Rh5DG132400

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

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_samantha
Chr5D
OG0000343
Physical Location & Seq
Reverse (-)
13029300 .. 13030718
1419 bp
Loading structure...
UTR
Exon/CDS
Intron
Rh5DG132400.1

Sequence Viewer

Length: 639 bp
ATGAAAATGTTCTGTTTGAAGGCTTCAGCTAGTAACTCAGACGGCGAGGACCGCAAGTTGACAAGAAAGGAGAAGGACGGAGGATGTAAGATCGAGTACACTACTGAAAAACCAGCCACGCCATTGCTGGACACAATCAATTACCCAGCTCACATGAAGAATCTATCAACACAGGATCTCGAACAACTAGCAGCAGAGCTCAGAATGGATATTGTTCACAGTGTTTCACAGACAGGTGGGCATCTCAGTTTTAGCTTGGGTGTGGTGGAGCTATCAGTGGCATTGCATCATGTGTTCAGCACCCCTGACGATAAAATCATATGGGATGTTGGTCATCAGGATATCCAAGTTAGAAAAAAGCCAGGATTGTCCACTGATGACATATTCGATACGGTTTGTGCTTTTTGTGATAATGGTGGCAGCCTTTTGTGTTGTGAAGGGCGATGCCTAAGGTCCTTTCATGCAACTGTAAAGGACGGTGAGGGCTTTACTTGTGAATCTCTTGGATTTTCCCAGGATGAAGTAGATGCAATTCGAAAAATTGATTTCTACTGCAAGAACTGTCAATATAAACAGCATCAGTGCTATGCTTGTGGGAAGTTAGGATCCTTGGACAAATCTTTAGGTGCTGAGGTATGA
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

212

Amino Acids

23.41

Weight (kDa)

5.59

Isoelectric Point (pI)

