Rw3G003780

Type I 3-dehydroquinase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr3
OG0016868
Physical Location & Seq
Forward (+)
3257143 .. 3260709
3567 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw3G003780.1

Sequence Viewer

Length: 1506 bp
ATGGGAACCACAGTGGACCAAATGCTGATTGAGATGCACAAGGCTAAGGAAATTGGTTCTGATATTGTGGAGATCAGGCTTGACTGTTTGAGAAACTTTAACCCAAGTTCAGATCTTCAAATTCTTATCAAGCAGAGTCCTCTGCCTACTCTTGTCACCTACAGGCCAGTTTGGGAAGGCGGTCAATATGAAGGCGATGAAACCAAGCGACAAGATGCTCTTCGGTCAGCAATGGAATTGGGAGCTAACTATATTGATATTGAGCTTGAGGTTGCCCATGACTTCAACAATTCCATCTATGAAAAGAAGCCTGACAACTTCAAAGTCATTGTTTCTTCTCACAACTTTCACAACACTCCATCCTCCGAGGCAATCGGAAATCTTGTGGCTAGAATCCAAGCCACTGGAGCTGACATTGTGAAAATTGCAACTACTGCATTAGACATTACAGATTGTGCCAGAATTTTCCAGATTACCGTGCATTCACAGGTCCCAACAATAGGTATTGTTATGGGAGAGAGAGGTTTGATTTCACGACTACTTAGCCCCAAGTTTGGTGGATTTCTTACCTATGGTGCACTAGAAGCCGGTGCTATATCAGCTCCTGGGCAACCAACTGCGAGAGACTTGCTGGATTTATACAACTTCAGACTCATTAGACCTGATACCAAAGTATATGGGATTATTGGGAAGCCTGTTGGTCACAGCAAGAGTCCTCTACTATTCAATGCAGCATTCAAGTCAGTTGGCCTTAATGCAGTTTATGTTCATTTTCTGGTGGATGATGTCGAGAAGTTTTTCAACACATATTCATCCGTTGATTTTTCGGGATGCAGTTGTACTATTCCACATAAGGAGGCAGCACTCAAATGCATGGATGAGATTGATTCCATTGCCAAGAAAATTGGAGCTATCAACAACATTGTCAGGAAGCCTGATGGGAGGTTAGTTGCTTTCAACACCGACTACATTGGCTCCATCAGTGGCATTGAGGACGGACTACGAGGTTTGAACGGCGCCATTCCTGCTGGTAAATCACCCCTGGCTGGAAAGTTGTTTGTGGTCTTGGGAGCCGGTGGTGCTGGCAAGTCACTTGTGTATGGTGCTGCACAGAAAGGAGCAAGAGTTGTATGTGCCAACCGGACATATGAAAGAGCTAAGGAGCTGGCTGACAAAGTTGGGGGAAAAGCTATGACTCTTGAAGAAGTTGAAAATTTCCACCCGGAAGAGGGAATGATTCTTGCCAACACTACATCTGTGGGAATGAAGCCTAATGTTGATGATACCCCTATCTCCAAGCAAGCTCTGAAACACTATTGCTTAGTTTTTGATGCTATCTATACACCCAAAGAGACTAGACTCCTCCGGGAAGCAAAAGAGACTGGAGCAGAGGTTGTATATGGTACAGAGATGTTGATCAGGCAAGGGTTTGAACAATACAAGAACTTCACTGGTTTGCCAGCACCTGAAGAATTGTTTAGGGAGCTCATGGAGAAGCATGCATAA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko00400 ko01100 ko01110 ko01130 ko01230 map00400 map01100 map01110 map01130 map01230
Pfam Domains
Protein Families
DHquinase_I Shikimate_DH Shikimate_dh_N

Protein Analysis

501

Amino Acids

54.71

Weight (kDa)

6.06

Isoelectric Point (pI)

