Rh4BG122500

Protein ROOT PRIMORDIUM DEFECTIVE

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr4B
OG0014511
Physical Location & Seq
Reverse (-)
20513858 .. 20519222
5365 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh4BG122500.1

Sequence Viewer

Length: 1602 bp
ATGTCTCCCTTTCACTTCACCTTCCGCTCCGTCCTAAACCCCCACCACCGCCACCACCACCACCGCCACGTCAGCCGCAGAACCTTCGTGGACACCACCATAAACTGGGTCCGCGACCGCGGCCTCGACCACGTGGTCGAGCGGGAGAGAAACCTCCGGCCAATCATCAACATCAAGAACCTCATCAAATCAGAGCCCTCCAAATCCCTCCCCATTTCCCTCCTCACCAAATCCCGCCACTCCCTCATGATCCCCACCCGCCCCGTCGAGTTCGTCCGCCAATACCCCTCCATTTTCGAGGAGTTCCTCCCCGCCGTCCAGCCCCACGTCCGCCTCACCCCGCAAGTCCTCGACATCGACGCCAACGAGCAGTTGATGTATCAGAGCGTGACCTACACGCACCAAGCCGCCGATCGCCTCTTCAAGCTGCTAATGCTGGTGAGAAGCAACAAACTGCCGCTGAATATCATTGAGCTTTTCAAATGGGATTTGGGGCTTCCTCAAGATTACGTGGACACCATAGTGCCGGAGTTTCCGGATTACTTTAAGATTGTAGTGGGGAAATATGGGCAGCCGGAGTTGGAGATGGTGTGTTGGAGTGATGAGCTGGCCACTTCGGTTATGGAGAAGAAAGCAAAACAGGGCTATGTCAAGGGAATGCCGCTTGCTTTTCCTATGCAGTTTTCGAGAGGTTTCGAGATGGATAAGAAGCTGAAGAAGTGGATTGATGTGTGGCAGAAGTTGCCGTATGTGTCTCCTTATGAAAATGCAGCTCATCTGTCGTCTCAGAGTGACGAGTCGGATAAGTGGGCCGTTGCGGTTTTGCATGAGCTTCTGCATATTTTGGTTCCGAAGAAGACAGACAGGGAGAATGTTTTGGCTCTGGGAGAGTATTTGGGGATTAGATCGAGGTTTAAGCGGGCATTGCTTCACCATCCGGGAATATTGTATGTGTCGAGCAAGATTAGGACTTATACAGTTGTGTTGAGAGAAGGGTATAAGAGGGGTGCCATTATTGAAAATCATCCGCTGATGGACATAAGAAACCAGTATATTCACCTCATGAATGCTGTGAAGGAAGATGGTAAAACGATAAGTTCCAAGGAGAAGAAGACGAAGGGAATTGAAGATTCTAAAGGAGAGGATGTAGAAGAGGAAGATGATGACAATGAGGAAGAGCTGGAAGGGGAGCTGTGTGATTCGTCTGATGCTGAAGTGGAGCATGACAATGTTGACAGTGAAGATGGCGATGAAGAAGAGGATGAAGACGATGAAGAAGAAGAGAGTATGACAAGCATTCGAATGAATGATGCTAATACTAGAGGAAGAAGAGCTAGGAAATCTAATTATGATGTCATGACACCTTCCAGAAATGCTGGAAGAGGAAGTTCAGGTCAAAGAAGAGCTTGGAAATCTGATAATACTGAGAGAAGGAGGTCCGGTGGACAATACCCTCTTAGGAGCGGGGATGAAGTCTCAGCAGAAACTTCTAGAAGAACACAAGCTGATGTTAGGCATAATGTCCACCAAAATTCAAGAGAAAGATCAAATCGCTCCAGAAGCAGGGGGAGTTCTTCACCAGACAAGAAGAATTATGTTTAG
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

533

Amino Acids

61.81

Weight (kDa)

6.54

Isoelectric Point (pI)

57.67

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PORR PF11955 37 - 358 3.1e-114 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: OG0014511)

