Rh6DG332000

Protein ROOT PRIMORDIUM DEFECTIVE 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr6D
OG0014611
Physical Location & Seq
Reverse (-)
53733984 .. 53735171
1188 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh6DG332000.1

Sequence Viewer

Length: 1188 bp
ATGCTCTCCAAGACTCGAACCATCTCGTCCTATCTGCACAGCCACGGCACCACTCTCACATCGCACGCGAACCCAGAAATCCACCTTCAGATCAAACCCATTTCGAGTCTGAAGGTGGTGTGGCGCAAAGACCCAAAGCTAGACCAGGCCATAGAGAACGACAAGCCGTACAAGCTCTGCGCCCGGGTCGTGAAGGAGGTCCTAAACGAACCGGGCCAGAAAATCCCACTCCGGTACCTCGAAAAAAGGCGCGAGAGATTGCGCCTCAGAACCAAAGCCACAACCTTTATTGGCAAAAACCCAGGTTTATTTGAGGTCTATTATGATAGAATCAAACCCAAAATTGAGAAGGTTCAGTTTCTTAGGGTTAGTGATAGGCTGAGAGAGTTTCTTGAAGAAGAGAAGAGGATTAATGTGGAAAATGAGGGTTTGATTGTGTCTAAGTTGTGTAAATTGTTGATGATGGCCAATAATAAGGTGGTTAGTGCTGATAAATTGGTTGATGTGAAGAGGGAATTTGGGTTCCCTAATGATTTTATGGTGAATTTGGTGCCTAAATATTCGCAGTATTTTCGGCTGGTTGGGGGTTCCGGCGAGGGGAAGTCATTCTTGGAATTGGTTGATTGGAACCCCGAGTTTGCGAAATCTGTGATTGATAGGAGAGCAGAAGAGGAGTCAAGCTTGACAGGGATCCGGGTTCGGCCTAATTTTGATTACAAGCTTCCACAAGGGTTTGTGTTGAAGAAGGAAATGAGGGAGTGGGTTAGGGATTGGATGGAAATGGATTATATGTCGCCGTATGAGGATGTTTCGAAGTTGGATCAAGCGTCCCCAGAAATGGAGAAGAGGACGGTTGGGGTTTTCCATGAGTTGTTGTCATTGTCTTTGTTGAAGAGGATGCCTGTGCCCATACTGGGAAAATTTTGTGATGAGTATAGGTTTTCAAATGCATTCCCGAATGTATTCACAAGGCATTCGGGGTTGTTTTATGTGTCACAGAAAGGAGGGATCAAGACGGCGGTGCTGAGGGAAGCTTACAAGGATGACCAGTTGATTGATCGGGATCCGCTGCTACAGATTAAGGATAAGTTTGTTGAGCTATTGGAGGAAGGATGGCGGGAGAGCACACAGCAGTTGAGGTTGCAAAGGGAAGAAGTTAAGGGGATGGCTGTGAGGAATGAAGAATAG
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

395

Amino Acids

46.3

Weight (kDa)

9.22

Isoelectric Point (pI)

