Rh6CG344900

Protein ROOT PRIMORDIUM DEFECTIVE 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6C
OG0014611
Physical Location & Seq
Reverse (-)
53568192 .. 53570644
2453 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6CG344900.1

Sequence Viewer

Length: 1305 bp
ATGAACACTTTTTGTTACAATTCAGTCCTTTTCCTTTCGAGTAAAACCCTGAACCCTATGATTCGTTTCGAAAATCGAAAGTCGTTGTTTTCACTCTGTGAGTGGCTCCAGTCTCTGATTCCGATTCCAGGTATGCTCTCCAAGACTCGAACCATCTCTTCCTATCTGCACAGCCGCGCCACATCGCACGCGAACCCAGAAATCCACCTTGAGATCAAACCCATTTCGAGTCTGAAGGTGGTGTGGCGCAAAGACCCAAAGCTAGACCAGGCCATAGAGAACGACAAGCCGTACAAGCTCTGCGCCCGGGTCGTGAAGGAGGTCCTAAACGAGCCGGGCCAGAAAATCCCACTCCGGTACCTCGAAAAAAGGCGCGAGAGATTGCGCCTCAGAACCAAAGCCACAACCTTTATTGGCAAAAACCCAGGTTTATTTGAGGTCTACTACGATAGAATCAAACCCAAAACTGAGAAGGTTCAGTTTCTTAGGGTTAGTGATAGGCTGAGAGAGTTTCTTGAGGAAGAGAAGAGGATTAATGTGGAAAATGAGGGTTTGATAGTGTCTAAGTTGTGTAAATTGTTGATGATGGCCAAGAATAAGGTGGTTAGTGCTGATAAATTGGTTGATGTGAAGAGGGAATTTGGGTTCCCTAATGATTTTATGGTGAATTTGGTGCCTAAATATTCGCAGTATTTTCGGCTGGTTGGGGGTTCCAGCGAGGGCAAGTCATTCTTGGAATTGGTTGATTGGAACCCCGAGTTTGCGAAATCTGTGATTGAGAGGAGAGCAGAAGAGGAGTCAAGCTTGACAGGGATCCGGGTTCGGCCTAATTTTGATTACAAACTTCCACAAGGGTTTGTGTTGAACAAGGCAATGAGGGAGTGGGTTAGGGATTGGATGGAAATGGATTATATGTCGCCGTATGAGGATGTTTCCAAGTTGGATCAAGCGTCCCCAGAAATGGAGAAGCGGACGGTTGGGGTTTTCCATGAGTTATTGTCATTGTCTTTGTTGAAGAGGATGCCTGTGCCCATACTGGGAAAATTTTGTGATGAGTATAGGTTTTCAAATGCATTCCCGAATGTATTCACAAGGCATTCGGGGTTGTTTTATGTCTCACAGAAAGGAGGGATCAAGACGGCGGTGCTGAGGGAAGCTTACAAGGATGACCAGTTGATTGATCGGGATCCGCTGCTACAGATTAAGGATAAGTTTGTTGAGCTATTGGAGGAAGGATGGCGCGAGAGCACACAGCAGTTGAGGTTGCAAAGGGAAGAAGTTAAAGGGCATGGCTGTGAGGAATGA
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

434

Amino Acids

50.84

Weight (kDa)

9.2

Isoelectric Point (pI)

42.43

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 84 - 413 2.1e-107 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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Orthologous Genes (Group: OG0014611)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G63090
fragaria_vesca FvH4_2g23842
malus_domestica MD03G1268200.v1.1 MD11G1289000.v1.1
prunus_persica Prupe.8G243800_v2.0.a1
pyrus_communis pycom03g21410 pycom11g25640
rosa_chinensis RchiOBHm_Chr6g0291451
rosa_laevigata RLG00000012113
rosa_multiflora Rmu_sc0003296.1_g000003
rosa_roxburghii Rroxscaffold_7G00176040
rosa_rugosa Rorug06G0219500
rosa_samantha Rh6AG331800 Rh6BG338700 Rh6CG344900 Rh6DG332000
rosa_wichuraiana Rw6G028800