Species Orthologous Gene IDs
arabidopsis_thaliana AT1G71850
fragaria_vesca FvH4_4g08630 FvH4_4g08630
malus_domestica MD10G1045200.v1.1
prunus_persica Prupe.8G052100_v2.0.a1
pyrus_communis pycom10g03160
rosa_chinensis RchiOBHm_Chr4g0405141
rosa_laevigata RLG00000008869
rosa_multiflora Rmu_co8338777.1_g000001 Rmu_ssc0000255.1_g000039
rosa_roxburghii Rroxscaffold_5G00349370
rosa_rugosa Rorug04G0054000 Rorug04G0054100
rosa_samantha Rh4BG122500 Rh4CG136300 Rh4DG122700
rosa_wichuraiana Rw4G010430

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 1 cut(s) 134
AccB1I GGYRCC 1 cut(s) 1007
AccB7I CCANNNNNTGG 1 cut(s) 105
AccBSI CCGCTC 3 cut(s) 27, 142, 1464
AccII CGCG 2 cut(s) 114, 120
AccIII TCCGGA 1 cut(s) 535
AclWI GGATC 1 cut(s) 244
AcoI YGGCCR 2 cut(s) 158, 609
AcsI RAATTY 1 cut(s) 1531
AcuI CTGAAG 2 cut(s) 734, 1233
AcvI CACGTG 1 cut(s) 133
AcyI GRCGYC 1 cut(s) 360
AfiI CCNNNNNNNGG 2 cut(s) 105, 1563
AgsI TTSAA 5 cut(s) 424, 481, 1019, 1127, 1536
AjiI CACGTC 2 cut(s) 70, 328
AleI CACNNNNGTG 1 cut(s) 521
Alw26I GTCTC 4 cut(s) 9, 759, 789, 1480
AlwI GGATC 1 cut(s) 244
Aor13HI TCCGGA 1 cut(s) 535
AoxI GGCC 4 cut(s) 121, 158, 609, 810
ApeKI GCWGC 3 cut(s) 427, 571, 770
ApoI RAATTY 1 cut(s) 1531
AspS9I GGNCC 3 cut(s) 109, 810, 1437
AsuC2I CCSGG 1 cut(s) 939
AsuHPI GGTGA 7 cut(s) 10, 217, 328, 451, 923, 1049, 1569
AsuII TTCGAA 1 cut(s) 1300
AvaII GGWCC 2 cut(s) 109, 1437
BalI TGGCCA 1 cut(s) 611
BanI GGYRCC 1 cut(s) 1007
BanII GRGCYC 1 cut(s) 198
BbrPI CACGTG 1 cut(s) 133
BbsI GAAGAC 3 cut(s) 863, 1118, 1272
BbvI GCAGC 3 cut(s) 414, 583, 782
BccI CCATC 6 cut(s) 580, 694, 942, 1027, 1076, 1238
BceAI ACGGC 3 cut(s) 299, 730, 797
BcgI CGANNNNNNTGC 2 cut(s) 67, 101
BcnI CCSGG 1 cut(s) 939
BcoDI GTCTC 4 cut(s) 9, 759, 789, 1480
BfaI CTAG 3 cut(s) 1320, 1335, 1491
BisI GCNGC 8 cut(s) 76, 121, 408, 428, 458, 572, 662, 771
BlsI GCNGC 8 cut(s) 77, 122, 409, 429, 459, 573, 663, 772
Bme1390I CCNGG 1 cut(s) 939
Bme18I GGWCC 2 cut(s) 109, 1437
BmgBI CACGTC 2 cut(s) 70, 328
BmgT120I GGNCC 3 cut(s) 109, 810, 1437
BmiI GGNNCC 3 cut(s) 110, 849, 1009
BmrFI CCNGG 1 cut(s) 939
BmrI ACTGGG 1 cut(s) 115