40.97

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 43 - 372 2.3e-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) 234
AccB1I GGYRCC 3 cut(s) 47, 234, 550
AccII CGCG 2 cut(s) 68, 252
AciI CCGC 3 cut(s) 1019, 1067, 1117
AclWI GGATC 6 cut(s) 685, 698, 828, 1016, 1058, 1071
AcoI YGGCCR 1 cut(s) 465
AcsI RAATTY 3 cut(s) 515, 544, 920
AcuI CTGAAG 2 cut(s) 71, 131
AfaI GTAC 2 cut(s) 170, 236
AfiI CCNNNNNNNGG 3 cut(s) 597, 838, 914
AgsI TTSAA 4 cut(s) 395, 742, 892, 945
AjnI CCWGG 2 cut(s) 144, 301
AjuI GAANNNNNNNTTGG 2 cut(s) 593, 625
AloI GAACNNNNNNTCC 2 cut(s) 506, 538
AluBI AGCT 6 cut(s) 139, 175, 681, 721, 1034, 1099
AluI AGCT 6 cut(s) 139, 175, 681, 721, 1034, 1099
Alw21I GWGCWC 1 cut(s) 1127
AlwI GGATC 6 cut(s) 685, 698, 828, 1016, 1058, 1071
Ama87I CYCGRG 2 cut(s) 183, 632
AoxI GGCC 4 cut(s) 147, 214, 465, 701
ApeKI GCWGC 1 cut(s) 1069
ApoI RAATTY 3 cut(s) 515, 544, 920
AseI ATTAAT 1 cut(s) 411
Asp700I GAANNNNTTC 2 cut(s) 605, 962
Asp718I GGTACC 1 cut(s) 234
AspLEI GCGC 4 cut(s) 126, 182, 252, 264
AspS9I GGNCC 2 cut(s) 199, 214
AsuC2I CCSGG 4 cut(s) 184, 185, 213, 695
AsuHPI GGTGA 1 cut(s) 553
AsuII TTCGAA 1 cut(s) 812
AvaI CYCGRG 2 cut(s) 183, 632
AvaII GGWCC 1 cut(s) 199
BaeGI GKGCMC 1 cut(s) 909
BaeI ACNNNNGTAYC 2 cut(s) 218, 251
BalI TGGCCA 1 cut(s) 467
BamHI GGATCC 2 cut(s) 690, 1063
BanI GGYRCC 3 cut(s) 47, 234, 550
Bbv12I GWGCWC 1 cut(s) 1127
BbvCI CCTCAGC 1 cut(s) 1025
BbvI GCAGC 1 cut(s) 1056
BccI CCATC 5 cut(s) 29, 457, 769, 1107, 1159
BceAI ACGGC 4 cut(s) 61, 151, 781, 1032
BcgI CGANNNNNNTGC 2 cut(s) 554, 588
BciT130I CCWGG 2 cut(s) 146, 303
BcnI CCSGG 4 cut(s) 184, 185, 213, 695
BfaI CTAG 1 cut(s) 140
BfmI CTRYAG 1 cut(s) 1073
BisI GCNGC 1 cut(s) 1070
BlsI GCNGC 1 cut(s) 1071
Bme1390I CCNGG 6 cut(s) 146, 184, 185, 213, 303, 695
Bme18I GGWCC 1 cut(s) 199
BmeT110I CYCGRG 2 cut(s) 183, 632
BmgT120I GGNCC 2 cut(s) 199, 214
BmiI GGNNCC 8 cut(s) 49, 236, 524, 552, 589, 629, 692, 1065
BmrFI CCNGG 6 cut(s) 146, 184, 185, 213, 303, 695
BmrI ACTGGG 1 cut(s) 923
BmsI GCATC 1 cut(s) 888
BmuI ACTGGG 1 cut(s) 923
Bpu10I CCTNAGC 1 cut(s) 1025
Bpu14I TTCGAA 1 cut(s) 812
BpuMI CCSGG 4 cut(s) 184, 185, 213, 695
BsaBI GATNNNNATC 1 cut(s) 1062
BsaJI CCNNGG 3 cut(s) 43, 183, 301
BsaWI WCCGGW 1 cut(s) 231
Bsc4I CCNNNNNNNGG 3 cut(s) 597, 838, 914
Bse1I ACTGG 2 cut(s) 918, 1048