27.41

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DHquinase_I PF01487 1 - 214 3.2e-66 Type I 3-dehydroquinase
Shikimate_dh_N PF08501 228 - 308 9e-25 Shikimate dehydrogenase substrate binding domain
Shikimate_DH PF01488 348 - 419 4.2e-08 Shikimate / quinate 5-dehydrogenase
SDH_C PF18317 468 - 497 4.4e-08 Shikimate 5'-dehydrogenase C-terminal 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: OG0016868)

Species Orthologous Gene IDs
fragaria_vesca FvH4_6g04660 FvH4_6g04660
rosa_chinensis RchiOBHm_Chr3g0453131
rosa_laevigata RLG00000025535
rosa_multiflora Rmu_co8513087.1_g000001 Rmu_sc0007132.1_g000002 Rmu_sc0013481.1_g000006
rosa_roxburghii Rroxscaffold_6G00430190
rosa_rugosa Rorug02G0646700
rosa_samantha Rh3AG049300 Rh3BG050500 Rh3CG050600 Rh3DG051300
rosa_wichuraiana Rw3G003780

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 1016
AciI CCGC 1 cut(s) 180
AcsI RAATTY 3 cut(s) 120, 462, 1213
AcuI CTGAAG 2 cut(s) 631, 1488
AcyI GRCGYC 1 cut(s) 1017
AfaI GTAC 2 cut(s) 841, 1405
AfiI CCNNNNNNNGG 5 cut(s) 500, 554, 1046, 1228, 1229
AjnI CCWGG 2 cut(s) 604, 1041
Alw21I GWGCWC 2 cut(s) 580, 1488
Alw26I GTCTC 3 cut(s) 618, 1346, 1373
Alw44I GTGCAC 1 cut(s) 576
AlwNI CAGNNNCTG 2 cut(s) 605, 1466
AoxI GGCC 2 cut(s) 164, 748
ApaLI GTGCAC 1 cut(s) 576
ApeKI GCWGC 3 cut(s) 731, 860, 1106
ApoI RAATTY 3 cut(s) 120, 462, 1213
Asp700I GAANNNNTTC 1 cut(s) 797
AspLEI GCGC 1 cut(s) 1019
AspS9I GGNCC 2 cut(s) 16, 490
AsuC2I CCSGG 2 cut(s) 1223, 1367
AsuHPI GGTGA 2 cut(s) 148, 1029
AvaII GGWCC 2 cut(s) 16, 490
BaeGI GKGCMC 1 cut(s) 580
BaeI ACNNNNGTAYC 2 cut(s) 657, 690
BanI GGYRCC 1 cut(s) 1016
BanII GRGCYC 1 cut(s) 1488
Bbv12I GWGCWC 2 cut(s) 580, 1488
BbvI GCAGC 3 cut(s) 743, 872, 1093
BccI CCATC 4 cut(s) 302, 367, 932, 986
BceAI ACGGC 1 cut(s) 1030
BcgI CGANNNNNNTGC 2 cut(s) 610, 644
BciT130I CCWGG 2 cut(s) 606, 1043
BclI TGATCA 1 cut(s) 1416
BcnI CCSGG 2 cut(s) 1223, 1367
BcoDI GTCTC 3 cut(s) 618, 1346, 1373
BfaI CTAG 3 cut(s) 390, 581, 1356
BfmI CTRYAG 1 cut(s) 160
BfoI RGCGCY 1 cut(s) 1020
BglII AGATCT 1 cut(s) 112
BisI GCNGC 3 cut(s) 732, 861, 1107
BlsI GCNGC 3 cut(s) 733, 862, 1108
