Rw2G017080

1-deoxy-D-xylulose-5-phosphate synthase 2

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr2
OG0000901
Physical Location & Seq
Forward (+)
20835798 .. 20839968
4171 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw2G017080.1

Sequence Viewer

Length: 1866 bp
ATGCTCAACAGGTCACGCCCTTCTCCCCCTTCCCCTGTCTCCACCCAGATTCCATTAGCTATGGCGGTCTCTGGTACATTCATTAGACCAAATCAGTACTTCTCTTCATGCGTCAATACTCCAAGTCCAAGACTAAGACTAAATCCCAGTTGCAGAAAACAGTTCTGTTTGAAGGCTTCAGCTGGTAACTCAGACGGCGAGGACCGCAAGTTGACAAGAAAGGAGAAAGACGGAGGATGTAAGATCGAGTACACTACTGAAAAACCAGCCACGCCATTGCTGGACACAATCAATTACCCAGCTCACATGAAGAATCTATCAACACAGGATCTCGAACAACTAGCAGCAGAGCTCAGAATGGATATTGTTCACAGTGTTTCACAGACAGGTGGGCATCTCAGTTCTAGCTTGGGTGTGGTGGAGCTATCAGTGGCACTGCATCATGTGTTCAGCACCCCTGACGATAAAATCATATGGGATGTTGGTCATCAGGCTTATCCTCATAAAATTCTCACAGGAAGGAGGTCCAAGATGCATACAATGAGGAAAACTTCAGGTCTTGCAGGATTTCCCAAAAGGGATGAGAGCGTTCATGATGCTTTTGGTGTCGGGCACAGTTCTACAAGCATATCTGCTGGTTTAGGTATGGCAGTCGCAAGAGATCTACTTGGGAAGGACAACAGTATCATTTCAGTGATTGGAGATGGAGCCATGACAGCAGGACAAGCATATGAAGCCATGAACAACGCAGGATACCTTGACGCTAATCTGATCGTCATACTGAATGACAATAAGCAAGTCTCTTTACCCACCGCCACCCTTGATGGCCCTGCAACGCCAGTTGGAGCCCTCAGCAGTGCTCTAACCAAACTCCAAGCAAGCACCCAGTTTCGCAAACTTCGAGAAGCTGCAAAAAGCATTACGAAGCAAATCGGAGGACAAACACATGAAGTTGCAGCTAAAGTAGATGAGTATGCAAGAGGAATGATTAGTGCTTCTGGATCCACTCTCTTCGAGGAGCTTGGATTGTATTATATTGGTCCAGTAGACGGTCACAATGTTGCAGACTTGGTCAACATTTTCCAGAGAGTGAAAGCCATGCCTGCCCCGGGGCCAGTTTTGATCCACATCATAACAGAGAAAGGAAAAGGCTACCCCCCAGCCGAGGCCGCAGCTGATAGAATGCATGGGGTTGTCAAGTTTGACCCACCAACAGGCCAGCAATTTAAGACCAAATCCCCTACGCTTTCATATACTCAGTACTTTGCTGAATCTCTGATAAAGGAAGCTGAAACAGATGAGAAAATTGTAGCGATCCATGCAGCAATGGGTGGCGGCACTGGTCTAAATTACTTCCAGAAGAGGTTTCCAGATCGTTGCTTTGATGTGGGGATTGCTGAGCAACATGCTGTCACATTTGCAGCTGGTTTAGCTGCAGAAGGTCTCAAGCCATTCTGTGCTATCTACTCAACATTCCTGCAACGAGGATATGATCAGGTGGTCCATGATGTAGATCTTCAAAAACTACCTGTCCGCTTTGCAATGGATCGAGCTGGCTTGGTTGGTGCAGATGGTCCCACCCACTGTGGAGCATTTGATATCACATACATGGCTTGCTTGCCCAATATGGTGGTTATGGCTCCATCTGATGAAGCTGAACTGATGCACATGGTCGCCACAGCAGCAGTTATAGATGATAGACCAAGCTGCTTTAGATTTCCAAGAGGCAATGGTATTGGAGCAGTTCTTCCTGCCCATAACAAAGGAACTCCAATTGAGGTTATTATAAACAAAATTCCAATTGTAAGTGAAAGATACATAATAGATAGCTTAATCATATCTTTCTTCAATATTATGATTGAATAG
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00730 ko00900 ko01100 ko01110 ko01130 map00730 map00900 map01100 map01110 map01130
Pfam Domains
Protein Families
DXP_synthase_N Transket_pyr Transketolase_C

