CCNGG 4 cut(s) 464, 512, 616, 972
Bme18I GGWCC 2 cut(s) 508, 625
BmgT120I GGNCC 6 cut(s) 4, 471, 472, 508, 625, 931
BmiI GGNNCC 5 cut(s) 296, 473, 509, 1109, 1167
BmrFI CCNGG 4 cut(s) 464, 512, 616, 972
BmsI GCATC 1 cut(s) 790
BpiI GAAGAC 2 cut(s) 248, 684
BplI GAGNNNNNCTC 2 cut(s) 1226, 1258
Bpu14I TTCGAA 1 cut(s) 442
BpuEI CTTGAG 2 cut(s) 146, 428
BsaBI GATNNNNATC 1 cut(s) 1164
BsaJI CCNNGG 5 cut(s) 49, 462, 511, 615, 1262
BsaXI ACNNNNNCTCC 2 cut(s) 1111, 1141
Bsc4I CCNNNNNNNGG 4 cut(s) 356, 468, 469, 840
Bse118I RCCGGY 1 cut(s) 225
Bse1I ACTGG 2 cut(s) 7, 707
Bse8I GATNNNNATC 1 cut(s) 1164
BseBI CCWGG 4 cut(s) 464, 512, 616, 972
BseDI CCNNGG 5 cut(s) 49, 462, 511, 615, 1262
BseGI GGATG 2 cut(s) 59, 967
BseJI GATNNNNATC 1 cut(s) 1164
BseLI CCNNNNNNNGG 4 cut(s) 356, 468, 469, 840
BseMII CTCAG 4 cut(s) 141, 218, 953, 1257
BseNI ACTGG 2 cut(s) 7, 707
BseSI GKGCMC 1 cut(s) 475
BseXI GCAGC 2 cut(s) 154, 222
BsgI GTGCAG 1 cut(s) 229
Bsh1236I CGCG 1 cut(s) 85
Bsh1285I CGRYCG 1 cut(s) 1068
BshFI GGCC 3 cut(s) 5, 473, 932
BshNI GGYRCC 1 cut(s) 294
BsiEI CGRYCG 1 cut(s) 1068
BsiSI CCGG 1 cut(s) 226
BslFI GGGAC 3 cut(s) 258, 332, 521
BslI CCNNNNNNNGG 4 cut(s) 356, 468, 469, 840
BsmAI GTCTC 1 cut(s) 640
BsmFI GGGAC 3 cut(s) 258, 332, 521
BsmI GAATGC 1 cut(s) 174
BsnI GGCC 3 cut(s) 5, 473, 932
Bsp119I TTCGAA 1 cut(s) 442
Bsp120I GGGCCC 1 cut(s) 471
Bsp1286I GDGCHC 1 cut(s) 475
Bsp1407I TGTACA 2 cut(s) 574, 1131
Bsp143I GATC 4 cut(s) 157, 265, 814, 1165
BspACI CCGC 2 cut(s) 33, 333
BspANI GGCC 3 cut(s) 5, 473, 932
BspCNI CTCAG 4 cut(s) 142, 217, 952, 1256
BspFNI CGCG 1 cut(s) 85
BspLI GGNNCC 5 cut(s) 296, 473, 509, 1109, 1167
BspPI GGATC 4 cut(s) 165, 809, 1160, 1173
BspT104I TTCGAA 1 cut(s) 442
BspT107I GGYRCC 1 cut(s) 294
BsrFI RCCGGY 1 cut(s) 225
BsrGI TGTACA 2 cut(s) 574, 1131
BsrI ACTGG 2 cut(s) 7, 707
BssAI RCCGGY 1 cut(s) 225
BssECI CCNNGG 5 cut(s) 49, 462, 511, 615, 1262
BssMI GATC 4 cut(s) 157, 265, 814, 1165
BssNAI GTATAC 1 cut(s) 223
BssSI CACGAG 2 cut(s) 342, 860
BssT1I CCWWGG 1 cut(s) 1262
Bst1107I GTATAC 1 cut(s) 223
Bst2BI CACGAG 2 cut(s) 342, 860
Bst2UI CCWGG 4 cut(s) 464, 512, 616, 972
