Rorug04G0010100

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000004
OG0000595
Physical Location & Seq
Forward (+)
1648723 .. 1649433
711 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug04G0010100.1

Sequence Viewer

Length: 423 bp
ATGGAACCACAAACCCAGCAACCAACCGAGGATGGAGGAAGCAACAAAGCAGCCGGGAGTAATGCTAACATGCTGCGGGGGCGGAACAGGTGGAATCCCACTACAGATCAGATAAGAATCCTCAATGAGCTTTTCTACAATAAGGGAGTTAGGTCCCCAACTATAGAGCAGATTCAGAGGATCTGTCTCCAGCTGAAATGGTACGGCAAGATCGAGTTCAAGAACGTCTATTTTTGGTTCGTGAACCAAAGGGCTCGGGAGAAGCGGAAGAAGAGGTCCACTTCGGATGTTCATGTGCCCATGCAAAGTTCAGGGCTTACTACTTCCGATGGAGGTGGCGGTCACGGTGGTGGCTCTCACATTTCCCTTGAGCTCAGCCTTTCCTGCGAGGGCAAAGCTGGAAAAAGTTTCTGGAGCCGCTGA
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
No domains found.

Protein Analysis

140

Amino Acids

15.76

Weight (kDa)

9.95

Isoelectric Point (pI)

66.39

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Homeodomain PF00046 28 - 89 2.1e-10 Homeodomain
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: OG0000595)

Species Orthologous Gene IDs
fragaria_vesca FvH4_4g37100 FvH4_4g37100 FvH4_4g37100
malus_domestica MD13G1238300.v1.1 MD16G1243100.v1.1 MD16G1243200.v1.1
prunus_persica Prupe.1G070100_v2.0.a1 Prupe.1G070200_v2.0.a1 Prupe.1G070300_v2.0.a1 Prupe.1G070300_v2.0.a1
pyrus_communis pycom13g21070 pycom16g20390 pycom16g20400
rosa_chinensis RchiOBHm_Chr1g0318071 RchiOBHm_Chr1g0318111 RchiOBHm_Chr4g0446861 RchiOBHm_Chr4g0446881 RchiOBHm_Chr4g0446891
rosa_laevigata RLG00000005623 RLG00000005624 RLG00000009337 RLG00000030560 RLG00000030566
rosa_multiflora Rmu_co8177450.1_g000001 Rmu_sc0001753.1_g000012 Rmu_sc0001753.1_g000013 Rmu_sc0001753.1_g000014 Rmu_sc0001753.1_g000015 Rmu_sc0011424.1_g000009 Rmu_sc0011424.1_g000020 Rmu_sc0034555.1_g000001 Rmu_ssc0000008.1_g000002
rosa_roxburghii Rroxscaffold_4G00329530 Rroxscaffold_4G00329590 Rroxscaffold_4G00329800 Rroxscaffold_4G00329810 Rroxscaffold_4G00329860 Rroxscaffold_4G00329910 Rroxscaffold_4G00330030 Rroxscaffold_5G00343610 Rroxscaffold_5G00348280 Rroxscaffold_5G00387220 Rroxscaffold_5G00387230
rosa_rugosa Rorug01G0019100 Rorug01G0019100 Rorug01G0019500 Rorug01G0019600 Rorug04G0010100 Rorug04G0375200 Rorug04G0375300 Rorug04G0375400 Rorug04G0375500 Rorug04G0375600 Rorug04G0375700
rosa_samantha Rh1AG030700 Rh1AG030900 Rh1BG026900 Rh1CG029500 Rh1CG029700 Rh1DG040500 Rh4AG088100 Rh4AG436700 Rh4AG436800 Rh4AG436900 Rh4BG084700 Rh4BG445800 Rh4BG445900 Rh4BG446100 Rh4CG096300 Rh4CG463100 Rh4CG463200 Rh4CG463400 Rh4DG444500 Rh4DG444600 Rh4DG444700
rosa_wichuraiana Rw1G002420 Rw1G002440 Rw1G002480 Rw4G037360 Rw4G037370 Rw4G037380