25.54

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DXP_synthase_N PF13292 43 - 113 3.2e-28 1-deoxy-D-xylulose-5-phosphate synthase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000343)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G48090 AT5G48090 AT5G48090 AT5G55390 AT5G55390 AT5G55390
fragaria_vesca FvH4_3g23690 FvH4_4g08730 FvH4_4g08730 FvH4_4g08730 FvH4_4g08730 FvH4_4g08730 FvH4_4g08730 FvH4_5g31160 FvH4_5g31160 FvH4_5g31160 FvH4_5g31160 FvH4_5g31160
malus_domestica MD03G1191000.v1.1 MD11G1207800.v1.1 MD11G1208000.v1.1
prunus_persica Prupe.4G227500_v2.0.a1 Prupe.4G227500_v2.0.a1 Prupe.4G227500_v2.0.a1 Prupe.4G227500_v2.0.a1 Prupe.4G227500_v2.0.a1 Prupe.4G227500_v2.0.a1 Prupe.4G227600_v2.0.a1 Prupe.4G227700_v2.0.a1 Prupe.4G227800_v2.0.a1 Prupe.4G227800_v2.0.a1 Prupe.4G227800_v2.0.a1 Prupe.4G227800_v2.0.a1 Prupe.4G227800_v2.0.a1
pyrus_communis pycom01g03400 pycom03g14420 pycom11g18100 pycom11g18140 pycom11g18150 pycom11g18160
rosa_chinensis RchiOBHm_Chr2g0145981 RchiOBHm_Chr4g0405241 RchiOBHm_Chr4g0405271 RchiOBHm_Chr5g0016201 RchiOBHm_Chr5g0041831 RchiOBHm_Chr5g0041871 RchiOBHm_Chr5g0041881 RchiOBHm_Chr5g0059241
rosa_laevigata RLG00000002117 RLG00000008861 RLG00000008862 RLG00000011000 RLG00000033216 RLG00000034097 RLG00000034101
rosa_multiflora Rmu_sc0000161.1_g000001 Rmu_sc0000861.1_g000040 Rmu_sc0007522.1_g000003 Rmu_sc0009443.1_g000015 Rmu_sc0022129.1_g000001 Rmu_sc0042315.1_g000001
rosa_roxburghii Rroxscaffold_1G00038660 Rroxscaffold_1G00038690 Rroxscaffold_5G00349560 Rroxscaffold_5G00349610 Rroxscaffold_6G00388370 Rroxscaffold_7G00188740
rosa_rugosa Rorug03G0199700 Rorug04G0055400 Rorug04G0055500 Rorug04G0055900 Rorug04G0056000 Rorug04G0056100 Rorug04G0056100 Rorug04G0056200 Rorug05G0195600 Rorug05G0195700 Rorug05G0195800 Rorug05G0195900 Rorug05G0196800 Rorug05G0385000
rosa_samantha Rh4AG129900 Rh4AG130100 Rh4BG124200 Rh4BG124400 Rh4BG124500 Rh4CG137200 Rh4CG137300 Rh4DG123500 Rh4DG123700 Rh5AG280800 Rh5AG281400 Rh5BG286700 Rh5BG287000 Rh5BG397800 Rh5CG318100 Rh5CG318600 Rh5CG421600 Rh5DG132300 Rh5DG132400 Rh5DG295400 Rh5DG295700 Rh7BG475300
rosa_wichuraiana Rw0G001330 Rw0G005730 Rw4G008670 Rw4G010510 Rw4G010540 Rw5G026450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 1 cut(s) 52
AclWI GGATC 3 cut(s) 183, 600, 613
AcuI CTGAAG 1 cut(s) 9
AfaI GTAC 1 cut(s) 98
AgsI TTSAA 1 cut(s) 19
AjnI CCWGG 2 cut(s) 361, 513
AluBI AGCT 5 cut(s) 29, 149, 199, 255, 271
AluI AGCT 5 cut(s) 29, 149, 199, 255, 271
Alw21I GWGCWC 1 cut(s) 201
AlwI GGATC 3 cut(s) 183, 600, 613
ApeKI GCWGC 2 cut(s) 191, 420
Asp700I GAANNNNTTC 1 cut(s) 8
AspS9I GGNCC 2 cut(s) 49, 453
AsuHPI GGTGA 1 cut(s) 491
AsuII TTCGAA 1 cut(s) 535
AvaII GGWCC 2 cut(s) 49, 453