Bme1390I CCNGG 4 cut(s) 606, 1043, 1223, 1367
Bme18I GGWCC 2 cut(s) 16, 490
BmgT120I GGNCC 2 cut(s) 16, 490
BmiI GGNNCC 5 cut(s) 7, 492, 976, 1018, 1072
BmrFI CCNGG 4 cut(s) 606, 1043, 1223, 1367
BmsI GCATC 4 cut(s) 24, 205, 821, 1321
BpmI CTGGAG 2 cut(s) 426, 1404
Bpu10I CCTNAGC 2 cut(s) 45, 1158
BpuEI CTTGAG 1 cut(s) 287
BpuMI CCSGG 2 cut(s) 1223, 1367
BsaBI GATNNNNATC 1 cut(s) 1415
BsaHI GRCGYC 1 cut(s) 1017
BsaJI CCNNGG 3 cut(s) 366, 605, 1041
BsaWI WCCGGW 1 cut(s) 1140
BsaXI ACNNNNNCTCC 6 cut(s) 959, 989, 1110, 1140, 1377, 1407
Bsc4I CCNNNNNNNGG 5 cut(s) 500, 554, 1046, 1228, 1229
Bse118I RCCGGY 2 cut(s) 587, 1073
Bse1I ACTGG 4 cut(s) 167, 409, 1387, 1456
Bse3DI GCAATG 2 cut(s) 237, 891
Bse8I GATNNNNATC 1 cut(s) 1415
BseBI CCWGG 2 cut(s) 606, 1043
BseDI CCNNGG 3 cut(s) 366, 605, 1041
BseGI GGATG 5 cut(s) 359, 787, 812, 836, 883
BseJI GATNNNNATC 1 cut(s) 1415
BseLI CCNNNNNNNGG 5 cut(s) 500, 554, 1046, 1228, 1229
BseMI GCAATG 2 cut(s) 237, 891
BseNI ACTGG 4 cut(s) 167, 409, 1387, 1456
BseRI GAGGAG 1 cut(s) 1352
BseSI GKGCMC 1 cut(s) 580
BseXI GCAGC 3 cut(s) 743, 872, 1093
BsgI GTGCAG 1 cut(s) 1092
BshFI GGCC 2 cut(s) 166, 750
BshNI GGYRCC 1 cut(s) 1016
BsiHKAI GWGCWC 2 cut(s) 580, 1488
BsiSI CCGG 5 cut(s) 588, 1074, 1141, 1223, 1366
BslFI GGGAC 1 cut(s) 476
BslI CCNNNNNNNGG 5 cut(s) 500, 554, 1046, 1228, 1229
BsmAI GTCTC 3 cut(s) 618, 1346, 1373
BsmFI GGGAC 1 cut(s) 476
BsmI GAATGC 2 cut(s) 481, 734
BsnI GGCC 2 cut(s) 166, 750
Bsp1286I GDGCHC 2 cut(s) 580, 1488
Bsp143I GATC 3 cut(s) 72, 112, 1416
BspACI CCGC 1 cut(s) 180
BspANI GGCC 2 cut(s) 166, 750
BspLI GGNNCC 5 cut(s) 7, 492, 976, 1018, 1072
BspQI GCTCTTC 1 cut(s) 225
BspT107I GGYRCC 1 cut(s) 1016
BsrDI GCAATG 2 cut(s) 237, 891
BsrFI RCCGGY 2 cut(s) 587, 1073
BsrI ACTGG 4 cut(s) 167, 409, 1387, 1456
BssAI RCCGGY 2 cut(s) 587, 1073
BssECI CCNNGG 3 cut(s) 366, 605, 1041
BssMI GATC 3 cut(s) 72, 112, 1416
BssNI GRCGYC 1 cut(s) 1017
Bst2UI CCWGG 2 cut(s) 606, 1043
Bst4CI ACNGT 3 cut(s) 13, 86, 478
Bst6I CTCTTC 2 cut(s) 225, 1221
BstACI GRCGYC 1 cut(s) 1017
BstAPI GCANNNNNTGC 1 cut(s) 434
BstC8I GCNNGC 5 cut(s) 1084, 1167, 1302, 1461, 1500