Bst4CI ACNGT 4 cut(s) 593, 1012, 1037, 1066
Bst6I CTCTTC 3 cut(s) 731, 833, 1206
BstAUI TGTACA 2 cut(s) 574, 1131
BstBI TTCGAA 1 cut(s) 442
BstC8I GCNNGC 2 cut(s) 172, 276
BstDEI CTNAG 5 cut(s) 150, 204, 939, 1019, 1243
BstDSI CCRYGG 1 cut(s) 49
BstF5I GGATG 2 cut(s) 59, 967
BstFNI CGCG 1 cut(s) 85
BstH2I RGCGCY 2 cut(s) 342, 967
BstHHI GCGC 2 cut(s) 341, 966
BstKTI GATC 4 cut(s) 160, 268, 817, 1168
BstMAI GTCTC 1 cut(s) 640
BstMBI GATC 4 cut(s) 157, 265, 814, 1165
BstMCI CGRYCG 1 cut(s) 1068
BstMWI GCNNNNNNNGC 1 cut(s) 918
BstNI CCWGG 4 cut(s) 464, 512, 616, 972
BstSCI CCNGG 4 cut(s) 462, 510, 614, 970
BstSLI GKGCMC 1 cut(s) 475
BstUI CGCG 1 cut(s) 85
BstV1I GCAGC 2 cut(s) 154, 222
BstV2I GAAGAC 2 cut(s) 248, 684
BstX2I RGATCY 3 cut(s) 157, 814, 1165
BstYI RGATCY 3 cut(s) 157, 814, 1165
BstZ17I GTATAC 1 cut(s) 223
BsuI GTATCC 1 cut(s) 841
BsuRI GGCC 3 cut(s) 5, 473, 932
BtgI CCRYGG 1 cut(s) 49
BtsCI GGATG 2 cut(s) 59, 967
BtsI GCAGTG 1 cut(s) 553
BtsIMutI CAGTG 3 cut(s) 14, 212, 553
Cac8I GCNNGC 2 cut(s) 172, 276
CfoI GCGC 2 cut(s) 341, 966
Cfr10I RCCGGY 1 cut(s) 225
Cfr13I GGNCC 6 cut(s) 4, 471, 472, 508, 625, 931
Csp6I GTAC 5 cut(s) 295, 575, 793, 822, 1132
CviAII CATG 4 cut(s) 351, 454, 748, 1256
CviQI GTAC 5 cut(s) 295, 575, 793, 822, 1132
DdeI CTNAG 5 cut(s) 150, 204, 939, 1019, 1243
DpnI GATC 4 cut(s) 159, 267, 816, 1167
DpnII GATC 4 cut(s) 157, 265, 814, 1165
DrdI GACNNNNNNGTC 2 cut(s) 252, 632
DseDI GACNNNNNNGTC 2 cut(s) 252, 632
Eam1104I CTCTTC 3 cut(s) 731, 833, 1206
EarI CTCTTC 3 cut(s) 731, 833, 1206
EciI GGCGGA 1 cut(s) 348
Eco130I CCWWGG 1 cut(s) 1262
Eco24I GRGCYC 1 cut(s) 475
Eco47I GGWCC 2 cut(s) 508, 625
Eco57I CTGAAG 3 cut(s) 290, 390, 1227
EcoO109I RGGNCCY 3 cut(s) 472, 508, 625
EcoRII CCWGG 4 cut(s) 462, 510, 614, 970
EcoT14I CCWWGG 1 cut(s) 1262
EcoT22I ATGCAT 1 cut(s) 749
EcoT38I GRGCYC 1 cut(s) 475
ErhI CCWWGG 1 cut(s) 1262
FaeI CATG 4 cut(s) 354, 457, 751, 1259
FaqI GGGAC 3 cut(s) 258, 332, 521
FatI CATG 4 cut(s) 350, 453, 747, 1255
FauI CCCGC 1 cut(s) 26
FauNDI CATATG 2 cut(s) 523, 1171
FblI GTMKAC 1 cut(s) 222
Fnu4HI GCNGC 2 cut(s) 168, 211