BmsI GCATC 2 cut(s) 1198, 1300
BmuI ACTGGG 1 cut(s) 115
BpiI GAAGAC 3 cut(s) 863, 1118, 1272
BpmI CTGGAG 1 cut(s) 1540
Bpu14I TTCGAA 1 cut(s) 1300
BpuEI CTTGAG 1 cut(s) 486
BpuMI CCSGG 1 cut(s) 939
BsaAI YACGTR 2 cut(s) 133, 511
BsaHI GRCGYC 1 cut(s) 360
BsaJI CCNNGG 2 cut(s) 118, 1101
BsaWI WCCGGW 2 cut(s) 535, 1439
BsaXI ACNNNNNCTCC 6 cut(s) 575, 605, 1131, 1161, 1426, 1456
Bsc4I CCNNNNNNNGG 2 cut(s) 105, 1563
Bse1I ACTGG 2 cut(s) 110, 1048
Bse3DI GCAATG 1 cut(s) 923
BseAI TCCGGA 1 cut(s) 535
BseDI CCNNGG 2 cut(s) 118, 1101
BseGI GGATG 5 cut(s) 934, 1024, 1150, 1267, 1474
BseLI CCNNNNNNNGG 2 cut(s) 105, 1563
BseMI GCAATG 1 cut(s) 923
BseMII CTCAG 3 cut(s) 800, 1416, 1491
BseNI ACTGG 2 cut(s) 110, 1048
BseRI GAGGAG 2 cut(s) 212, 314
BseXI GCAGC 3 cut(s) 414, 583, 782
Bsh1236I CGCG 2 cut(s) 114, 120
Bsh1285I CGRYCG 2 cut(s) 118, 415
BshFI GGCC 4 cut(s) 123, 160, 611, 812
BshNI GGYRCC 1 cut(s) 1007
BsiEI CGRYCG 2 cut(s) 118, 415
BsiSI CCGG 6 cut(s) 157, 527, 536, 575, 938, 1440
BslI CCNNNNNNNGG 2 cut(s) 105, 1563
BsmAI GTCTC 4 cut(s) 9, 759, 789, 1480
BsmBI CGTCTC 1 cut(s) 789
BsmI GAATGC 3 cut(s) 663, 1072, 1296
BsnI GGCC 4 cut(s) 123, 160, 611, 812
Bsp119I TTCGAA 1 cut(s) 1300
Bsp1286I GDGCHC 1 cut(s) 198
Bsp13I TCCGGA 1 cut(s) 535
Bsp143I GATC 4 cut(s) 249, 412, 905, 1544
BspANI GGCC 4 cut(s) 123, 160, 611, 812
BspCNI CTCAG 3 cut(s) 799, 1417, 1490
BspEI TCCGGA 1 cut(s) 535
BspFNI CGCG 2 cut(s) 114, 120
BspHI TCATGA 3 cut(s) 246, 1062, 1356
BspLI GGNNCC 3 cut(s) 110, 849, 1009
BspPI GGATC 1 cut(s) 244
BspQI GCTCTTC 3 cut(s) 1170, 1324, 1396
BspT104I TTCGAA 1 cut(s) 1300
BspT107I GGYRCC 1 cut(s) 1007
BsrBI CCGCTC 3 cut(s) 27, 142, 1464
BsrDI GCAATG 1 cut(s) 923
BsrI ACTGG 2 cut(s) 110, 1048
BssECI CCNNGG 2 cut(s) 118, 1101
BssMI GATC 4 cut(s) 249, 412, 905, 1544
BssNI GRCGYC 1 cut(s) 360
BssT1I CCWWGG 1 cut(s) 1101
Bst4CI ACNGT 2 cut(s) 979, 1238
Bst6I CTCTTC 8 cut(s) 425, 1146, 1170, 1251, 1275, 1324, 1375, 1396
BstACI GRCGYC 1 cut(s) 360
BstAPI GCANNNNNTGC 1 cut(s) 742
BstBAI YACGTR 2 cut(s) 133, 511
BstBI TTCGAA 1 cut(s) 1300
BstC8I GCNNGC 3 cut(s) 609, 666, 921