BstDEI CTNAG 4 cut(s) 45, 542, 1158, 1321
BstF5I GGATG 5 cut(s) 359, 787, 812, 836, 883
BstH2I RGCGCY 1 cut(s) 1020
BstHHI GCGC 1 cut(s) 1019
BstKTI GATC 3 cut(s) 75, 115, 1419
BstMAI GTCTC 3 cut(s) 618, 1346, 1373
BstMBI GATC 3 cut(s) 72, 112, 1416
BstMWI GCNNNNNNNGC 6 cut(s) 407, 434, 584, 599, 1025, 1079
BstNI CCWGG 2 cut(s) 606, 1043
BstNSI RCATGY 1 cut(s) 1502
BstSCI CCNGG 4 cut(s) 604, 1041, 1221, 1365
BstSFI CTRYAG 1 cut(s) 160
BstSLI GKGCMC 1 cut(s) 580
BstV1I GCAGC 3 cut(s) 743, 872, 1093
BstX2I RGATCY 1 cut(s) 112
BstXI CCANNNNNNTGG 1 cut(s) 404
BstYI RGATCY 1 cut(s) 112
BsuRI GGCC 2 cut(s) 166, 750
BtgZI GCGATG 1 cut(s) 210
BtsCI GGATG 5 cut(s) 359, 787, 812, 836, 883
BtsIMutI CAGTG 4 cut(s) 18, 402, 988, 1449
Cac8I GCNNGC 5 cut(s) 1084, 1167, 1302, 1461, 1500
CaiI CAGNNNCTG 2 cut(s) 605, 1466
CfoI GCGC 1 cut(s) 1019
Cfr10I RCCGGY 2 cut(s) 587, 1073
Cfr13I GGNCC 2 cut(s) 16, 490
Csp6I GTAC 2 cut(s) 840, 1404
CspCI CAANNNNNGTGG 2 cut(s) 538, 573
CviAII CATG 4 cut(s) 278, 874, 1489, 1499
CviQI GTAC 2 cut(s) 840, 1404
DdeI CTNAG 4 cut(s) 45, 542, 1158, 1321
DinI GGCGCC 1 cut(s) 1018
DpnI GATC 3 cut(s) 74, 114, 1418
DpnII GATC 3 cut(s) 72, 112, 1416
Eam1104I CTCTTC 2 cut(s) 225, 1221
EarI CTCTTC 2 cut(s) 225, 1221
Ecl136II GAGCTC 1 cut(s) 1486
Eco24I GRGCYC 1 cut(s) 1488
Eco47I GGWCC 2 cut(s) 16, 490
Eco53kI GAGCTC 1 cut(s) 1486
Eco57I CTGAAG 2 cut(s) 631, 1488
EcoICRI GAGCTC 1 cut(s) 1486
EcoO109I RGGNCCY 1 cut(s) 490
EcoRII CCWGG 2 cut(s) 604, 1041
EcoT22I ATGCAT 2 cut(s) 875, 1504
EcoT38I GRGCYC 1 cut(s) 1488
EgeI GGCGCC 1 cut(s) 1018
EheI GGCGCC 1 cut(s) 1018
FaeI CATG 4 cut(s) 281, 877, 1492, 1502
FalI AAGNNNNNCTT 2 cut(s) 204, 236
FaqI GGGAC 1 cut(s) 476
FatI CATG 4 cut(s) 277, 873, 1488, 1498
FauNDI CATATG 1 cut(s) 1147
FbaI TGATCA 1 cut(s) 1416
Fnu4HI GCNGC 3 cut(s) 732, 861, 1107
FokI GGATG 5 cut(s) 346, 794, 799, 843, 890
FriOI GRGCYC 1 cut(s) 1488
Fsp4HI GCNGC 3 cut(s) 732, 861, 1107
FspBI CTAG 3 cut(s) 390, 581, 1356
GlaI GCGC 1 cut(s) 1018
GluI GCNGC 3 cut(s) 732, 861, 1107
GsuI CTGGAG 2 cut(s) 426, 1404
HaeII RGCGCY 1 cut(s) 1020
HaeIII GGCC 2 cut(s) 166, 750