Bse8I GATNNNNATC 1 cut(s) 1062
BseBI CCWGG 2 cut(s) 146, 303
BseDI CCNNGG 3 cut(s) 43, 183, 301
BseGI GGATG 6 cut(s) 780, 811, 903, 1048, 1118, 1170
BseJI GATNNNNATC 1 cut(s) 1062
BseLI CCNNNNNNNGG 3 cut(s) 597, 838, 914
BseMII CTCAG 3 cut(s) 280, 371, 1016
BseNI ACTGG 2 cut(s) 918, 1048
BseRI GAGGAG 1 cut(s) 686
BseSI GKGCMC 1 cut(s) 909
BseXI GCAGC 1 cut(s) 1056
BsgI GTGCAG 1 cut(s) 20
Bsh1236I CGCG 2 cut(s) 68, 252
BshFI GGCC 4 cut(s) 149, 216, 467, 703
BshNI GGYRCC 3 cut(s) 47, 234, 550
BsiHKAI GWGCWC 1 cut(s) 1127
BsiHKCI CYCGRG 2 cut(s) 183, 632
BsiSI CCGG 5 cut(s) 184, 212, 232, 591, 694
BslFI GGGAC 1 cut(s) 814
BslI CCNNNNNNNGG 3 cut(s) 597, 838, 914
BsmFI GGGAC 1 cut(s) 814
BsmI GAATGC 2 cut(s) 950, 973
BsnI GGCC 4 cut(s) 149, 216, 467, 703
BsoBI CYCGRG 2 cut(s) 183, 632
Bsp119I TTCGAA 1 cut(s) 812
Bsp1286I GDGCHC 2 cut(s) 909, 1127
Bsp143I GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
BspACI CCGC 3 cut(s) 1019, 1067, 1117
BspANI GGCC 4 cut(s) 149, 216, 467, 703
BspCNI CTCAG 3 cut(s) 279, 372, 1017
BspFNI CGCG 2 cut(s) 68, 252
BspLI GGNNCC 8 cut(s) 49, 236, 524, 552, 589, 629, 692, 1065
BspPI GGATC 6 cut(s) 685, 698, 828, 1016, 1058, 1071
BspT104I TTCGAA 1 cut(s) 812
BspT107I GGYRCC 3 cut(s) 47, 234, 550
BsrI ACTGG 2 cut(s) 918, 1048
BssECI CCNNGG 3 cut(s) 43, 183, 301
BssMI GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
Bst2UI CCWGG 2 cut(s) 146, 303
Bst4CI ACNGT 1 cut(s) 853
Bst6I CTCTTC 6 cut(s) 393, 398, 503, 663, 839, 887
BstBI TTCGAA 1 cut(s) 812
BstC8I GCNNGC 1 cut(s) 66
BstDEI CTNAG 5 cut(s) 266, 362, 380, 441, 1025
BstDSI CCRYGG 1 cut(s) 43
BstF5I GGATG 6 cut(s) 780, 811, 903, 1048, 1118, 1170
BstFNI CGCG 2 cut(s) 68, 252
BstHHI GCGC 4 cut(s) 126, 182, 252, 264
BstKTI GATC 6 cut(s) 93, 693, 823, 1011, 1060, 1066
BstMBI GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
BstMWI GCNNNNNNNGC 1 cut(s) 172
BstNI CCWGG 2 cut(s) 146, 303
BstSCI CCNGG 6 cut(s) 144, 182, 183, 211, 301, 693
BstSFI CTRYAG 1 cut(s) 1073
BstSLI GKGCMC 1 cut(s) 909
BstUI CGCG 2 cut(s) 68, 252
BstV1I GCAGC 1 cut(s) 1056
BstX2I RGATCY 2 cut(s) 690, 1063
BstYI RGATCY 2 cut(s) 690, 1063
BsuRI GGCC 4 cut(s) 149, 216, 467, 703
BtgI CCRYGG 1 cut(s) 43
BtgZI GCGATG 1 cut(s) 45
BtsCI GGATG 6 cut(s) 780, 811, 903, 1048, 1118, 1170
Cac8I GCNNGC 1 cut(s) 66
CfoI GCGC 4 cut(s) 126, 182, 252, 264