Protein Analysis

621

Amino Acids

67.01

Weight (kDa)

7.05

Isoelectric Point (pI)

42.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DXP_synthase_N PF13292 94 - 379 3.1e-109 1-deoxy-D-xylulose-5-phosphate synthase
E1_dh PF00676 202 - 265 5.6e-06 Dehydrogenase E1 component
Transket_pyr PF02779 416 - 577 4.3e-49 Transketolase, pyrimidine binding 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)
AanI TTATAA 1 cut(s) 1787
AccI GTMKAC 1 cut(s) 1047
AciI CCGC 6 cut(s) 65, 205, 813, 1170, 1335, 1534
AclWI GGATC 6 cut(s) 336, 996, 1009, 1117, 1309, 1554
AcsI RAATTY 2 cut(s) 507, 1794
AcuI CTGAAG 2 cut(s) 162, 537
AfaI GTAC 4 cut(s) 76, 98, 251, 1262
AfiI CCNNNNNNNGG 4 cut(s) 1049, 1109, 1165, 1214
AgsI TTSAA 4 cut(s) 172, 1520, 1849, 1862
Alw21I GWGCWC 2 cut(s) 354, 862
Alw26I GTCTC 4 cut(s) 43, 73, 805, 1448
AlwI GGATC 6 cut(s) 336, 996, 1009, 1117, 1309, 1554
Ama87I CYCGRG 1 cut(s) 1108
AoxI GGCC 4 cut(s) 826, 1112, 1167, 1216
ApeKI GCWGC 9 cut(s) 344, 908, 956, 1172, 1322, 1421, 1433, 1682, 1707
ApoI RAATTY 2 cut(s) 507, 1794
AspS9I GGNCC 7 cut(s) 202, 525, 827, 1040, 1112, 1501, 1574
AsuC2I CCSGG 2 cut(s) 1109, 1110
AvaI CYCGRG 1 cut(s) 1108
AvaII GGWCC 5 cut(s) 202, 525, 1040, 1501, 1574
BaeGI GKGCMC 1 cut(s) 615
BaeI ACNNNNGTAYC 2 cut(s) 667, 700
BamHI GGATCC 1 cut(s) 1001
BanII GRGCYC 2 cut(s) 354, 850
Bbv12I GWGCWC 2 cut(s) 354, 862
BbvCI CCTCAGC 1 cut(s) 851
BbvI GCAGC 9 cut(s) 356, 895, 968, 1184, 1334, 1420, 1433, 1694, 1694
BccI CCATC 4 cut(s) 698, 818, 1565, 1651
BceAI ACGGC 1 cut(s) 211
BciVI GTATCC 1 cut(s) 746
BclI TGATCA 1 cut(s) 1492
BcnI CCSGG 2 cut(s) 1109, 1110
BcoDI GTCTC 4 cut(s) 43, 73, 805, 1448
BfaI CTAG 2 cut(s) 341, 405
BfmI CTRYAG 1 cut(s) 1434
BfuI GTATCC 1 cut(s) 746
BglII AGATCT 2 cut(s) 661, 1513
BlpI GCTNAGC 1 cut(s) 1398
BmcAI AGTACT 2 cut(s) 98, 1262
Bme1390I CCNGG 2 cut(s) 1109, 1110
Bme18I GGWCC 5 cut(s) 202, 525, 1040, 1501, 1574
BmeT110I CYCGRG 1 cut(s) 1108
BmgT120I GGNCC 7 cut(s) 202, 525, 827, 1040, 1112, 1501, 1574