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 5 cut(s) 76, 82, 265, 339, 418
AclWI GGATC 1 cut(s) 188
AfaI GTAC 1 cut(s) 203
AgsI TTSAA 1 cut(s) 220
AleI CACNNNNGTG 1 cut(s) 348
AluBI AGCT 4 cut(s) 130, 193, 373, 398
AluI AGCT 4 cut(s) 130, 193, 373, 398
Alw21I GWGCWC 1 cut(s) 375
Alw26I GTCTC 1 cut(s) 191
AlwI GGATC 1 cut(s) 188
Ama87I CYCGRG 1 cut(s) 255
ApeKI GCWGC 2 cut(s) 50, 73
AspS9I GGNCC 2 cut(s) 153, 276
AsuC2I CCSGG 1 cut(s) 55
AvaI CYCGRG 1 cut(s) 255
AvaII GGWCC 2 cut(s) 153, 276
BaeGI GKGCMC 1 cut(s) 300
BanII GRGCYC 2 cut(s) 256, 375
Bbv12I GWGCWC 1 cut(s) 375
BbvI GCAGC 2 cut(s) 60, 62
BccI CCATC 2 cut(s) 26, 323
BceAI ACGGC 1 cut(s) 220
BcnI CCSGG 1 cut(s) 55
BcoDI GTCTC 1 cut(s) 191
BfmI CTRYAG 2 cut(s) 102, 162
BisI GCNGC 3 cut(s) 51, 74, 418
BlpI GCTNAGC 1 cut(s) 374
BlsI GCNGC 3 cut(s) 52, 75, 419
Bme1390I CCNGG 1 cut(s) 55
Bme18I GGWCC 2 cut(s) 153, 276
BmeT110I CYCGRG 1 cut(s) 255
BmgT120I GGNCC 2 cut(s) 153, 276
BmiI GGNNCC 3 cut(s) 6, 155, 416
BmrFI CCNGG 1 cut(s) 55
BpmI CTGGAG 1 cut(s) 173
Bpu1102I GCTNAGC 1 cut(s) 374
BpuEI CTTGAG 1 cut(s) 389
BpuMI CCSGG 1 cut(s) 55
BsaBI GATNNNNATC 1 cut(s) 116
BsaJI CCNNGG 1 cut(s) 27
Bse8I GATNNNNATC 1 cut(s) 116
BseDI CCNNGG 1 cut(s) 27
BseGI GGATG 2 cut(s) 37, 292
BseJI GATNNNNATC 1 cut(s) 116
BseMII CTCAG 1 cut(s) 388
BseSI GKGCMC 1 cut(s) 300
BseXI GCAGC 2 cut(s) 60, 62
BseYI CCCAGC 1 cut(s) 15
BsiHKAI GWGCWC 1 cut(s) 375
BsiHKCI CYCGRG 1 cut(s) 255
BsiSI CCGG 1 cut(s) 54
BslFI GGGAC 1 cut(s) 139
BsmAI GTCTC 1 cut(s) 191
BsmFI GGGAC 1 cut(s) 139
BsoBI CYCGRG 1 cut(s) 255
Bsp1286I GDGCHC 3 cut(s) 256, 300, 375
Bsp143I GATC 3 cut(s) 106, 180, 210
Bsp1720I GCTNAGC 1 cut(s) 374
BspACI CCGC 5 cut(s) 76, 82, 265, 339, 418
BspCNI CTCAG 1 cut(s) 387
BspLI GGNNCC 3 cut(s) 6, 155, 416
BspPI GGATC 1 cut(s) 188
BssECI CCNNGG 1 cut(s) 27
BssMI GATC 3 cut(s) 106, 180, 210
Bst4CI ACNGT 1 cut(s) 347
Bst6I CTCTTC 1 cut(s) 266
BstDEI CTNAG 1 cut(s) 374
BstF5I GGATG 2 cut(s) 37, 292
BstKTI GATC 3 cut(s) 109, 183, 213
BstMAI GTCTC 1 cut(s) 191
BstMBI GATC 3 cut(s) 106, 180, 210
BstMWI GCNNNNNNNGC 2 cut(s) 79, 384
BstNSI RCATGY 1 cut(s) 73
BstSCI CCNGG 1 cut(s) 53
BstSFI CTRYAG 2 cut(s) 102, 162
BstSLI GKGCMC 1 cut(s) 300
BstV1I GCAGC 2 cut(s) 60, 62
BstX2I RGATCY 1 cut(s) 180
BstYI RGATCY 1 cut(s) 180
BtsCI GGATG 2 cut(s) 37, 292
Cfr13I GGNCC 2 cut(s) 153, 276
Csp6I GTAC 1 cut(s) 202
CviAII CATG 3 cut(s) 70, 293, 301
CviQI GTAC 1 cut(s) 202
DdeI CTNAG 1 cut(s) 374
DpnI GATC 3 cut(s) 108, 182, 212
DpnII GATC 3 cut(s) 106, 180, 210
Eam1104I CTCTTC 1 cut(s) 266
EarI CTCTTC 1 cut(s) 266
EciI GGCGGA 1 cut(s) 97
Ecl136II GAGCTC 1 cut(s) 373
Eco24I GRGCYC 2 cut(s) 256, 375
Eco47I GGWCC 2 cut(s) 153, 276
Eco53kI GAGCTC 1 cut(s) 373
Eco88I CYCGRG 1 cut(s) 255
EcoICRI GAGCTC 1 cut(s) 373
EcoO109I RGGNCCY 1 cut(s) 153
EcoT38I GRGCYC 2 cut(s) 256, 375