AxyI CCTNAGG 1 cut(s) 449
BamHI GGATCC 1 cut(s) 605
BanII GRGCYC 1 cut(s) 201
Bbv12I GWGCWC 1 cut(s) 201
BbvCI CCTCAGC 1 cut(s) 630
BbvI GCAGC 2 cut(s) 203, 432
BceAI ACGGC 1 cut(s) 58
BciT130I CCWGG 2 cut(s) 363, 515
BfaI CTAG 2 cut(s) 30, 188
BisI GCNGC 2 cut(s) 192, 421
BlsI GCNGC 2 cut(s) 193, 422
Bme1390I CCNGG 2 cut(s) 363, 515
Bme18I GGWCC 2 cut(s) 49, 453
BmgT120I GGNCC 2 cut(s) 49, 453
BmiI GGNNCC 1 cut(s) 607
BmrFI CCNGG 2 cut(s) 363, 515
BmsI GCATC 5 cut(s) 250, 295, 434, 517, 586
Bpu10I CCTNAGC 1 cut(s) 630
Bpu14I TTCGAA 1 cut(s) 535
BsaJI CCNNGG 2 cut(s) 513, 609
Bse21I CCTNAGG 1 cut(s) 449
Bse3DI GCAATG 2 cut(s) 122, 281
BseBI CCWGG 2 cut(s) 363, 515
BseDI CCNNGG 2 cut(s) 513, 609
BseGI GGATG 3 cut(s) 89, 331, 523
BseMI GCAATG 2 cut(s) 122, 281
BseMII CTCAG 4 cut(s) 51, 214, 259, 621
BseXI GCAGC 2 cut(s) 203, 432
BseYI CCCAGC 1 cut(s) 145
BsiHKAI GWGCWC 1 cut(s) 201
Bsp119I TTCGAA 1 cut(s) 535
Bsp1286I GDGCHC 1 cut(s) 201
Bsp143I GATC 3 cut(s) 90, 175, 605
BspACI CCGC 1 cut(s) 52
BspCNI CTCAG 4 cut(s) 50, 213, 258, 622
BspLI GGNNCC 1 cut(s) 607
BspPI GGATC 3 cut(s) 183, 600, 613
BspT104I TTCGAA 1 cut(s) 535
BsrDI GCAATG 2 cut(s) 122, 281
BssECI CCNNGG 2 cut(s) 513, 609
BssMI GATC 3 cut(s) 90, 175, 605
BssT1I CCWWGG 1 cut(s) 609
Bst2UI CCWGG 2 cut(s) 363, 515
Bst4CI ACNGT 5 cut(s) 221, 394, 469, 479, 563
BstBI TTCGAA 1 cut(s) 535
BstDEI CTNAG 5 cut(s) 37, 200, 245, 449, 630
BstF5I GGATG 3 cut(s) 89, 331, 523
BstKTI GATC 3 cut(s) 93, 178, 608
BstMBI GATC 3 cut(s) 90, 175, 605
BstMWI GCNNNNNNNGC 1 cut(s) 51
BstNI CCWGG 2 cut(s) 363, 515
BstSCI CCNGG 2 cut(s) 361, 513
BstV1I GCAGC 2 cut(s) 203, 432
BstX2I RGATCY 2 cut(s) 175, 605
BstYI RGATCY 2 cut(s) 175, 605
Bsu36I CCTNAGG 1 cut(s) 449
BtgZI GCGATG 1 cut(s) 457
BtsCI GGATG 3 cut(s) 89, 331, 523
BtsIMutI CAGTG 4 cut(s) 226, 282, 372, 587
Cfr13I GGNCC 2 cut(s) 49, 453
Csp6I GTAC 1 cut(s) 97
CviAII CATG 3 cut(s) 154, 290, 461
CviQI GTAC 1 cut(s) 97
DdeI CTNAG 5 cut(s) 37, 200, 245, 449, 630
DpnI GATC 3 cut(s) 92, 177, 607
DpnII GATC 3 cut(s) 90, 175, 605
Ecl136II GAGCTC 1 cut(s) 199
Eco130I CCWWGG 1 cut(s) 609
Eco24I GRGCYC 1 cut(s) 201
Eco32I GATATC 1 cut(s) 343
Eco47I GGWCC 2 cut(s) 49, 453
Eco53kI GAGCTC 1 cut(s) 199
Eco57I CTGAAG 1 cut(s) 9
Eco81I CCTNAGG 1 cut(s) 449
EcoICRI GAGCTC 1 cut(s) 199
EcoO109I RGGNCCY 1 cut(s) 453
EcoRII CCWGG 2 cut(s) 361, 513
EcoRV GATATC 1 cut(s) 343
EcoT14I CCWWGG 1 cut(s) 609
EcoT38I GRGCYC 1 cut(s) 201
ErhI CCWWGG 1 cut(s) 609
FaeI CATG 3 cut(s) 157, 293, 464
FaiI YATR 9 cut(s) 155, 291, 320, 322, 383, 462, 570, 588, 637
FatI CATG 3 cut(s) 153, 289, 460
FauNDI CATATG 1 cut(s) 320
Fnu4HI GCNGC 2 cut(s) 192, 421
FokI GGATG 3 cut(s) 96, 338, 530
FriOI GRGCYC 1 cut(s) 201
