Rh3AG280800

Stachyose

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr3A
OG0002202
Physical Location & Seq
Reverse (-)
32757598 .. 32759014
1417 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh3AG280800.1

Sequence Viewer

Length: 1338 bp
ATGGCACCTCCTAATGATCCTCTTAGTCCAGTTTTCAAGGCGTTCCGGTCCGAGAGTTCTGGACAATACTTTGACCTCTCTAATGGAAAGCTTAGTGTCAAAGGTGTTCCATTGCTCTCTGAAGTTCCAAGCAATGTAACTTTCAGGGACTTCCACTCACCCTGCCAATCCTCTGATGCTCCACTTCCTCTGCTCCAACGGGTTCGTGCTTCATCCCACAAGGGTGCTTTCCTTGGATTCAACAAGGAGGTTCCCTCAGATAGGCTGCTCAACTCCTTGGGGAAACTCAGTAACAGGGATTTCCTTAGCATCTTTAGGTTCAAGACATGGTGGTCTACCATGTGGGTAGGAAACTCTGGTTCAAACTTGCAAATGGAAACCCAATGGGTGCTCTTAGATGTCCCGGAGATCAAGTCCTATGTTATAATCATACCGATCATTGAAGCCAATTTCAGGTCTGCTCTTCATCCTGGCAGTGATGACCATGTCATGATCTGTGCCGAGAGTGGTTCTAGTCAAGTAAAAGCGTCGAATTTCGATGCCATTGCTTATGTTAATGCTTCTGACAATCCCTACAACTTGATGAAAGAAGCCTATAGTGCTGTTAGAGTCCATCTCAATAGTTTTAGGCTCTTGGAAGAGAAGACGGTCCCAAATCTAGTTAACAAATTCGGTTGGTGCACTTGGGATGCATTCTACTTAAATGTAGAACCTGTTGGTGTCTGGCATGGTCTGAATGAATTTATTGAAGGCGGTGTGTCCCCGCGGTTTCTCATCATTGATGATGGTTGGCAAAGCATCAATATGGATGATGAGGACCTGAAGGAGGAAACGAAAAAACTAGTTCATGGTGGTACTAAAATGATTGCTAGGCTTCACAGGTTTGAGGAGTGCAAGAAGTTCAGGAACTACAGAGAGCATGCTGAGAAGGATTGCGACAAGGCCCTTCATTCTGGAGTCACTGAGTTATCTGTGTTTGAAACTAAACTTCAGAAGCTGAAGATAGAGTTGAATGAGATCATTGGTGGAGGAGAGAGCAGTGCTCCTAGTGAAGGCCGTGGAACCAGTTCTTGCAGTGATGAAAATTATGGAATGAGGGCTTTCACCGGTGACTTGAGAACCAAGTTTAAAGGTTTGGATGATATATATGTATGGCATGCCATTTGTGGTGCCTGGGGTGGTGTTAGGCCAGGTTCAACTCATCTCAGTTCAAAGATCATTCCTTGCAAAGTCTCACCTGGACTAGACGGGACAATGAATGATTCCGCTGTGGTGAAAATCGTTGAGAGCGGGATTGGGCTTGTTCATCCTGATGAAGCTGATAGTTTCTATGACTAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
GO:0003674 GO:0003824 GO:0006950 GO:0006979 GO:0008150 GO:0008378 GO:0009628 GO:0016740 GO:0016757 GO:0016758 GO:0047268 GO:0050896 GO:0080167
KEGG Pathways
Metabolic & Signaling
ko00052 map00052
Pfam Domains
Protein Families
Raffinose_syn

Protein Analysis

445

Amino Acids

49.49

Weight (kDa)

5.76

Isoelectric Point (pI)