BstDEI CTNAG 4 cut(s) 786, 1425, 1457, 1477
BstDSI CCRYGG 1 cut(s) 118
BstF5I GGATG 5 cut(s) 934, 1024, 1150, 1267, 1474
BstFNI CGCG 2 cut(s) 114, 120
BstKTI GATC 4 cut(s) 252, 415, 908, 1547
BstMAI GTCTC 4 cut(s) 9, 759, 789, 1480
BstMBI GATC 4 cut(s) 249, 412, 905, 1544
BstMCI CGRYCG 2 cut(s) 118, 415
BstMWI GCNNNNNNNGC 6 cut(s) 72, 120, 433, 742, 925, 1560
BstSCI CCNGG 1 cut(s) 937
BstUI CGCG 2 cut(s) 114, 120
BstV1I GCAGC 3 cut(s) 414, 583, 782
BstV2I GAAGAC 3 cut(s) 863, 1118, 1272
BsuRI GGCC 4 cut(s) 123, 160, 611, 812
BtgI CCRYGG 1 cut(s) 118
BtgZI GCGATG 1 cut(s) 1263
BtrI CACGTC 2 cut(s) 70, 328
BtsCI GGATG 5 cut(s) 934, 1024, 1150, 1267, 1474
BtsIMutI CAGTG 1 cut(s) 1243
Cac8I GCNNGC 3 cut(s) 609, 666, 921
CciI TCATGA 3 cut(s) 246, 1062, 1356
Cfr13I GGNCC 3 cut(s) 109, 810, 1437
Cfr42I CCGCGG 1 cut(s) 121
CseI GACGC 1 cut(s) 368
CviAII CATG 5 cut(s) 247, 827, 1063, 1223, 1357
DdeI CTNAG 4 cut(s) 786, 1425, 1457, 1477
DpnI GATC 4 cut(s) 251, 414, 907, 1546
DpnII GATC 4 cut(s) 249, 412, 905, 1544
DrdI GACNNNNNNGTC 1 cut(s) 134
DseDI GACNNNNNNGTC 1 cut(s) 134
EaeI YGGCCR 2 cut(s) 158, 609
Eam1104I CTCTTC 8 cut(s) 425, 1146, 1170, 1251, 1275, 1324, 1375, 1396
EarI CTCTTC 8 cut(s) 425, 1146, 1170, 1251, 1275, 1324, 1375, 1396
EciI GGCGGA 2 cut(s) 266, 320
Eco130I CCWWGG 1 cut(s) 1101
Eco24I GRGCYC 1 cut(s) 198
Eco47I GGWCC 2 cut(s) 109, 1437
Eco57I CTGAAG 2 cut(s) 734, 1233
Eco72I CACGTG 1 cut(s) 133
EcoT14I CCWWGG 1 cut(s) 1101
EcoT38I GRGCYC 1 cut(s) 198
ErhI CCWWGG 1 cut(s) 1101
Esp3I CGTCTC 1 cut(s) 789
FaeI CATG 5 cut(s) 250, 830, 1066, 1226, 1360
FalI AAGNNNNNCTT 2 cut(s) 1390, 1422
FatI CATG 5 cut(s) 246, 826, 1062, 1222, 1356
FauI CCCGC 7 cut(s) 135, 242, 266, 319, 348, 912, 1457
Fnu4HI GCNGC 8 cut(s) 76, 121, 408, 428, 458, 572, 662, 771
FokI GGATG 5 cut(s) 921, 1011, 1157, 1274, 1481
FriOI GRGCYC 1 cut(s) 198
Fsp4HI GCNGC 8 cut(s) 76, 121, 408, 428, 458, 572, 662, 771
FspBI CTAG 3 cut(s) 1320, 1335, 1491
GluI GCNGC 8 cut(s) 76, 121, 408, 428, 458, 572, 662, 771
GsuI CTGGAG 1 cut(s) 1540
HaeIII GGCC 4 cut(s) 123, 160, 611, 812
HapII CCGG 6 cut(s) 157, 527, 536, 575, 938, 1440