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 357
AccB1I GGYRCC 2 cut(s) 357, 673
AccI GTMKAC 1 cut(s) 441
AccII CGCG 4 cut(s) 177, 191, 375, 1242
AciI CCGC 4 cut(s) 175, 970, 1142, 1190
AclWI GGATC 6 cut(s) 808, 821, 951, 1139, 1181, 1194
AcoI YGGCCR 1 cut(s) 588
AcsI RAATTY 3 cut(s) 638, 667, 1043
AcuI CTGAAG 1 cut(s) 254
AdeI CACNNNGTG 1 cut(s) 98
AfaI GTAC 2 cut(s) 293, 359
AfiI CCNNNNNNNGG 3 cut(s) 128, 961, 1037
AgsI TTSAA 3 cut(s) 865, 1015, 1068
AjnI CCWGG 3 cut(s) 127, 267, 424
AloI GAACNNNNNNTCC 2 cut(s) 629, 661
AluBI AGCT 5 cut(s) 262, 298, 804, 1157, 1222
AluI AGCT 5 cut(s) 262, 298, 804, 1157, 1222
Alw21I GWGCWC 1 cut(s) 1250
Alw26I GTCTC 2 cut(s) 117, 1120
AlwI GGATC 6 cut(s) 808, 821, 951, 1139, 1181, 1194
AlwNI CAGNNNCTG 1 cut(s) 115
Ama87I CYCGRG 2 cut(s) 306, 755
AoxI GGCC 4 cut(s) 270, 337, 588, 824
ApeKI GCWGC 1 cut(s) 1192
ApoI RAATTY 3 cut(s) 638, 667, 1043
AseI ATTAAT 1 cut(s) 534
Asp700I GAANNNNTTC 1 cut(s) 1085
Asp718I GGTACC 1 cut(s) 357
AspLEI GCGC 6 cut(s) 179, 249, 305, 375, 387, 1242
AspS9I GGNCC 2 cut(s) 322, 337
AsuC2I CCSGG 4 cut(s) 307, 308, 336, 818
AsuHPI GGTGA 1 cut(s) 676
AsuII TTCGAA 1 cut(s) 69
AvaI CYCGRG 2 cut(s) 306, 755
AvaII GGWCC 1 cut(s) 322
BaeGI GKGCMC 1 cut(s) 1032
BaeI ACNNNNGTAYC 2 cut(s) 341, 374
BalI TGGCCA 1 cut(s) 590
BamHI GGATCC 2 cut(s) 813, 1186
BanI GGYRCC 2 cut(s) 357, 673
Bbv12I GWGCWC 1 cut(s) 1250
BbvCI CCTCAGC 1 cut(s) 1148
BbvI GCAGC 1 cut(s) 1179
BccI CCATC 4 cut(s) 161, 580, 892, 1230
BceAI ACGGC 3 cut(s) 274, 904, 1155
BcgI CGANNNNNNTGC 2 cut(s) 677, 711
BciT130I CCWGG 3 cut(s) 129, 269, 426
BcnI CCSGG 4 cut(s) 307, 308, 336, 818
BcoDI GTCTC 2 cut(s) 117, 1120
BfaI CTAG 1 cut(s) 263
BfmI CTRYAG 1 cut(s) 1196
BisI GCNGC 2 cut(s) 175, 1193
BlsI GCNGC 2 cut(s) 176, 1194
Bme1390I CCNGG 7 cut(s) 129, 269, 307, 308, 336, 426, 818
Bme18I GGWCC 1 cut(s) 322
BmeT110I CYCGRG 2 cut(s) 306, 755
BmgT120I GGNCC 2 cut(s) 322, 337
BmiI GGNNCC 8 cut(s) 107, 359, 647, 675, 712, 752, 815, 1188
BmrFI CCNGG 7 cut(s) 129, 269, 307, 308, 336, 426, 818
BmrI ACTGGG 1 cut(s) 1046
BmsI GCATC 1 cut(s) 1011
BmuI ACTGGG 1 cut(s) 1046
BpmI CTGGAG 1 cut(s) 92
Bpu10I CCTNAGC 1 cut(s) 1148
Bpu14I TTCGAA 1 cut(s) 69
BpuEI CTTGAG 2 cut(s) 230, 536
BpuMI CCSGG 4 cut(s) 307, 308, 336, 818
BsaBI GATNNNNATC 1 cut(s) 1185
BsaJI CCNNGG 2 cut(s) 306, 424
BsaWI WCCGGW 1 cut(s) 354
Bsc4I CCNNNNNNNGG 3 cut(s) 128, 961, 1037
Bse1I ACTGG 3 cut(s) 109, 1041, 1171
Bse3DI GCAATG 1 cut(s) 879
Bse8I GATNNNNATC 1 cut(s) 1185
BseBI CCWGG 3 cut(s) 129, 269, 426