40.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Raffinose_syn PF05691 24 - 445 2.3e-136 Raffinose synthase or seed imbibition protein Sip1
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)
AanI TTATAA 1 cut(s) 425
AasI GACNNNNNNGTC 1 cut(s) 331
AccB1I GGYRCC 2 cut(s) 4, 1169
AccBSI CCGCTC 1 cut(s) 1290
AccI GTMKAC 1 cut(s) 335
AccII CGCG 1 cut(s) 766
AciI CCGC 5 cut(s) 753, 764, 766, 1266, 1290
AclWI GGATC 1 cut(s) 11
AcsI RAATTY 3 cut(s) 532, 668, 740
AcuI CTGAAG 4 cut(s) 141, 842, 974, 1019
AfaI GTAC 1 cut(s) 856
AfiI CCNNNNNNNGG 4 cut(s) 261, 453, 826, 1052
AgeI ACCGGT 1 cut(s) 1106
AhlI ACTAGT 1 cut(s) 841
AjnI CCWGG 4 cut(s) 469, 1172, 1189, 1237
AleI CACNNNNGTG 1 cut(s) 222
AluBI AGCT 3 cut(s) 91, 997, 1319
AluI AGCT 3 cut(s) 91, 997, 1319
Alw21I GWGCWC 3 cut(s) 393, 683, 1045
Alw26I GTCTC 1 cut(s) 1237
Alw44I GTGCAC 1 cut(s) 679
AlwI GGATC 1 cut(s) 11
AlwNI CAGNNNCTG 1 cut(s) 997
AoxI GGCC 3 cut(s) 942, 1054, 1187
ApaLI GTGCAC 1 cut(s) 679
ApeKI GCWGC 1 cut(s) 265
ApoI RAATTY 3 cut(s) 532, 668, 740
AsiGI ACCGGT 1 cut(s) 1106
Asp700I GAANNNNTTC 1 cut(s) 1066
AspS9I GGNCC 4 cut(s) 48, 649, 817, 943
AsuC2I CCSGG 1 cut(s) 404
AsuHPI GGTGA 5 cut(s) 150, 1096, 1121, 1227, 1285
AvaII GGWCC 3 cut(s) 48, 649, 817
BaeGI GKGCMC 1 cut(s) 683
BanI GGYRCC 2 cut(s) 4, 1169
BbsI GAAGAC 1 cut(s) 650
Bbv12I GWGCWC 3 cut(s) 393, 683, 1045
BbvI GCAGC 1 cut(s) 252
BccI CCATC 2 cut(s) 621, 779
BceAI ACGGC 1 cut(s) 1041
BcgI CGANNNNNNTGC 2 cut(s) 527, 561
BciT130I CCWGG 4 cut(s) 471, 1174, 1191, 1239
BcnI CCSGG 1 cut(s) 404
BcoDI GTCTC 1 cut(s) 1237
BcuI ACTAGT 1 cut(s) 841
BfaI CTAG 6 cut(s) 513, 659, 842, 870, 1047, 1244
BfmI CTRYAG 2 cut(s) 595, 910
BisI GCNGC 1 cut(s) 266
BlsI GCNGC 1 cut(s) 267
Bme1390I CCNGG 5 cut(s) 404, 471, 1174, 1191, 1239
Bme18I GGWCC 3 cut(s) 48, 649, 817
BmgT120I GGNCC 4 cut(s) 48, 649, 817, 943
BmiI GGNNCC 5 cut(s) 6, 252, 651, 1063, 1171
BmrFI CCNGG 5 cut(s) 404, 471, 1174, 1191, 1239
BmsI GCATC 5 cut(s) 166, 318, 529, 679, 807
BpiI GAAGAC 1 cut(s) 650
BplI GAGNNNNNCTC 6 cut(s) 239, 271, 600, 632, 1027, 1059
BpmI CTGGAG 1 cut(s) 975
Bpu10I CCTNAGC 1 cut(s) 305
BpuEI CTTGAG 1 cut(s) 1135
BpuMI CCSGG 1 cut(s) 404
BsaJI CCNNGG 5 cut(s) 232, 276, 764, 1057, 1173