Cfr13I GGNCC 2 cut(s) 199, 214
Cfr9I CCCGGG 1 cut(s) 183
CseI GACGC 1 cut(s) 816
Csp6I GTAC 2 cut(s) 169, 235
CviAII CATG 1 cut(s) 866
CviQI GTAC 2 cut(s) 169, 235
DdeI CTNAG 5 cut(s) 266, 362, 380, 441, 1025
DpnI GATC 6 cut(s) 92, 692, 822, 1010, 1059, 1065
DpnII GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
EaeI YGGCCR 1 cut(s) 465
Eam1104I CTCTTC 6 cut(s) 393, 398, 503, 663, 839, 887
EarI CTCTTC 6 cut(s) 393, 398, 503, 663, 839, 887
Eco47I GGWCC 1 cut(s) 199
Eco57I CTGAAG 2 cut(s) 71, 131
Eco88I CYCGRG 2 cut(s) 183, 632
EcoO109I RGGNCCY 1 cut(s) 199
EcoRII CCWGG 2 cut(s) 144, 301
EcoT22I ATGCAT 1 cut(s) 952
FaeI CATG 1 cut(s) 869
FalI AAGNNNNNCTT 2 cut(s) 593, 625
FaqI GGGAC 1 cut(s) 814
FatI CATG 1 cut(s) 865
FauI CCCGC 1 cut(s) 1110
Fnu4HI GCNGC 1 cut(s) 1070
FokI GGATG 6 cut(s) 787, 818, 910, 1055, 1125, 1177
Fsp4HI GCNGC 1 cut(s) 1070
FspBI CTAG 1 cut(s) 140
GlaI GCGC 4 cut(s) 125, 181, 251, 263
GluI GCNGC 1 cut(s) 1070
HaeIII GGCC 4 cut(s) 149, 216, 467, 703
HapII CCGG 5 cut(s) 184, 212, 232, 591, 694
HgaI GACGC 1 cut(s) 816
HhaI GCGC 4 cut(s) 126, 182, 252, 264
Hin1II CATG 1 cut(s) 869
Hin6I GCGC 4 cut(s) 124, 180, 250, 262
HinP1I GCGC 4 cut(s) 124, 180, 250, 262
HindIII AAGCTT 3 cut(s) 679, 719, 1032
HinfI GANTC 4 cut(s) 13, 106, 330, 674
HpaII CCGG 5 cut(s) 184, 212, 232, 591, 694
HphI GGTGA 1 cut(s) 553
Hpy188I TCNGA 3 cut(s) 90, 111, 269
Hpy188III TCNNGA 5 cut(s) 190, 392, 955, 1012, 1061
HpyAV CCTTC 6 cut(s) 95, 106, 187, 343, 739, 1103
HpyCH4III ACNGT 1 cut(s) 853
HpyCH4V TGCA 3 cut(s) 37, 950, 1144
HpyF10VI GCNNNNNNNGC 1 cut(s) 172
HpyF3I CTNAG 5 cut(s) 266, 362, 380, 441, 1025
Hsp92II CATG 1 cut(s) 869
HspAI GCGC 4 cut(s) 124, 180, 250, 262
KpnI GGTACC 1 cut(s) 238
Kzo9I GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
Lsp1109I GCAGC 1 cut(s) 1056
LweI GCATC 1 cut(s) 888
MaeI CTAG 1 cut(s) 140
MaeIII GTNAC 1 cut(s) 993
MalI GATC 6 cut(s) 92, 692, 822, 1010, 1059, 1065
MboI GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
MboII GAAGA 9 cut(s) 407, 410, 415, 520, 680, 754, 856, 904, 1163
MflI RGATCY 2 cut(s) 690, 1063
MhlI GDGCHC 2 cut(s) 909, 1127
MlsI TGGCCA 1 cut(s) 467
MluCI AATT 8 cut(s) 342, 452, 494, 515, 544, 614, 706, 920
MluNI TGGCCA 1 cut(s) 467
MlyI GAGTC 3 cut(s) 7, 115, 683
MmeI TCCRAC 1 cut(s) 798
Mox20I TGGCCA 1 cut(s) 467
Mph1103I ATGCAT 1 cut(s) 952