FokI GGATG 2 cut(s) 66, 954
FriOI GRGCYC 1 cut(s) 475
Fsp4HI GCNGC 2 cut(s) 168, 211
FspBI CTAG 2 cut(s) 1112, 1263
GlaI GCGC 2 cut(s) 340, 965
GluI GCNGC 2 cut(s) 168, 211
HaeII RGCGCY 2 cut(s) 342, 967
HaeIII GGCC 3 cut(s) 5, 473, 932
HapII CCGG 1 cut(s) 226
HhaI GCGC 2 cut(s) 341, 966
Hin1II CATG 4 cut(s) 354, 457, 751, 1259
Hin6I GCGC 2 cut(s) 339, 964
HinP1I GCGC 2 cut(s) 339, 964
HindIII AAGCTT 1 cut(s) 272
HinfI GANTC 7 cut(s) 314, 364, 415, 544, 1214, 1241, 1267
HpaII CCGG 1 cut(s) 226
HphI GGTGA 4 cut(s) 127, 192, 451, 1160
Hpy166II GTNNAC 3 cut(s) 223, 577, 948
Hpy188I TCNGA 8 cut(s) 151, 270, 799, 835, 942, 1207, 1219, 1246
Hpy188III TCNNGA 4 cut(s) 263, 368, 407, 860
Hpy8I GTNNAC 3 cut(s) 223, 577, 948
HpyAV CCTTC 3 cut(s) 485, 664, 926
HpyCH4III ACNGT 4 cut(s) 593, 1012, 1037, 1066
HpyCH4IV ACGT 3 cut(s) 531, 681, 898
HpyCH4V TGCA 6 cut(s) 61, 210, 646, 747, 1051, 1088
HpyF10VI GCNNNNNNNGC 1 cut(s) 918
HpyF3I CTNAG 5 cut(s) 150, 204, 939, 1019, 1243
HpySE526I ACGT 3 cut(s) 531, 681, 898
Hsp92II CATG 4 cut(s) 354, 457, 751, 1259
HspAI GCGC 2 cut(s) 339, 964
KpnI GGTACC 1 cut(s) 298
Kzo9I GATC 4 cut(s) 157, 265, 814, 1165
LmnI GCTCC 1 cut(s) 1119
Lsp1109I GCAGC 2 cut(s) 154, 222
LweI GCATC 1 cut(s) 790
MaeI CTAG 2 cut(s) 1112, 1263
MaeII ACGT 3 cut(s) 531, 681, 898
MalI GATC 4 cut(s) 159, 267, 816, 1167
MboI GATC 4 cut(s) 157, 265, 814, 1165
MboII GAAGA 9 cut(s) 186, 248, 686, 689, 748, 850, 860, 1220, 1223
MfeI CAATTG 1 cut(s) 641
MflI RGATCY 3 cut(s) 157, 814, 1165
MhlI GDGCHC 1 cut(s) 475
MluCI AATT 5 cut(s) 65, 641, 1070, 1196, 1222
MluI ACGCGT 1 cut(s) 83
MlyI GAGTC 4 cut(s) 323, 358, 1223, 1235
MmeI TCCRAC 1 cut(s) 691
Mph1103I ATGCAT 1 cut(s) 749
MseI TTAA 3 cut(s) 24, 69, 432
MslI CAYNNNNRTG 1 cut(s) 205
MspI CCGG 1 cut(s) 226
MspR9I CCNGG 4 cut(s) 464, 512, 616, 972
MunI CAATTG 1 cut(s) 641
Mva1269I GAATGC 1 cut(s) 174
MvaI CCWGG 4 cut(s) 464, 512, 616, 972
MvnI CGCG 1 cut(s) 85
MwoI GCNNNNNNNGC 1 cut(s) 918
NdeI CATATG 2 cut(s) 523, 1171
NdeII GATC 4 cut(s) 157, 265, 814, 1165
NlaIII CATG 4 cut(s) 354, 457, 751, 1259
NlaIV GGNNCC 5 cut(s) 296, 473, 509, 1109, 1167