BsaWI WCCGGW 2 cut(s) 45, 1106
BsaXI ACNNNNNCTCC 2 cut(s) 398, 428
Bsc4I CCNNNNNNNGG 4 cut(s) 261, 453, 826, 1052
Bse118I RCCGGY 1 cut(s) 1106
Bse1I ACTGG 2 cut(s) 29, 1065
Bse3DI GCAATG 3 cut(s) 110, 139, 543
BseBI CCWGG 4 cut(s) 471, 1174, 1191, 1239
BseDI CCNNGG 5 cut(s) 232, 276, 764, 1057, 1173
BseGI GGATG 6 cut(s) 212, 466, 694, 814, 1144, 1306
BseLI CCNNNNNNNGG 4 cut(s) 261, 453, 826, 1052
BseMI GCAATG 3 cut(s) 110, 139, 543
BseMII CTCAG 5 cut(s) 270, 301, 915, 954, 1219
BseNI ACTGG 2 cut(s) 29, 1065
BseRI GAGGAG 2 cut(s) 902, 1044
BseSI GKGCMC 1 cut(s) 683
BseXI GCAGC 1 cut(s) 252
Bsh1236I CGCG 1 cut(s) 766
BshFI GGCC 3 cut(s) 944, 1056, 1189
BshNI GGYRCC 2 cut(s) 4, 1169
BshTI ACCGGT 1 cut(s) 1106
BsiHKAI GWGCWC 3 cut(s) 393, 683, 1045
BsiSI CCGG 3 cut(s) 46, 404, 1107
BslFI GGGAC 5 cut(s) 161, 386, 635, 745, 1264
BslI CCNNNNNNNGG 4 cut(s) 261, 453, 826, 1052
BsmAI GTCTC 1 cut(s) 1237
BsmFI GGGAC 5 cut(s) 161, 386, 635, 745, 1264
BsmI GAATGC 1 cut(s) 692
BsnI GGCC 3 cut(s) 944, 1056, 1189
Bsp1286I GDGCHC 3 cut(s) 393, 683, 1045
Bsp143I GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
BspACI CCGC 5 cut(s) 753, 764, 766, 1266, 1290
BspANI GGCC 3 cut(s) 944, 1056, 1189
BspCNI CTCAG 5 cut(s) 269, 300, 916, 955, 1218
BspFNI CGCG 1 cut(s) 766
BspHI TCATGA 1 cut(s) 489
BspLI GGNNCC 5 cut(s) 6, 252, 651, 1063, 1171
BspPI GGATC 1 cut(s) 11
BspQI GCTCTTC 1 cut(s) 468
BspT107I GGYRCC 2 cut(s) 4, 1169
BsrBI CCGCTC 1 cut(s) 1290
BsrDI GCAATG 3 cut(s) 110, 139, 543
BsrFI RCCGGY 1 cut(s) 1106
BsrI ACTGG 2 cut(s) 29, 1065
BssAI RCCGGY 1 cut(s) 1106
BssECI CCNNGG 5 cut(s) 232, 276, 764, 1057, 1173
BssMI GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
BssT1I CCWWGG 2 cut(s) 232, 276
Bst2UI CCWGG 4 cut(s) 471, 1174, 1191, 1239
Bst4CI ACNGT 1 cut(s) 649
Bst6I CTCTTC 2 cut(s) 468, 633
BstC8I GCNNGC 2 cut(s) 921, 1158
BstDEI CTNAG 9 cut(s) 23, 92, 256, 287, 305, 394, 924, 963, 1205
BstDSI CCRYGG 2 cut(s) 764, 1057
BstENI CCTNNNNNAGG 3 cut(s) 259, 824, 1050
BstF5I GGATG 6 cut(s) 212, 466, 694, 814, 1144, 1306
BstFNI CGCG 1 cut(s) 766
BstKTI GATC 6 cut(s) 19, 411, 438, 495, 1020, 1218
BstMAI GTCTC 1 cut(s) 1237
BstMBI GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