BmiI GGNNCC 6 cut(s) 709, 847, 1003, 1113, 1576, 1641
BmrFI CCNGG 2 cut(s) 1109, 1110
BmrI ACTGGG 2 cut(s) 141, 880
BmsI GCATC 5 cut(s) 403, 448, 522, 586, 1653
BmuI ACTGGG 2 cut(s) 141, 880
Bpu10I CCTNAGC 1 cut(s) 851
Bpu1102I GCTNAGC 1 cut(s) 1398
BpuEI CTTGAG 1 cut(s) 1430
BpuMI CCSGG 2 cut(s) 1109, 1110
BsaBI GATNNNNATC 2 cut(s) 1127, 1512
BsaI GGTCTC 2 cut(s) 73, 1448
BsaJI CCNNGG 4 cut(s) 1107, 1108, 1109, 1164
Bsc4I CCNNNNNNNGG 4 cut(s) 1049, 1109, 1165, 1214
Bse1I ACTGG 6 cut(s) 147, 839, 886, 1043, 1115, 1345
Bse3DI GCAATG 4 cut(s) 275, 1332, 1548, 1735
Bse8I GATNNNNATC 2 cut(s) 1127, 1512
BseDI CCNNGG 4 cut(s) 1107, 1108, 1109, 1164
BseGI GGATG 3 cut(s) 242, 484, 586
BseJI GATNNNNATC 2 cut(s) 1127, 1512
BseLI CCNNNNNNNGG 4 cut(s) 1049, 1109, 1165, 1214
BseMI GCAATG 4 cut(s) 275, 1332, 1548, 1735
BseMII CTCAG 6 cut(s) 204, 367, 412, 865, 1271, 1389
BseNI ACTGG 6 cut(s) 147, 839, 886, 1043, 1115, 1345
BseRI GAGGAG 1 cut(s) 1031
BseSI GKGCMC 1 cut(s) 615
BseXI GCAGC 9 cut(s) 356, 895, 968, 1184, 1334, 1420, 1433, 1694, 1694
BseYI CCCAGC 2 cut(s) 298, 1159
BsgI GTGCAG 1 cut(s) 1587
BshFI GGCC 4 cut(s) 828, 1114, 1169, 1218
BsiHKAI GWGCWC 2 cut(s) 354, 862
BsiHKCI CYCGRG 1 cut(s) 1108
BsiSI CCGG 1 cut(s) 1109
BslFI GGGAC 1 cut(s) 1560
BslI CCNNNNNNNGG 4 cut(s) 1049, 1109, 1165, 1214
BsmAI GTCTC 4 cut(s) 43, 73, 805, 1448
BsmFI GGGAC 1 cut(s) 1560
BsmI GAATGC 1 cut(s) 1188
BsnI GGCC 4 cut(s) 828, 1114, 1169, 1218
Bso31I GGTCTC 2 cut(s) 73, 1448
BsoBI CYCGRG 1 cut(s) 1108
Bsp1286I GDGCHC 4 cut(s) 354, 615, 850, 862
Bsp1720I GCTNAGC 1 cut(s) 1398
BspACI CCGC 6 cut(s) 65, 205, 813, 1170, 1335, 1534
BspANI GGCC 4 cut(s) 828, 1114, 1169, 1218
BspCNI CTCAG 6 cut(s) 203, 366, 411, 864, 1270, 1390
BspHI TCATGA 1 cut(s) 592
BspLI GGNNCC 6 cut(s) 709, 847, 1003, 1113, 1576, 1641
BspMAI CTGCAG 1 cut(s) 1438
BspPI GGATC 6 cut(s) 336, 996, 1009, 1117, 1309, 1554
BspTNI GGTCTC 2 cut(s) 73, 1448
BsrDI GCAATG 4 cut(s) 275, 1332, 1548, 1735
BsrI ACTGG 6 cut(s) 147, 839, 886, 1043, 1115, 1345