MroXI GAANNNNTTC 2 cut(s) 605, 962
MscI TGGCCA 1 cut(s) 467
MseI TTAA 3 cut(s) 411, 1080, 1158
Msp20I TGGCCA 1 cut(s) 467
MspA1I CMGCKG 1 cut(s) 1069
MspI CCGG 5 cut(s) 184, 212, 232, 591, 694
MspR9I CCNGG 6 cut(s) 146, 184, 185, 213, 303, 695
Mva1269I GAATGC 2 cut(s) 950, 973
MvaI CCWGG 2 cut(s) 146, 303
MvnI CGCG 2 cut(s) 68, 252
MwoI GCNNNNNNNGC 1 cut(s) 172
NciI CCSGG 4 cut(s) 184, 185, 213, 695
NdeII GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
NlaIII CATG 1 cut(s) 869
NlaIV GGNNCC 8 cut(s) 49, 236, 524, 552, 589, 629, 692, 1065
NmuCI GTSAC 1 cut(s) 993
NsiI ATGCAT 1 cut(s) 952
NspV TTCGAA 1 cut(s) 812
PctI GAATGC 2 cut(s) 950, 973
PdmI GAANNNNTTC 2 cut(s) 605, 962
PfeI GAWTC 1 cut(s) 330
PkrI GCNGC 1 cut(s) 1071
PleI GAGTC 3 cut(s) 7, 114, 682
PpsI GAGTC 3 cut(s) 7, 114, 682
PpuMI RGGWCCY 1 cut(s) 199
PshBI ATTAAT 1 cut(s) 411
Psp5II RGGWCCY 1 cut(s) 199
Psp6I CCWGG 2 cut(s) 144, 301
PspGI CCWGG 2 cut(s) 144, 301
PspN4I GGNNCC 8 cut(s) 49, 236, 524, 552, 589, 629, 692, 1065
PspPI GGNCC 2 cut(s) 199, 214
PspPPI RGGWCCY 1 cut(s) 199
PsuI RGATCY 2 cut(s) 690, 1063
RsaI GTAC 2 cut(s) 170, 236
RsaNI GTAC 2 cut(s) 169, 235
SaqAI TTAA 3 cut(s) 411, 1080, 1158
SatI GCNGC 1 cut(s) 1070
Sau3AI GATC 6 cut(s) 90, 690, 820, 1008, 1057, 1063
Sau96I GGNCC 2 cut(s) 199, 214
SchI GAGTC 3 cut(s) 7, 115, 683
ScrFI CCNGG 6 cut(s) 146, 184, 185, 213, 303, 695
SduI GDGCHC 2 cut(s) 909, 1127
SfaNI GCATC 1 cut(s) 888
SfcI CTRYAG 1 cut(s) 1073
SfuI TTCGAA 1 cut(s) 812
SinI GGWCC 1 cut(s) 199
SmaI CCCGGG 1 cut(s) 185
Sse9I AATT 8 cut(s) 342, 452, 494, 515, 544, 614, 706, 920
SsiI CCGC 3 cut(s) 1019, 1067, 1117
SspI AATATT 1 cut(s) 560
SspMI CTAG 1 cut(s) 140
StyD4I CCNGG 6 cut(s) 144, 182, 183, 211, 301, 693
TaaI ACNGT 1 cut(s) 853
TaqI TCGA 4 cut(s) 16, 104, 240, 812
TasI AATT 8 cut(s) 342, 452, 494, 515, 544, 614, 706, 920
TfiI GAWTC 1 cut(s) 330
Tru1I TTAA 3 cut(s) 411, 1080, 1158
Tru9I TTAA 3 cut(s) 411, 1080, 1158
TseFI GTSAC 1 cut(s) 993
TseI GCWGC 1 cut(s) 1069
Tsp45I GTSAC 1 cut(s) 993
TspMI CCCGGG 1 cut(s) 183
VpaK11BI GGWCC 1 cut(s) 199
VspI ATTAAT 1 cut(s) 411
XapI RAATTY 3 cut(s) 515, 544, 920
XcmI CCANNNNNNNNNTGG 1 cut(s) 475
XmaI CCCGGG 1 cut(s) 183
XmnI GAANNNNTTC 2 cut(s) 605, 962
XspI CTAG 1 cut(s) 140
Zsp2I ATGCAT 1 cut(s) 952
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.