BstMWI GCNNNNNNNGC 1 cut(s) 599
BstNI CCWGG 4 cut(s) 471, 1174, 1191, 1239
BstNSI RCATGY 2 cut(s) 923, 1160
BstSCI CCNGG 5 cut(s) 402, 469, 1172, 1189, 1237
BstSFI CTRYAG 2 cut(s) 595, 910
BstSLI GKGCMC 1 cut(s) 683
BstUI CGCG 1 cut(s) 766
BstV1I GCAGC 1 cut(s) 252
BstV2I GAAGAC 1 cut(s) 650
BsuRI GGCC 3 cut(s) 944, 1056, 1189
BtgI CCRYGG 2 cut(s) 764, 1057
BtsCI GGATG 6 cut(s) 212, 466, 694, 814, 1144, 1306
BtsI GCAGTG 3 cut(s) 481, 1045, 1081
BtsIMutI CAGTG 4 cut(s) 481, 960, 1045, 1081
Cac8I GCNNGC 2 cut(s) 921, 1158
CaiI CAGNNNCTG 1 cut(s) 997
CciI TCATGA 1 cut(s) 489
Cfr10I RCCGGY 1 cut(s) 1106
Cfr13I GGNCC 4 cut(s) 48, 649, 817, 943
Cfr42I CCGCGG 1 cut(s) 767
CpoI CGGWCCG 1 cut(s) 48
CseI GACGC 1 cut(s) 516
Csp6I GTAC 1 cut(s) 855
CspAI ACCGGT 1 cut(s) 1106
CspI CGGWCCG 1 cut(s) 48
CviAII CATG 8 cut(s) 327, 340, 485, 490, 728, 848, 920, 1157
CviQI GTAC 1 cut(s) 855
DdeI CTNAG 9 cut(s) 23, 92, 256, 287, 305, 394, 924, 963, 1205
DpnI GATC 6 cut(s) 18, 410, 437, 494, 1019, 1217
DpnII GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
DraI TTTAAA 1 cut(s) 1129
DrdI GACNNNNNNGTC 1 cut(s) 331
DseDI GACNNNNNNGTC 1 cut(s) 331
Eam1104I CTCTTC 2 cut(s) 468, 633
EarI CTCTTC 2 cut(s) 468, 633
Eco130I CCWWGG 2 cut(s) 232, 276
Eco47I GGWCC 3 cut(s) 48, 649, 817
Eco57I CTGAAG 4 cut(s) 141, 842, 974, 1019
EcoNI CCTNNNNNAGG 3 cut(s) 259, 824, 1050
EcoO109I RGGNCCY 2 cut(s) 817, 943
EcoRII CCWGG 4 cut(s) 469, 1172, 1189, 1237
EcoT14I CCWWGG 2 cut(s) 232, 276
EcoT22I ATGCAT 1 cut(s) 694
ErhI CCWWGG 2 cut(s) 232, 276
FaeI CATG 8 cut(s) 330, 343, 488, 493, 731, 851, 923, 1160
FaqI GGGAC 5 cut(s) 161, 386, 635, 745, 1264
FatI CATG 8 cut(s) 326, 339, 484, 489, 727, 847, 919, 1156
FauI CCCGC 2 cut(s) 771, 1283
FblI GTMKAC 1 cut(s) 335
Fnu4HI GCNGC 1 cut(s) 266
FokI GGATG 6 cut(s) 199, 453, 701, 821, 1151, 1293
Fsp4HI GCNGC 1 cut(s) 266
FspBI CTAG 6 cut(s) 513, 659, 842, 870, 1047, 1244
GluI GCNGC 1 cut(s) 266
GsuI CTGGAG 1 cut(s) 975
HaeIII GGCC 3 cut(s) 944, 1056, 1189
HapII CCGG 3 cut(s) 46, 404, 1107
HgaI GACGC 1 cut(s) 516
Hin1II CATG 8 cut(s) 330, 343, 488, 493, 731, 851, 923, 1160
HincII GTYRAC 1 cut(s) 664
HindII GTYRAC 1 cut(s) 664
HindIII AAGCTT 1 cut(s) 89
HinfI GANTC 4 cut(s) 237, 609, 957, 1262