HapII CCGG 5 cut(s) 588, 1074, 1141, 1223, 1366
HhaI GCGC 1 cut(s) 1019
Hin1I GRCGYC 1 cut(s) 1017
Hin1II CATG 4 cut(s) 281, 877, 1492, 1502
Hin6I GCGC 1 cut(s) 1017
HinP1I GCGC 1 cut(s) 1017
HinfI GANTC 8 cut(s) 136, 393, 651, 712, 887, 1195, 1237, 1359
HpaII CCGG 5 cut(s) 588, 1074, 1141, 1223, 1366
HphI GGTGA 2 cut(s) 148, 1029
Hpy166II GTNNAC 2 cut(s) 16, 578
Hpy188I TCNGA 6 cut(s) 61, 112, 367, 377, 650, 1308
Hpy188III TCNNGA 6 cut(s) 469, 534, 790, 828, 928, 1199
Hpy8I GTNNAC 2 cut(s) 16, 578
HpyAV CCTTC 2 cut(s) 170, 185
HpyCH4III ACNGT 3 cut(s) 13, 86, 478
HpyF10VI GCNNNNNNNGC 6 cut(s) 407, 434, 584, 599, 1025, 1079
HpyF3I CTNAG 4 cut(s) 45, 542, 1158, 1321
Hsp92I GRCGYC 1 cut(s) 1017
Hsp92II CATG 4 cut(s) 281, 877, 1492, 1502
HspAI GCGC 1 cut(s) 1017
KasI GGCGCC 1 cut(s) 1016
Ksp22I TGATCA 1 cut(s) 1416
Kzo9I GATC 3 cut(s) 72, 112, 1416
LguI GCTCTTC 1 cut(s) 225
Lsp1109I GCAGC 3 cut(s) 743, 872, 1093
LweI GCATC 4 cut(s) 24, 205, 821, 1321
MaeI CTAG 3 cut(s) 390, 581, 1356
MaeIII GTNAC 3 cut(s) 154, 701, 1089
MalI GATC 3 cut(s) 74, 114, 1418
MboI GATC 3 cut(s) 72, 112, 1416
MboII GAAGA 6 cut(s) 107, 212, 327, 1214, 1238, 1481
MflI RGATCY 1 cut(s) 112
MhlI GDGCHC 2 cut(s) 580, 1488
MluCI AATT 9 cut(s) 51, 120, 236, 289, 423, 462, 903, 1213, 1472
Mly113I GGCGCC 1 cut(s) 1017
MlyI GAGTC 5 cut(s) 145, 645, 721, 1189, 1353
Mph1103I ATGCAT 2 cut(s) 875, 1504
MroXI GAANNNNTTC 1 cut(s) 797
MseI TTAA 2 cut(s) 99, 753
MslI CAYNNNNRTG 1 cut(s) 868
MspI CCGG 5 cut(s) 588, 1074, 1141, 1223, 1366
MspR9I CCNGG 4 cut(s) 606, 1043, 1223, 1367
Mva1269I GAATGC 2 cut(s) 481, 734
MvaI CCWGG 2 cut(s) 606, 1043
MwoI GCNNNNNNNGC 6 cut(s) 407, 434, 584, 599, 1025, 1079
NarI GGCGCC 1 cut(s) 1017
NciI CCSGG 2 cut(s) 1223, 1367
NdeI CATATG 1 cut(s) 1147
NdeII GATC 3 cut(s) 72, 112, 1416
NlaIII CATG 4 cut(s) 281, 877, 1492, 1502
NlaIV GGNNCC 5 cut(s) 7, 492, 976, 1018, 1072
NmuCI GTSAC 3 cut(s) 154, 701, 1089
NsiI ATGCAT 2 cut(s) 875, 1504
NspI RCATGY 1 cut(s) 1502
PaeI GCATGC 1 cut(s) 1502
PciSI GCTCTTC 1 cut(s) 225
PctI GAATGC 2 cut(s) 481, 734
PdmI GAANNNNTTC 1 cut(s) 797
PfeI GAWTC 3 cut(s) 393, 887, 1237