BssECI CCNNGG 4 cut(s) 1107, 1108, 1109, 1164
Bst4CI ACNGT 6 cut(s) 162, 374, 617, 683, 1052, 1586
Bst6I CTCTTC 3 cut(s) 109, 1016, 1355
BstC8I GCNNGC 6 cut(s) 880, 1104, 1220, 1555, 1615, 1619
BstDEI CTNAG 7 cut(s) 134, 190, 353, 398, 851, 1257, 1398
BstF5I GGATG 3 cut(s) 242, 484, 586
BstMAI GTCTC 4 cut(s) 43, 73, 805, 1448
BstMWI GCNNNNNNNGC 9 cut(s) 204, 716, 725, 734, 1103, 1169, 1319, 1430, 1682
BstNSI RCATGY 1 cut(s) 1409
BstSCI CCNGG 2 cut(s) 1107, 1108
BstSFI CTRYAG 1 cut(s) 1434
BstSLI GKGCMC 1 cut(s) 615
BstV1I GCAGC 9 cut(s) 356, 895, 968, 1184, 1334, 1420, 1433, 1694, 1694
BstX2I RGATCY 4 cut(s) 328, 661, 1001, 1513
BstXI CCANNNNNNTGG 1 cut(s) 1630
BstYI RGATCY 4 cut(s) 328, 661, 1001, 1513
BsuI GTATCC 1 cut(s) 746
BsuRI GGCC 4 cut(s) 828, 1114, 1169, 1218
BtsCI GGATG 3 cut(s) 242, 484, 586
BtsI GCAGTG 2 cut(s) 434, 862
BtsIMutI CAGTG 7 cut(s) 379, 434, 435, 699, 862, 1338, 1582
Cac8I GCNNGC 6 cut(s) 880, 1104, 1220, 1555, 1615, 1619
CciI TCATGA 1 cut(s) 592
Cfr13I GGNCC 7 cut(s) 202, 525, 827, 1040, 1112, 1501, 1574
Cfr9I CCCGGG 1 cut(s) 1108
CseI GACGC 2 cut(s) 100, 770
Csp6I GTAC 4 cut(s) 75, 97, 250, 1261
CviQI GTAC 4 cut(s) 75, 97, 250, 1261
DdeI CTNAG 7 cut(s) 134, 190, 353, 398, 851, 1257, 1398
Eam1104I CTCTTC 3 cut(s) 109, 1016, 1355
EarI CTCTTC 3 cut(s) 109, 1016, 1355
Ecl136II GAGCTC 1 cut(s) 352
Eco24I GRGCYC 2 cut(s) 354, 850
Eco31I GGTCTC 2 cut(s) 73, 1448
Eco32I GATATC 1 cut(s) 1600
Eco47I GGWCC 5 cut(s) 202, 525, 1040, 1501, 1574
Eco53kI GAGCTC 1 cut(s) 352
Eco57I CTGAAG 2 cut(s) 162, 537
Eco88I CYCGRG 1 cut(s) 1108
EcoICRI GAGCTC 1 cut(s) 352
EcoRV GATATC 1 cut(s) 1600
EcoT22I ATGCAT 2 cut(s) 537, 1188
EcoT38I GRGCYC 2 cut(s) 354, 850
FaqI GGGAC 1 cut(s) 1560
FauNDI CATATG 2 cut(s) 473, 730
FbaI TGATCA 1 cut(s) 1492
FblI GTMKAC 1 cut(s) 1047
FokI GGATG 3 cut(s) 249, 491, 593
FriOI GRGCYC 2 cut(s) 354, 850
FspBI CTAG 2 cut(s) 341, 405
GsaI CCCAGC 2 cut(s) 302, 1163
HaeIII GGCC 4 cut(s) 828, 1114, 1169, 1218
HapII CCGG 1 cut(s) 1109
HgaI GACGC 2 cut(s) 100, 770