HpaI GTTAAC 1 cut(s) 664
HpaII CCGG 3 cut(s) 46, 404, 1107
HphI GGTGA 5 cut(s) 150, 1096, 1121, 1227, 1285
Hpy166II GTNNAC 3 cut(s) 336, 664, 681
Hpy188I TCNGA 7 cut(s) 52, 121, 175, 259, 565, 735, 993
Hpy188III TCNNGA 6 cut(s) 60, 322, 490, 904, 954, 1310
Hpy8I GTNNAC 3 cut(s) 336, 664, 681
Hpy99I CGWCG 1 cut(s) 532
HpyAV CCTTC 5 cut(s) 743, 817, 922, 956, 1046
HpyCH4III ACNGT 1 cut(s) 649
HpyCH4V TGCA 6 cut(s) 370, 681, 692, 894, 1074, 1227
HpyF10VI GCNNNNNNNGC 1 cut(s) 599
HpyF3I CTNAG 9 cut(s) 23, 92, 256, 287, 305, 394, 924, 963, 1205
Hsp92II CATG 8 cut(s) 330, 343, 488, 493, 731, 851, 923, 1160
KspAI GTTAAC 1 cut(s) 664
KspI CCGCGG 1 cut(s) 767
Kzo9I GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
LguI GCTCTTC 1 cut(s) 468
LmnI GCTCC 3 cut(s) 184, 198, 1048
Lsp1109I GCAGC 1 cut(s) 252
LweI GCATC 5 cut(s) 166, 318, 529, 679, 807
MaeI CTAG 6 cut(s) 513, 659, 842, 870, 1047, 1244
MaeIII GTNAC 4 cut(s) 136, 290, 958, 1109
MalI GATC 6 cut(s) 18, 410, 437, 494, 1019, 1217
MbiI CCGCTC 1 cut(s) 1290
MboI GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
MboII GAAGA 4 cut(s) 455, 650, 655, 1012
MhlI GDGCHC 3 cut(s) 393, 683, 1045
MluCI AATT 5 cut(s) 448, 532, 668, 740, 1084
MlyI GAGTC 2 cut(s) 618, 966
MmeI TCCRAC 1 cut(s) 220
Mph1103I ATGCAT 1 cut(s) 694
MroXI GAANNNNTTC 1 cut(s) 1066
MseI TTAA 4 cut(s) 555, 663, 701, 1128
MslI CAYNNNNRTG 3 cut(s) 222, 803, 1311
MspA1I CMGCKG 2 cut(s) 766, 1268
MspI CCGG 3 cut(s) 46, 404, 1107
MspR9I CCNGG 5 cut(s) 404, 471, 1174, 1191, 1239
Mva1269I GAATGC 1 cut(s) 692
MvaI CCWGG 4 cut(s) 471, 1174, 1191, 1239
MvnI CGCG 1 cut(s) 766
MwoI GCNNNNNNNGC 1 cut(s) 599
NciI CCSGG 1 cut(s) 404
NdeII GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
NlaIII CATG 8 cut(s) 330, 343, 488, 493, 731, 851, 923, 1160
NlaIV GGNNCC 5 cut(s) 6, 252, 651, 1063, 1171
NmeAIII GCCGAG 1 cut(s) 526
NmuCI GTSAC 2 cut(s) 958, 1109
NsiI ATGCAT 1 cut(s) 694
NspI RCATGY 2 cut(s) 923, 1160
OliI CACNNNNGTG 1 cut(s) 222
PaeI GCATGC 2 cut(s) 923, 1160
PagI TCATGA 1 cut(s) 489
PciSI GCTCTTC 1 cut(s) 468
PctI GAATGC 1 cut(s) 692
PdmI GAANNNNTTC 1 cut(s) 1066
PfeI GAWTC 2 cut(s) 237, 1262
PflFI GACNNNGTC 1 cut(s) 485
PfoI TCCNGGA 1 cut(s) 402