BseDI CCNNGG 2 cut(s) 306, 424
BseGI GGATG 5 cut(s) 903, 934, 1026, 1171, 1241
BseJI GATNNNNATC 1 cut(s) 1185
BseLI CCNNNNNNNGG 3 cut(s) 128, 961, 1037
BseMI GCAATG 1 cut(s) 879
BseMII CTCAG 4 cut(s) 403, 459, 494, 1139
BseNI ACTGG 3 cut(s) 109, 1041, 1171
BseRI GAGGAG 2 cut(s) 796, 809
BseSI GKGCMC 1 cut(s) 1032
BseXI GCAGC 1 cut(s) 1179
BsgI GTGCAG 1 cut(s) 152
Bsh1236I CGCG 4 cut(s) 177, 191, 375, 1242
BshFI GGCC 4 cut(s) 272, 339, 590, 826
BshNI GGYRCC 2 cut(s) 357, 673
BsiHKAI GWGCWC 1 cut(s) 1250
BsiHKCI CYCGRG 2 cut(s) 306, 755
BsiSI CCGG 4 cut(s) 307, 335, 355, 817
BslFI GGGAC 1 cut(s) 937
BslI CCNNNNNNNGG 3 cut(s) 128, 961, 1037
BsmAI GTCTC 2 cut(s) 117, 1120
BsmFI GGGAC 1 cut(s) 937
BsmI GAATGC 2 cut(s) 1073, 1096
BsnI GGCC 4 cut(s) 272, 339, 590, 826
BsoBI CYCGRG 2 cut(s) 306, 755
Bsp119I TTCGAA 1 cut(s) 69
Bsp1286I GDGCHC 2 cut(s) 1032, 1250
Bsp143I GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
BspACI CCGC 4 cut(s) 175, 970, 1142, 1190
BspANI GGCC 4 cut(s) 272, 339, 590, 826
BspCNI CTCAG 4 cut(s) 402, 460, 495, 1140
BspFNI CGCG 4 cut(s) 177, 191, 375, 1242
BspLI GGNNCC 8 cut(s) 107, 359, 647, 675, 712, 752, 815, 1188
BspPI GGATC 6 cut(s) 808, 821, 951, 1139, 1181, 1194
BspT104I TTCGAA 1 cut(s) 69
BspT107I GGYRCC 2 cut(s) 357, 673
BsrDI GCAATG 1 cut(s) 879
BsrI ACTGG 3 cut(s) 109, 1041, 1171
BssECI CCNNGG 2 cut(s) 306, 424
BssMI GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
Bst2UI CCWGG 3 cut(s) 129, 269, 426
Bst4CI ACNGT 1 cut(s) 976
Bst6I CTCTTC 6 cut(s) 163, 516, 521, 626, 786, 1010
BstBI TTCGAA 1 cut(s) 69
BstC8I GCNNGC 1 cut(s) 189
BstDEI CTNAG 6 cut(s) 389, 468, 485, 503, 564, 1148
BstF5I GGATG 5 cut(s) 903, 934, 1026, 1171, 1241
BstFNI CGCG 4 cut(s) 177, 191, 375, 1242
BstHHI GCGC 6 cut(s) 179, 249, 305, 375, 387, 1242
BstKTI GATC 6 cut(s) 216, 816, 946, 1134, 1183, 1189
BstMAI GTCTC 2 cut(s) 117, 1120
BstMBI GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
BstMWI GCNNNNNNNGC 1 cut(s) 295
BstNI CCWGG 3 cut(s) 129, 269, 426
BstSCI CCNGG 7 cut(s) 127, 267, 305, 306, 334, 424, 816
BstSFI CTRYAG 1 cut(s) 1196
BstSLI GKGCMC 1 cut(s) 1032
BstUI CGCG 4 cut(s) 177, 191, 375, 1242
BstV1I GCAGC 1 cut(s) 1179
BstX2I RGATCY 2 cut(s) 813, 1186
BstYI RGATCY 2 cut(s) 813, 1186
BsuRI GGCC 4 cut(s) 272, 339, 590, 826
BtgZI GCGATG 1 cut(s) 168
BtsCI GGATG 5 cut(s) 903, 934, 1026, 1171, 1241
Cac8I GCNNGC 1 cut(s) 189
CaiI CAGNNNCTG 1 cut(s) 115
CfoI GCGC 6 cut(s) 179, 249, 305, 375, 387, 1242
Cfr13I GGNCC 2 cut(s) 322, 337
Cfr9I CCCGGG 1 cut(s) 306
CseI GACGC 1 cut(s) 939
Csp6I GTAC 2 cut(s) 292, 358