FaeI CATG 3 cut(s) 73, 296, 304
FaiI YATR 4 cut(s) 71, 164, 294, 302
FaqI GGGAC 1 cut(s) 139
FatI CATG 3 cut(s) 69, 292, 300
FauI CCCGC 1 cut(s) 69
Fnu4HI GCNGC 3 cut(s) 51, 74, 418
FokI GGATG 2 cut(s) 44, 299
FriOI GRGCYC 2 cut(s) 256, 375
Fsp4HI GCNGC 3 cut(s) 51, 74, 418
GluI GCNGC 3 cut(s) 51, 74, 418
GsaI CCCAGC 1 cut(s) 19
GsuI CTGGAG 1 cut(s) 173
HapII CCGG 1 cut(s) 54
Hin1II CATG 3 cut(s) 73, 296, 304
HinfI GANTC 3 cut(s) 94, 117, 172
HpaII CCGG 1 cut(s) 54
Hpy166II GTNNAC 2 cut(s) 244, 279
Hpy188I TCNGA 4 cut(s) 111, 177, 286, 328
Hpy188III TCNNGA 4 cut(s) 220, 241, 257, 412
Hpy8I GTNNAC 2 cut(s) 244, 279
HpyCH4III ACNGT 1 cut(s) 347
HpyCH4IV ACGT 1 cut(s) 225
HpyCH4V TGCA 1 cut(s) 304
HpyF10VI GCNNNNNNNGC 2 cut(s) 79, 384
HpyF3I CTNAG 1 cut(s) 374
HpySE526I ACGT 1 cut(s) 225
Hsp92II CATG 3 cut(s) 73, 296, 304
Kzo9I GATC 3 cut(s) 106, 180, 210
LmnI GCTCC 1 cut(s) 414
LpnPI CCDG 8 cut(s) 29, 67, 73, 203, 297, 384, 397, 397
Lsp1109I GCAGC 2 cut(s) 60, 62
MaeII ACGT 1 cut(s) 225
MaeIII GTNAC 1 cut(s) 341
MalI GATC 3 cut(s) 108, 182, 212
MboI GATC 3 cut(s) 106, 180, 210
MboII GAAGA 2 cut(s) 280, 283
MflI RGATCY 1 cut(s) 180
MhlI GDGCHC 3 cut(s) 256, 300, 375
MnlI CCTC 7 cut(s) 22, 29, 131, 171, 267, 326, 382
MslI CAYNNNNRTG 1 cut(s) 348
MspA1I CMGCKG 2 cut(s) 193, 420
MspI CCGG 1 cut(s) 54
MspR9I CCNGG 1 cut(s) 55
MwoI GCNNNNNNNGC 2 cut(s) 79, 384
NciI CCSGG 1 cut(s) 55
NdeII GATC 3 cut(s) 106, 180, 210
NlaIII CATG 3 cut(s) 73, 296, 304
NlaIV GGNNCC 3 cut(s) 6, 155, 416
NmuCI GTSAC 1 cut(s) 341
NspI RCATGY 1 cut(s) 73
OliI CACNNNNGTG 1 cut(s) 348
PcsI WCGNNNNNNNCGW 1 cut(s) 210
PfeI GAWTC 3 cut(s) 94, 117, 172
PkrI GCNGC 3 cut(s) 52, 75, 419
PpuMI RGGWCCY 1 cut(s) 153
Psp124BI GAGCTC 1 cut(s) 375
Psp5II RGGWCCY 1 cut(s) 153
PspFI CCCAGC 1 cut(s) 15
PspN4I GGNNCC 3 cut(s) 6, 155, 416
PspPI GGNCC 2 cut(s) 153, 276
PspPPI RGGWCCY 1 cut(s) 153
PsuI RGATCY 1 cut(s) 180
PvuII CAGCTG 1 cut(s) 193
RsaI GTAC 1 cut(s) 203
RsaNI GTAC 1 cut(s) 202
RseI CAYNNNNRTG 1 cut(s) 348
SacI GAGCTC 1 cut(s) 375
SatI GCNGC 3 cut(s) 51, 74, 418
Sau3AI GATC 3 cut(s) 106, 180, 210
Sau96I GGNCC 2 cut(s) 153, 276
ScrFI CCNGG 1 cut(s) 55
SduI GDGCHC 3 cut(s) 256, 300, 375
SetI ASST 9 cut(s) 92, 132, 155, 195, 228, 278, 337, 375, 400
SfcI CTRYAG 2 cut(s) 102, 162
SinI GGWCC 2 cut(s) 153, 276
SmiMI CAYNNNNRTG 1 cut(s) 348
SmlI CTYRAG 1 cut(s) 368
SmoI CTYRAG 1 cut(s) 368
SsiI CCGC 5 cut(s) 76, 82, 265, 339, 418
SstI GAGCTC 1 cut(s) 375
StyD4I CCNGG 1 cut(s) 53
TaaI ACNGT 1 cut(s) 347
TaiI ACGT 1 cut(s) 228
TaqI TCGA 1 cut(s) 213
TauI GCSGC 1 cut(s) 420
TfiI GAWTC 3 cut(s) 94, 117, 172
TseFI GTSAC 1 cut(s) 341
TseI GCWGC 2 cut(s) 50, 73
Tsp45I GTSAC 1 cut(s) 341
TspDTI ATGAA 1 cut(s) 281
VpaK11BI GGWCC 2 cut(s) 153, 276
XceI RCATGY 1 cut(s) 73
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.