HincII GTYRAC 2 cut(s) 213, 1075
HindII GTYRAC 2 cut(s) 213, 1075
HinfI GANTC 3 cut(s) 49, 313, 1271
HpaII CCGG 1 cut(s) 1109
Hpy166II GTNNAC 5 cut(s) 213, 252, 370, 1048, 1075
Hpy188I TCNGA 6 cut(s) 193, 356, 771, 935, 1278, 1648
Hpy188III TCNNGA 7 cut(s) 332, 593, 902, 999, 1084, 1357, 1370
Hpy8I GTNNAC 5 cut(s) 213, 252, 370, 1048, 1075
HpyAV CCTTC 6 cut(s) 30, 39, 166, 513, 667, 1433
HpyCH4III ACNGT 6 cut(s) 162, 374, 617, 683, 1052, 1586
HpyF10VI GCNNNNNNNGC 9 cut(s) 204, 716, 725, 734, 1103, 1169, 1319, 1430, 1682
HpyF3I CTNAG 7 cut(s) 134, 190, 353, 398, 851, 1257, 1398
Ksp22I TGATCA 1 cut(s) 1492
LmnI GCTCC 7 cut(s) 421, 707, 845, 1018, 1589, 1645, 1739
Lsp1109I GCAGC 9 cut(s) 356, 895, 968, 1184, 1334, 1420, 1433, 1694, 1694
LweI GCATC 5 cut(s) 403, 448, 522, 586, 1653
MaeI CTAG 2 cut(s) 341, 405
MaeIII GTNAC 4 cut(s) 12, 185, 1052, 1411
MboII GAAGA 7 cut(s) 96, 322, 1003, 1372, 1508, 1739, 1837
MfeI CAATTG 2 cut(s) 1773, 1800
MflI RGATCY 4 cut(s) 328, 661, 1001, 1513
MhlI GDGCHC 4 cut(s) 354, 615, 850, 862
MluCI AATT 8 cut(s) 292, 507, 1223, 1305, 1348, 1773, 1794, 1800
MmeI TCCRAC 1 cut(s) 823
Mph1103I ATGCAT 2 cut(s) 537, 1188
MseI TTAA 2 cut(s) 1227, 1832
MslI CAYNNNNRTG 2 cut(s) 692, 1607
MspA1I CMGCKG 3 cut(s) 182, 1175, 1424
MspI CCGG 1 cut(s) 1109
MspR9I CCNGG 2 cut(s) 1109, 1110
MunI CAATTG 2 cut(s) 1773, 1800
Mva1269I GAATGC 1 cut(s) 1188
MwoI GCNNNNNNNGC 9 cut(s) 204, 716, 725, 734, 1103, 1169, 1319, 1430, 1682
NciI CCSGG 2 cut(s) 1109, 1110
NdeI CATATG 2 cut(s) 473, 730
NlaIV GGNNCC 6 cut(s) 709, 847, 1003, 1113, 1576, 1641
NmeAIII GCCGAG 1 cut(s) 1189
NmuCI GTSAC 3 cut(s) 12, 1052, 1411
NsiI ATGCAT 2 cut(s) 537, 1188
NspI RCATGY 1 cut(s) 1409
PagI TCATGA 1 cut(s) 592
PcsI WCGNNNNNNNCGW 1 cut(s) 898
PctI GAATGC 1 cut(s) 1188
PfeI GAWTC 3 cut(s) 49, 313, 1271
PflFI GACNNNGTC 1 cut(s) 1070
PsiI TTATAA 1 cut(s) 1787
Psp124BI GAGCTC 1 cut(s) 354
PspFI CCCAGC 2 cut(s) 298, 1159
PspN4I GGNNCC 6 cut(s) 709, 847, 1003, 1113, 1576, 1641
PspPI GGNCC 7 cut(s) 202, 525, 827, 1040, 1112, 1501, 1574