PfoI TCCNGGA 1 cut(s) 1365
PkrI GCNGC 3 cut(s) 733, 862, 1108
PleI GAGTC 5 cut(s) 144, 645, 720, 1189, 1353
PluTI GGCGCC 1 cut(s) 1020
PpsI GAGTC 5 cut(s) 144, 645, 720, 1189, 1353
PpuMI RGGWCCY 1 cut(s) 490
Psp124BI GAGCTC 1 cut(s) 1488
Psp5II RGGWCCY 1 cut(s) 490
Psp6I CCWGG 2 cut(s) 604, 1041
PspGI CCWGG 2 cut(s) 604, 1041
PspN4I GGNNCC 5 cut(s) 7, 492, 976, 1018, 1072
PspPI GGNCC 2 cut(s) 16, 490
PspPPI RGGWCCY 1 cut(s) 490
PstNI CAGNNNCTG 2 cut(s) 605, 1466
PsuI RGATCY 1 cut(s) 112
RsaI GTAC 2 cut(s) 841, 1405
RsaNI GTAC 2 cut(s) 840, 1404
RseI CAYNNNNRTG 1 cut(s) 868
SacI GAGCTC 1 cut(s) 1488
SapI GCTCTTC 1 cut(s) 225
SaqAI TTAA 2 cut(s) 99, 753
SatI GCNGC 3 cut(s) 732, 861, 1107
Sau3AI GATC 3 cut(s) 72, 112, 1416
Sau96I GGNCC 2 cut(s) 16, 490
SchI GAGTC 5 cut(s) 145, 645, 721, 1189, 1353
ScrFI CCNGG 4 cut(s) 606, 1043, 1223, 1367
SduI GDGCHC 2 cut(s) 580, 1488
SfaNI GCATC 4 cut(s) 24, 205, 821, 1321
SfcI CTRYAG 1 cut(s) 160
SfoI GGCGCC 1 cut(s) 1018
SinI GGWCC 2 cut(s) 16, 490
SmiMI CAYNNNNRTG 1 cut(s) 868
SmlI CTYRAG 1 cut(s) 266
SmoI CTYRAG 1 cut(s) 266
SphI GCATGC 1 cut(s) 1502
Sse9I AATT 9 cut(s) 51, 120, 236, 289, 423, 462, 903, 1213, 1472
SsiI CCGC 1 cut(s) 180
SspDI GGCGCC 1 cut(s) 1016
SspMI CTAG 3 cut(s) 390, 581, 1356
SstI GAGCTC 1 cut(s) 1488
StyD4I CCNGG 4 cut(s) 604, 1041, 1221, 1365
TaaI ACNGT 3 cut(s) 13, 86, 478
TaqI TCGA 1 cut(s) 789
TaqII GACCGA 1 cut(s) 213
TasI AATT 9 cut(s) 51, 120, 236, 289, 423, 462, 903, 1213, 1472
TatI WGTACW 1 cut(s) 839
TfiI GAWTC 3 cut(s) 393, 887, 1237
Tru1I TTAA 2 cut(s) 99, 753
Tru9I TTAA 2 cut(s) 99, 753
TscAI CASTG 4 cut(s) 18, 409, 988, 1456
TseFI GTSAC 3 cut(s) 154, 701, 1089
TseI GCWGC 3 cut(s) 731, 860, 1106
Tsp45I GTSAC 3 cut(s) 154, 701, 1089
TspDTI ATGAA 7 cut(s) 204, 213, 315, 758, 801, 1164, 1280
TspGWI ACGGA 2 cut(s) 805, 1011
TspRI CASTG 4 cut(s) 18, 409, 988, 1456
VneI GTGCAC 1 cut(s) 576
VpaK11BI GGWCC 2 cut(s) 16, 490
XapI RAATTY 3 cut(s) 120, 462, 1213
XceI RCATGY 1 cut(s) 1502
XmnI GAANNNNTTC 1 cut(s) 797
XspI CTAG 3 cut(s) 390, 581, 1356
Zsp2I ATGCAT 2 cut(s) 875, 1504
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.