CviAII CATG 2 cut(s) 989, 1289
CviQI GTAC 2 cut(s) 292, 358
DdeI CTNAG 6 cut(s) 389, 468, 485, 503, 564, 1148
DpnI GATC 6 cut(s) 215, 815, 945, 1133, 1182, 1188
DpnII GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
DraIII CACNNNGTG 1 cut(s) 98
EaeI YGGCCR 1 cut(s) 588
Eam1104I CTCTTC 6 cut(s) 163, 516, 521, 626, 786, 1010
EarI CTCTTC 6 cut(s) 163, 516, 521, 626, 786, 1010
Eco47I GGWCC 1 cut(s) 322
Eco57I CTGAAG 1 cut(s) 254
Eco88I CYCGRG 2 cut(s) 306, 755
EcoO109I RGGNCCY 1 cut(s) 322
EcoRII CCWGG 3 cut(s) 127, 267, 424
EcoT22I ATGCAT 1 cut(s) 1075
FaeI CATG 2 cut(s) 992, 1292
FalI AAGNNNNNCTT 2 cut(s) 716, 748
FaqI GGGAC 1 cut(s) 937
FatI CATG 2 cut(s) 988, 1288
FblI GTMKAC 1 cut(s) 441
Fnu4HI GCNGC 2 cut(s) 175, 1193
FokI GGATG 5 cut(s) 910, 941, 1033, 1178, 1248
Fsp4HI GCNGC 2 cut(s) 175, 1193
FspBI CTAG 1 cut(s) 263
GlaI GCGC 6 cut(s) 178, 248, 304, 374, 386, 1241
GluI GCNGC 2 cut(s) 175, 1193
GsuI CTGGAG 1 cut(s) 92
HaeIII GGCC 4 cut(s) 272, 339, 590, 826
HapII CCGG 4 cut(s) 307, 335, 355, 817
HgaI GACGC 1 cut(s) 939
HhaI GCGC 6 cut(s) 179, 249, 305, 375, 387, 1242
Hin1II CATG 2 cut(s) 992, 1292
Hin6I GCGC 6 cut(s) 177, 247, 303, 373, 385, 1240
HinP1I GCGC 6 cut(s) 177, 247, 303, 373, 385, 1240
HindIII AAGCTT 2 cut(s) 802, 1155
HinfI GANTC 7 cut(s) 61, 118, 124, 145, 229, 453, 797
HpaII CCGG 4 cut(s) 307, 335, 355, 817
HphI GGTGA 1 cut(s) 676
Hpy166II GTNNAC 1 cut(s) 442
Hpy188I TCNGA 4 cut(s) 117, 123, 234, 392
Hpy188III TCNNGA 5 cut(s) 313, 515, 1078, 1135, 1184
Hpy8I GTNNAC 1 cut(s) 442
HpyAV CCTTC 4 cut(s) 229, 310, 466, 1226
HpyCH4III ACNGT 1 cut(s) 976
HpyCH4V TGCA 3 cut(s) 169, 1073, 1267
HpyF10VI GCNNNNNNNGC 1 cut(s) 295
HpyF3I CTNAG 6 cut(s) 389, 468, 485, 503, 564, 1148
Hsp92II CATG 2 cut(s) 992, 1292
HspAI GCGC 6 cut(s) 177, 247, 303, 373, 385, 1240
KpnI GGTACC 1 cut(s) 361
Kzo9I GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
LmnI GCTCC 1 cut(s) 111
Lsp1109I GCAGC 1 cut(s) 1179
LweI GCATC 1 cut(s) 1011
MaeI CTAG 1 cut(s) 263
MaeIII GTNAC 1 cut(s) 14
MalI GATC 6 cut(s) 215, 815, 945, 1133, 1182, 1188
MboI GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
MboII GAAGA 7 cut(s) 150, 533, 538, 643, 803, 1027, 1286
MflI RGATCY 2 cut(s) 813, 1186
MhlI GDGCHC 2 cut(s) 1032, 1250
MlsI TGGCCA 1 cut(s) 590
MluCI AATT 8 cut(s) 19, 575, 617, 638, 667, 737, 829, 1043
MluNI TGGCCA 1 cut(s) 590
MlyI GAGTC 3 cut(s) 139, 238, 806
MmeI TCCRAC 1 cut(s) 921
Mox20I TGGCCA 1 cut(s) 590
Mph1103I ATGCAT 1 cut(s) 1075
MroXI GAANNNNTTC 1 cut(s) 1085
MscI TGGCCA 1 cut(s) 590