PstI CTGCAG 1 cut(s) 1438
PsuI RGATCY 4 cut(s) 328, 661, 1001, 1513
PsyI GACNNNGTC 1 cut(s) 1070
PvuII CAGCTG 3 cut(s) 182, 1175, 1424
RsaI GTAC 4 cut(s) 76, 98, 251, 1262
RsaNI GTAC 4 cut(s) 75, 97, 250, 1261
RseI CAYNNNNRTG 2 cut(s) 692, 1607
SacI GAGCTC 1 cut(s) 354
SaqAI TTAA 2 cut(s) 1227, 1832
Sau96I GGNCC 7 cut(s) 202, 525, 827, 1040, 1112, 1501, 1574
ScaI AGTACT 2 cut(s) 98, 1262
ScrFI CCNGG 2 cut(s) 1109, 1110
SduI GDGCHC 4 cut(s) 354, 615, 850, 862
SfaNI GCATC 5 cut(s) 403, 448, 522, 586, 1653
SfcI CTRYAG 1 cut(s) 1434
SinI GGWCC 5 cut(s) 202, 525, 1040, 1501, 1574
SmaI CCCGGG 1 cut(s) 1110
SmiMI CAYNNNNRTG 2 cut(s) 692, 1607
SmlI CTYRAG 1 cut(s) 1445
SmoI CTYRAG 1 cut(s) 1445
Sse9I AATT 8 cut(s) 292, 507, 1223, 1305, 1348, 1773, 1794, 1800
SsiI CCGC 6 cut(s) 65, 205, 813, 1170, 1335, 1534
SspI AATATT 1 cut(s) 1852
SspMI CTAG 2 cut(s) 341, 405
SstI GAGCTC 1 cut(s) 354
StyD4I CCNGG 2 cut(s) 1107, 1108
TaaI ACNGT 6 cut(s) 162, 374, 617, 683, 1052, 1586
TaqI TCGA 5 cut(s) 246, 333, 901, 1014, 1549
TasI AATT 8 cut(s) 292, 507, 1223, 1305, 1348, 1773, 1794, 1800
TatI WGTACW 3 cut(s) 96, 249, 1260
TauI GCSGC 2 cut(s) 1172, 1338
TfiI GAWTC 3 cut(s) 49, 313, 1271
Tru1I TTAA 2 cut(s) 1227, 1832
Tru9I TTAA 2 cut(s) 1227, 1832
TscAI CASTG 7 cut(s) 379, 435, 441, 699, 862, 1345, 1589
TseFI GTSAC 3 cut(s) 12, 1052, 1411
TseI GCWGC 9 cut(s) 344, 908, 956, 1172, 1322, 1421, 1433, 1682, 1707
Tsp45I GTSAC 3 cut(s) 12, 1052, 1411
TspDTI ATGAA 9 cut(s) 70, 96, 323, 581, 747, 755, 963, 1239, 1665
TspGWI ACGGA 1 cut(s) 246
TspMI CCCGGG 1 cut(s) 1108
TspRI CASTG 7 cut(s) 379, 435, 441, 699, 862, 1345, 1589
Tth111I GACNNNGTC 1 cut(s) 1070
VpaK11BI GGWCC 5 cut(s) 202, 525, 1040, 1501, 1574
XapI RAATTY 2 cut(s) 507, 1794
XceI RCATGY 1 cut(s) 1409
XcmI CCANNNNNNNNNTGG 1 cut(s) 277
XmaI CCCGGG 1 cut(s) 1108
XmiI GTMKAC 1 cut(s) 1047
XspI CTAG 2 cut(s) 341, 405
ZrmI AGTACT 2 cut(s) 98, 1262
Zsp2I ATGCAT 2 cut(s) 537, 1188
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.