Fsp4HI GCNGC 2 cut(s) 192, 421
FspBI CTAG 2 cut(s) 30, 188
GluI GCNGC 2 cut(s) 192, 421
GsaI CCCAGC 1 cut(s) 149
Hin1II CATG 3 cut(s) 157, 293, 464
HincII GTYRAC 1 cut(s) 60
HindII GTYRAC 1 cut(s) 60
HinfI GANTC 2 cut(s) 160, 497
HphI GGTGA 1 cut(s) 491
Hpy166II GTNNAC 4 cut(s) 60, 99, 217, 372
Hpy188I TCNGA 2 cut(s) 40, 203
Hpy188III TCNNGA 2 cut(s) 179, 338
Hpy8I GTNNAC 4 cut(s) 60, 99, 217, 372
HpyAV CCTTC 3 cut(s) 13, 67, 431
HpyCH4III ACNGT 5 cut(s) 221, 394, 469, 479, 563
HpyCH4V TGCA 4 cut(s) 286, 464, 530, 555
HpyF10VI GCNNNNNNNGC 1 cut(s) 51
HpyF3I CTNAG 5 cut(s) 37, 200, 245, 449, 630
Hsp92II CATG 3 cut(s) 157, 293, 464
Kzo9I GATC 3 cut(s) 90, 175, 605
LmnI GCTCC 1 cut(s) 268
Lsp1109I GCAGC 2 cut(s) 203, 432
LweI GCATC 5 cut(s) 250, 295, 434, 517, 586
MaeI CTAG 2 cut(s) 30, 188
MaeIII GTNAC 1 cut(s) 32
MalI GATC 3 cut(s) 92, 177, 607
MboI GATC 3 cut(s) 90, 175, 605
MboII GAAGA 1 cut(s) 169
MflI RGATCY 2 cut(s) 175, 605
MhlI GDGCHC 1 cut(s) 201
MluCI AATT 3 cut(s) 139, 531, 540
MnlI CCTC 4 cut(s) 40, 74, 475, 625
MroXI GAANNNNTTC 1 cut(s) 8
MspR9I CCNGG 2 cut(s) 363, 515
MvaI CCWGG 2 cut(s) 363, 515
MwoI GCNNNNNNNGC 1 cut(s) 51
NdeI CATATG 1 cut(s) 320
NdeII GATC 3 cut(s) 90, 175, 605
NlaIII CATG 3 cut(s) 157, 293, 464
NlaIV GGNNCC 1 cut(s) 607
NspV TTCGAA 1 cut(s) 535
PdmI GAANNNNTTC 1 cut(s) 8
PfeI GAWTC 2 cut(s) 160, 497
PkrI GCNGC 2 cut(s) 193, 422
PpuMI RGGWCCY 1 cut(s) 453
Psp124BI GAGCTC 1 cut(s) 201
Psp5II RGGWCCY 1 cut(s) 453
Psp6I CCWGG 2 cut(s) 361, 513
PspFI CCCAGC 1 cut(s) 145
PspGI CCWGG 2 cut(s) 361, 513
PspN4I GGNNCC 1 cut(s) 607
PspPI GGNCC 2 cut(s) 49, 453
PspPPI RGGWCCY 1 cut(s) 453
PsuI RGATCY 2 cut(s) 175, 605
RsaI GTAC 1 cut(s) 98
RsaNI GTAC 1 cut(s) 97
SacI GAGCTC 1 cut(s) 201
SatI GCNGC 2 cut(s) 192, 421
Sau3AI GATC 3 cut(s) 90, 175, 605
Sau96I GGNCC 2 cut(s) 49, 453
ScrFI CCNGG 2 cut(s) 363, 515
SduI GDGCHC 1 cut(s) 201
SetI ASST 9 cut(s) 31, 151, 201, 238, 257, 273, 455, 628, 636
SfaNI GCATC 5 cut(s) 250, 295, 434, 517, 586
SfuI TTCGAA 1 cut(s) 535
SinI GGWCC 2 cut(s) 49, 453
Sse9I AATT 3 cut(s) 139, 531, 540
SsiI CCGC 1 cut(s) 52
SspMI CTAG 2 cut(s) 30, 188
SstI GAGCTC 1 cut(s) 201
StyD4I CCNGG 2 cut(s) 361, 513
StyI CCWWGG 1 cut(s) 609
TaaI ACNGT 5 cut(s) 221, 394, 469, 479, 563
TaqI TCGA 4 cut(s) 93, 180, 387, 535
TasI AATT 3 cut(s) 139, 531, 540
TatI WGTACW 1 cut(s) 96
TfiI GAWTC 2 cut(s) 160, 497
TscAI CASTG 4 cut(s) 226, 282, 379, 587
TseI GCWGC 2 cut(s) 191, 420
TspDTI ATGAA 4 cut(s) 17, 170, 449, 534
TspGWI ACGGA 1 cut(s) 93
TspRI CASTG 4 cut(s) 226, 282, 379, 587
VpaK11BI GGWCC 2 cut(s) 49, 453
XcmI CCANNNNNNNNNTGG 1 cut(s) 124
XmnI GAANNNNTTC 1 cut(s) 8
XspI CTAG 2 cut(s) 30, 188
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.