PinAI ACCGGT 1 cut(s) 1106
PkrI GCNGC 1 cut(s) 267
PleI GAGTC 2 cut(s) 617, 965
PpsI GAGTC 2 cut(s) 617, 965
PpuMI RGGWCCY 1 cut(s) 817
PsiI TTATAA 1 cut(s) 425
Psp5II RGGWCCY 1 cut(s) 817
Psp6I CCWGG 4 cut(s) 469, 1172, 1189, 1237
PspGI CCWGG 4 cut(s) 469, 1172, 1189, 1237
PspN4I GGNNCC 5 cut(s) 6, 252, 651, 1063, 1171
PspPI GGNCC 4 cut(s) 48, 649, 817, 943
PspPPI RGGWCCY 1 cut(s) 817
PstNI CAGNNNCTG 1 cut(s) 997
PsyI GACNNNGTC 1 cut(s) 485
RsaI GTAC 1 cut(s) 856
RsaNI GTAC 1 cut(s) 855
RseI CAYNNNNRTG 3 cut(s) 222, 803, 1311
Rsr2I CGGWCCG 1 cut(s) 48
RsrII CGGWCCG 1 cut(s) 48
SacII CCGCGG 1 cut(s) 767
SapI GCTCTTC 1 cut(s) 468
SaqAI TTAA 4 cut(s) 555, 663, 701, 1128
SatI GCNGC 1 cut(s) 266
Sau3AI GATC 6 cut(s) 16, 408, 435, 492, 1017, 1215
Sau96I GGNCC 4 cut(s) 48, 649, 817, 943
SchI GAGTC 2 cut(s) 618, 966
ScrFI CCNGG 5 cut(s) 404, 471, 1174, 1191, 1239
SduI GDGCHC 3 cut(s) 393, 683, 1045
SfaNI GCATC 5 cut(s) 166, 318, 529, 679, 807
SfcI CTRYAG 2 cut(s) 595, 910
Sfr303I CCGCGG 1 cut(s) 767
SgrAI CRCCGGYG 1 cut(s) 1106
SgrBI CCGCGG 1 cut(s) 767
SinI GGWCC 3 cut(s) 48, 649, 817
SmiMI CAYNNNNRTG 3 cut(s) 222, 803, 1311
SmlI CTYRAG 1 cut(s) 1114
SmoI CTYRAG 1 cut(s) 1114
SpeI ACTAGT 1 cut(s) 841
SphI GCATGC 2 cut(s) 923, 1160
Sse9I AATT 5 cut(s) 448, 532, 668, 740, 1084
SsiI CCGC 5 cut(s) 753, 764, 766, 1266, 1290
SspMI CTAG 6 cut(s) 513, 659, 842, 870, 1047, 1244
StyD4I CCNGG 5 cut(s) 402, 469, 1172, 1189, 1237
StyI CCWWGG 2 cut(s) 232, 276
TaaI ACNGT 1 cut(s) 649
TaqI TCGA 2 cut(s) 530, 537
TasI AATT 5 cut(s) 448, 532, 668, 740, 1084
TfiI GAWTC 2 cut(s) 237, 1262
Tru1I TTAA 4 cut(s) 555, 663, 701, 1128
Tru9I TTAA 4 cut(s) 555, 663, 701, 1128
TscAI CASTG 4 cut(s) 481, 967, 1045, 1081
TseFI GTSAC 2 cut(s) 958, 1109
TseI GCWGC 1 cut(s) 265
Tsp45I GTSAC 2 cut(s) 958, 1109
TspRI CASTG 4 cut(s) 481, 967, 1045, 1081
Tth111I GACNNNGTC 1 cut(s) 485
VneI GTGCAC 1 cut(s) 679
VpaK11BI GGWCC 3 cut(s) 48, 649, 817
XagI CCTNNNNNAGG 3 cut(s) 259, 824, 1050
XapI RAATTY 3 cut(s) 532, 668, 740
XceI RCATGY 2 cut(s) 923, 1160
XmiI GTMKAC 1 cut(s) 335
XmnI GAANNNNTTC 1 cut(s) 1066
XspI CTAG 6 cut(s) 513, 659, 842, 870, 1047, 1244
Zsp2I ATGCAT 1 cut(s) 694
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.