HgaI GACGC 1 cut(s) 368
Hin1I GRCGYC 1 cut(s) 360
Hin1II CATG 5 cut(s) 250, 830, 1066, 1226, 1360
HincII GTYRAC 1 cut(s) 1234
HindII GTYRAC 1 cut(s) 1234
HinfI GANTC 3 cut(s) 797, 1130, 1199
HpaII CCGG 6 cut(s) 157, 527, 536, 575, 938, 1440
HphI GGTGA 7 cut(s) 10, 217, 328, 451, 923, 1049, 1569
Hpy166II GTNNAC 5 cut(s) 91, 514, 1234, 1445, 1525
Hpy188I TCNGA 7 cut(s) 193, 384, 789, 802, 852, 1207, 1417
Hpy8I GTNNAC 5 cut(s) 91, 514, 1234, 1445, 1525
Hpy99I CGWCG 2 cut(s) 269, 362
HpyAV CCTTC 8 cut(s) 31, 94, 986, 1069, 1111, 1178, 1374, 1425
HpyCH4III ACNGT 2 cut(s) 979, 1238
HpyCH4IV ACGT 4 cut(s) 69, 132, 327, 510
HpyCH4V TGCA 4 cut(s) 679, 770, 826, 838
HpyF10VI GCNNNNNNNGC 6 cut(s) 72, 120, 433, 742, 925, 1560
HpyF3I CTNAG 4 cut(s) 786, 1425, 1457, 1477
HpySE526I ACGT 4 cut(s) 69, 132, 327, 510
Hsp92I GRCGYC 1 cut(s) 360
Hsp92II CATG 5 cut(s) 250, 830, 1066, 1226, 1360
Kpn2I TCCGGA 1 cut(s) 535
KspI CCGCGG 1 cut(s) 121
Kzo9I GATC 4 cut(s) 249, 412, 905, 1544
LguI GCTCTTC 3 cut(s) 1170, 1324, 1396
LmnI GCTCC 5 cut(s) 32, 1189, 1219, 1461, 1559
Lsp1109I GCAGC 3 cut(s) 414, 583, 782
LweI GCATC 2 cut(s) 1198, 1300
MaeI CTAG 3 cut(s) 1320, 1335, 1491
MaeII ACGT 4 cut(s) 69, 132, 327, 510
MaeIII GTNAC 2 cut(s) 388, 791
MalI GATC 4 cut(s) 251, 414, 907, 1546
MbiI CCGCTC 3 cut(s) 27, 142, 1464
MboI GATC 4 cut(s) 249, 412, 905, 1544
MhlI GDGCHC 1 cut(s) 198
MlsI TGGCCA 1 cut(s) 611
MluCI AATT 4 cut(s) 1122, 1345, 1531, 1591
MluNI TGGCCA 1 cut(s) 611
MlyI GAGTC 1 cut(s) 806
MmeI TCCRAC 3 cut(s) 561, 575, 780
Mox20I TGGCCA 1 cut(s) 611
MroI TCCGGA 1 cut(s) 535
MscI TGGCCA 1 cut(s) 611
MseI TTAA 2 cut(s) 546, 915
MslI CAYNNNNRTG 3 cut(s) 521, 1227, 1301
Msp20I TGGCCA 1 cut(s) 611
MspA1I CMGCKG 3 cut(s) 120, 460, 1030
MspI CCGG 6 cut(s) 157, 527, 536, 575, 938, 1440
MspR9I CCNGG 1 cut(s) 939
Mva1269I GAATGC 3 cut(s) 663, 1072, 1296
MvnI CGCG 2 cut(s) 114, 120
MwoI GCNNNNNNNGC 6 cut(s) 72, 120, 433, 742, 925, 1560
NciI CCSGG 1 cut(s) 939
NdeII GATC 4 cut(s) 249, 412, 905, 1544
NlaIII CATG 5 cut(s) 250, 830, 1066, 1226, 1360
NlaIV GGNNCC 3 cut(s) 110, 849, 1009