NsiI ATGCAT 1 cut(s) 749
NspV TTCGAA 1 cut(s) 442
OliI CACNNNNGTG 1 cut(s) 205
PctI GAATGC 1 cut(s) 174
PfeI GAWTC 3 cut(s) 415, 544, 1267
PflMI CCANNNNNTGG 1 cut(s) 356
PkrI GCNGC 2 cut(s) 169, 212
PleI GAGTC 4 cut(s) 322, 358, 1222, 1235
PpsI GAGTC 4 cut(s) 322, 358, 1222, 1235
PpuMI RGGWCCY 2 cut(s) 508, 625
PshBI ATTAAT 1 cut(s) 432
Psp5II RGGWCCY 2 cut(s) 508, 625
Psp6I CCWGG 4 cut(s) 462, 510, 614, 970
PspGI CCWGG 4 cut(s) 462, 510, 614, 970
PspN4I GGNNCC 5 cut(s) 296, 473, 509, 1109, 1167
PspOMI GGGCCC 1 cut(s) 471
PspPI GGNCC 6 cut(s) 4, 471, 472, 508, 625, 931
PspPPI RGGWCCY 2 cut(s) 508, 625
PsuI RGATCY 3 cut(s) 157, 814, 1165
RsaI GTAC 5 cut(s) 296, 576, 794, 823, 1133
RsaNI GTAC 5 cut(s) 295, 575, 793, 822, 1132
RseI CAYNNNNRTG 1 cut(s) 205
SaqAI TTAA 3 cut(s) 24, 69, 432
SatI GCNGC 2 cut(s) 168, 211
Sau3AI GATC 4 cut(s) 157, 265, 814, 1165
Sau96I GGNCC 6 cut(s) 4, 471, 472, 508, 625, 931
SchI GAGTC 4 cut(s) 323, 358, 1223, 1235
ScrFI CCNGG 4 cut(s) 464, 512, 616, 972
SduI GDGCHC 1 cut(s) 475
SfaNI GCATC 1 cut(s) 790
SfuI TTCGAA 1 cut(s) 442
SinI GGWCC 2 cut(s) 508, 625
SmiMI CAYNNNNRTG 1 cut(s) 205
SmlI CTYRAG 2 cut(s) 161, 407
SmoI CTYRAG 2 cut(s) 161, 407
Sse9I AATT 5 cut(s) 65, 641, 1070, 1196, 1222
SsiI CCGC 2 cut(s) 33, 333
SspMI CTAG 2 cut(s) 1112, 1263
StyD4I CCNGG 4 cut(s) 462, 510, 614, 970
StyI CCWWGG 1 cut(s) 1262
TaaI ACNGT 4 cut(s) 593, 1012, 1037, 1066
TaiI ACGT 3 cut(s) 534, 684, 901
TaqI TCGA 3 cut(s) 418, 442, 1068
TaqII GACCGA 1 cut(s) 242
TasI AATT 5 cut(s) 65, 641, 1070, 1196, 1222
TatI WGTACW 2 cut(s) 574, 1131
TfiI GAWTC 3 cut(s) 415, 544, 1267
Tru1I TTAA 3 cut(s) 24, 69, 432
Tru9I TTAA 3 cut(s) 24, 69, 432
TscAI CASTG 3 cut(s) 14, 212, 560
TseI GCWGC 2 cut(s) 167, 210
TspDTI ATGAA 5 cut(s) 418, 524, 860, 1259, 1272
TspGWI ACGGA 3 cut(s) 38, 175, 780
TspRI CASTG 3 cut(s) 14, 212, 560
Van91I CCANNNNNTGG 1 cut(s) 356
VpaK11BI GGWCC 2 cut(s) 508, 625
VspI ATTAAT 1 cut(s) 432
XapI RAATTY 1 cut(s) 65
XmaJI CCTAGG 1 cut(s) 1262
XmiI GTMKAC 1 cut(s) 222
XspI CTAG 2 cut(s) 1112, 1263
Zsp2I ATGCAT 1 cut(s) 749
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.