MseI TTAA 3 cut(s) 534, 1203, 1281
MslI CAYNNNNRTG 1 cut(s) 1293
Msp20I TGGCCA 1 cut(s) 590
MspA1I CMGCKG 1 cut(s) 1192
MspI CCGG 4 cut(s) 307, 335, 355, 817
MspR9I CCNGG 7 cut(s) 129, 269, 307, 308, 336, 426, 818
Mva1269I GAATGC 2 cut(s) 1073, 1096
MvaI CCWGG 3 cut(s) 129, 269, 426
MvnI CGCG 4 cut(s) 177, 191, 375, 1242
MwoI GCNNNNNNNGC 1 cut(s) 295
NciI CCSGG 4 cut(s) 307, 308, 336, 818
NdeII GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
NlaIII CATG 2 cut(s) 992, 1292
NlaIV GGNNCC 8 cut(s) 107, 359, 647, 675, 712, 752, 815, 1188
NsiI ATGCAT 1 cut(s) 1075
NspV TTCGAA 1 cut(s) 69
PctI GAATGC 2 cut(s) 1073, 1096
PdmI GAANNNNTTC 1 cut(s) 1085
PfeI GAWTC 4 cut(s) 61, 118, 124, 453
PkrI GCNGC 2 cut(s) 176, 1194
PleI GAGTC 3 cut(s) 139, 237, 805
PpsI GAGTC 3 cut(s) 139, 237, 805
PpuMI RGGWCCY 1 cut(s) 322
PshBI ATTAAT 1 cut(s) 534
Psp5II RGGWCCY 1 cut(s) 322
Psp6I CCWGG 3 cut(s) 127, 267, 424
PspGI CCWGG 3 cut(s) 127, 267, 424
PspN4I GGNNCC 8 cut(s) 107, 359, 647, 675, 712, 752, 815, 1188
PspPI GGNCC 2 cut(s) 322, 337
PspPPI RGGWCCY 1 cut(s) 322
PstNI CAGNNNCTG 1 cut(s) 115
PsuI RGATCY 2 cut(s) 813, 1186
RsaI GTAC 2 cut(s) 293, 359
RsaNI GTAC 2 cut(s) 292, 358
RseI CAYNNNNRTG 1 cut(s) 1293
SaqAI TTAA 3 cut(s) 534, 1203, 1281
SatI GCNGC 2 cut(s) 175, 1193
Sau3AI GATC 6 cut(s) 213, 813, 943, 1131, 1180, 1186
Sau96I GGNCC 2 cut(s) 322, 337
SchI GAGTC 3 cut(s) 139, 238, 806
ScrFI CCNGG 7 cut(s) 129, 269, 307, 308, 336, 426, 818
SduI GDGCHC 2 cut(s) 1032, 1250
SfaNI GCATC 1 cut(s) 1011
SfcI CTRYAG 1 cut(s) 1196
SfuI TTCGAA 1 cut(s) 69
SinI GGWCC 1 cut(s) 322
SmaI CCCGGG 1 cut(s) 308
SmiMI CAYNNNNRTG 1 cut(s) 1293
SmlI CTYRAG 2 cut(s) 209, 515
SmoI CTYRAG 2 cut(s) 209, 515
Sse9I AATT 8 cut(s) 19, 575, 617, 638, 667, 737, 829, 1043
SsiI CCGC 4 cut(s) 175, 970, 1142, 1190
SspI AATATT 1 cut(s) 683
SspMI CTAG 1 cut(s) 263
StyD4I CCNGG 7 cut(s) 127, 267, 305, 306, 334, 424, 816
TaaI ACNGT 1 cut(s) 976
TaqI TCGA 6 cut(s) 38, 69, 76, 148, 227, 363
TasI AATT 8 cut(s) 19, 575, 617, 638, 667, 737, 829, 1043
TauI GCSGC 1 cut(s) 177
TfiI GAWTC 4 cut(s) 61, 118, 124, 453
Tru1I TTAA 3 cut(s) 534, 1203, 1281
Tru9I TTAA 3 cut(s) 534, 1203, 1281
TseI GCWGC 1 cut(s) 1192
TspDTI ATGAA 1 cut(s) 17
TspMI CCCGGG 1 cut(s) 306
VpaK11BI GGWCC 1 cut(s) 322
VspI ATTAAT 1 cut(s) 534
XapI RAATTY 3 cut(s) 638, 667, 1043
XcmI CCANNNNNNNNNTGG 1 cut(s) 598
XmaI CCCGGG 1 cut(s) 306
XmiI GTMKAC 1 cut(s) 441
XmnI GAANNNNTTC 1 cut(s) 1085
XspI CTAG 1 cut(s) 263
Zsp2I ATGCAT 1 cut(s) 1075
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.