NmuCI GTSAC 2 cut(s) 388, 791
NspV TTCGAA 1 cut(s) 1300
OliI CACNNNNGTG 1 cut(s) 521
PagI TCATGA 3 cut(s) 246, 1062, 1356
PciSI GCTCTTC 3 cut(s) 1170, 1324, 1396
PcsI WCGNNNNNNNCGW 1 cut(s) 363
PctI GAATGC 3 cut(s) 663, 1072, 1296
PfeI GAWTC 2 cut(s) 1130, 1199
PflMI CCANNNNNTGG 1 cut(s) 105
PfoI TCCNGGA 1 cut(s) 937
PkrI GCNGC 8 cut(s) 77, 122, 409, 429, 459, 573, 663, 772
Ple19I CGATCG 1 cut(s) 415
PleI GAGTC 1 cut(s) 805
PmaCI CACGTG 1 cut(s) 133
PmlI CACGTG 1 cut(s) 133
PpsI GAGTC 1 cut(s) 805
Ppu21I YACGTR 2 cut(s) 133, 511
PspCI CACGTG 1 cut(s) 133
PspN4I GGNNCC 3 cut(s) 110, 849, 1009
PspPI GGNCC 3 cut(s) 109, 810, 1437
PvuI CGATCG 1 cut(s) 415
RseI CAYNNNNRTG 3 cut(s) 521, 1227, 1301
SacII CCGCGG 1 cut(s) 121
SapI GCTCTTC 3 cut(s) 1170, 1324, 1396
SaqAI TTAA 2 cut(s) 546, 915
SatI GCNGC 8 cut(s) 76, 121, 408, 428, 458, 572, 662, 771
Sau3AI GATC 4 cut(s) 249, 412, 905, 1544
Sau96I GGNCC 3 cut(s) 109, 810, 1437
SchI GAGTC 1 cut(s) 806
ScrFI CCNGG 1 cut(s) 939
SduI GDGCHC 1 cut(s) 198
SfaNI GCATC 2 cut(s) 1198, 1300
Sfr303I CCGCGG 1 cut(s) 121
SfuI TTCGAA 1 cut(s) 1300
SgrBI CCGCGG 1 cut(s) 121
SinI GGWCC 2 cut(s) 109, 1437
SmiMI CAYNNNNRTG 3 cut(s) 521, 1227, 1301
SmlI CTYRAG 1 cut(s) 501
SmoI CTYRAG 1 cut(s) 501
Sse9I AATT 4 cut(s) 1122, 1345, 1531, 1591
SspI AATATT 1 cut(s) 945
SspMI CTAG 3 cut(s) 1320, 1335, 1491
StyD4I CCNGG 1 cut(s) 937
StyI CCWWGG 1 cut(s) 1101
TaaI ACNGT 2 cut(s) 979, 1238
TaiI ACGT 4 cut(s) 72, 135, 330, 513
TasI AATT 4 cut(s) 1122, 1345, 1531, 1591
TauI GCSGC 5 cut(s) 78, 123, 410, 460, 664
TfiI GAWTC 2 cut(s) 1130, 1199
Tru1I TTAA 2 cut(s) 546, 915
Tru9I TTAA 2 cut(s) 546, 915
TscAI CASTG 1 cut(s) 1243
TseFI GTSAC 2 cut(s) 388, 791
TseI GCWGC 3 cut(s) 427, 571, 770
Tsp45I GTSAC 2 cut(s) 388, 791
TspDTI ATGAA 7 cut(s) 777, 1079, 1266, 1278, 1287, 1319, 1485
TspGWI ACGGA 1 cut(s) 19
TspRI CASTG 1 cut(s) 1243
Van91I CCANNNNNTGG 1 cut(s) 105
VpaK11BI GGWCC 2 cut(s) 109, 1437
XapI RAATTY 1 cut(s) 1531
XbaI TCTAGA 1 cut(s) 1490
XcmI CCANNNNNNNNNTGG 1 cut(s) 619
XspI CTAG 3 cut(s) 1320, 1335, 1491
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.