Rorug04G0375200

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000004
OG0000595
Physical Location & Seq
Reverse (-)
54556083 .. 54558479
2397 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug04G0375200.1

Sequence Viewer

Length: 1161 bp
ATGGTCTCGACCTTGGCTATCCAATGTGTTTGCTTAGTGCTATTGCTTGTAACCATTAACAAAGTTCAAGCTCAGTCCAAAGTTTACAATGTACTGGAACACGGGGCCGTTGCAGATGGAAAATTTGATAACAGCAAGGTCTTGAGTGAAGTGTGGAACCAATCCTGTCATCAAAACACTGGAGGTGGTGTTATTTTATTTCCACAAGGGACGTTCATGGTGGCTCCGGTGGTTCTACAAGGGCATTGCAAGGGACCAATGGAGTTGCAGGTACAGGGAACCATACAAGCTCCCGTGGACGTCCAATCTTCGGTTGGTGTGGACCATTGGATCAGCTTCAGATATGTTGAACACTTCGTAATTCATGGTGGTGGATTGTTGGACGGCCAAGGAGCCTCTGCTTGGGGAAAGAGCAAGGCACTTCCCACTACATTGAGGTTAGATTTTGTTTCTCATGCAAGCATCCGCCAAATAACATTTCTCAACAGCAAGAACACCCATATCAAAATTTTCACATGCAGTGTTGTAGTAATTAGCAACATCAACATATCGGCTCCCGGTGACAGTCCCAACACTGACGGAATCAAAGTAAGTAATTCCAAATACATCCAAATCTTGGATTCAGTGATATCCGTAGGGGACGACTGCATTGCCTGCCTTCCCAATTCAAAGAACATCAACATAACTAGAGTTCACTGTGGACCTGGACATGGATTTAGCATCGGAAGCATTTCTCGTGGTACTGTTACTAATTTGAACATAAGAAACAGCAGTTTACTTGGTACTCAGAATGGAGTGAGAATCAAGACAAAGGCTTATTCATCTCAGCCAGGCAACGTTGCATATGTTACATTTGAGCACATTGAAATGGATAATGTCGGCAACCCCATCATCATTGATCAAAACTATTGCCCTGATCACGGATGTAGCGGAAAGGAATCCTCACAAGTTCAGATTAAAAATGTTAAGTTTAATAACATTTGGGGAACTTCAAGAACAAAGACTGCAGTTAATTTCAACTGCAGCCAAAGTAAACCTTGCCATGAGATTGAGCTGAGAGACATCAACCTAAATTATAGAGATGGAGGACCTGCGAATTCGTCATGTTCATATGTGGATGGCAAAGCTTATGGCAAACAAAACCCTCCTTCTTGCCTATAA
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

386

Amino Acids

41.63

Weight (kDa)

8.47

Isoelectric Point (pI)

41.11

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Pect-lyase_RHGA_epim PF12708 29 - 257 3.7e-08 Rhamnogalacturonase A/epimerase, pectate lyase-like
Glyco_hydro_28 PF00295 65 - 374 5.8e-85 Glycosyl hydrolases family 28
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

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)
AatII GACGTC 1 cut(s) 303
Acc36I ACCTGC 2 cut(s) 259, 1099
AccB7I CCANNNNNTGG 1 cut(s) 616
AciI CCGC 2 cut(s) 466, 930
AclI AACGTT 1 cut(s) 837
AclWI GGATC 1 cut(s) 338
AcoI YGGCCR 1 cut(s) 385
AcsI RAATTY 3 cut(s) 122, 507, 1096
AcuI CTGAAG 1 cut(s) 322
AcyI GRCGYC 1 cut(s) 300
AfaI GTAC 4 cut(s) 93, 273, 742, 784
AfiI CCNNNNNNNGG 5 cut(s) 310, 402, 616, 710, 920
AgsI TTSAA 7 cut(s) 68, 350, 669, 757, 866, 993, 1018
AjnI CCWGG 2 cut(s) 703, 829
AjuI GAANNNNNNNTTGG 2 cut(s) 462, 494
AluBI AGCT 5 cut(s) 71, 290, 336, 1054, 1127
AluI AGCT 5 cut(s) 71, 290, 336, 1054, 1127
Alw21I GWGCWC 1 cut(s) 861
Alw26I GTCTC 2 cut(s) 10, 1053
AlwI GGATC 1 cut(s) 338
AoxI GGCC 2 cut(s) 105, 385
ApeKI GCWGC 1 cut(s) 1023
ApoI RAATTY 3 cut(s) 122, 507, 1096
Asp700I GAANNNNTTC 1 cut(s) 730
AspS9I GGNCC 5 cut(s) 105, 254, 322, 701, 1088
AsuC2I CCSGG 1 cut(s) 558
AsuHPI GGTGA 1 cut(s) 572
AvaII GGWCC 4 cut(s) 254, 322, 701, 1088
BauI CACGAG 1 cut(s) 735
Bbv12I GWGCWC 1 cut(s) 861
BbvI GCAGC 1 cut(s) 1035
BccI CCATC 4 cut(s) 110, 896, 1076, 1112
BceAI ACGGC 2 cut(s) 92, 400
BcgI CGANNNNNNTGC 2 cut(s) 632, 666
BciT130I CCWGG 2 cut(s) 705, 831
BclI TGATCA 2 cut(s) 898, 916
BcnI CCSGG 1 cut(s) 558
BcoDI GTCTC 2 cut(s) 10, 1053
BfaI CTAG 1 cut(s) 687
BfmI CTRYAG 2 cut(s) 1005, 1021
BfuAI ACCTGC 2 cut(s) 259, 1099
BisI GCNGC 1 cut(s) 1024
BlsI GCNGC 1 cut(s) 1025
Bme1390I CCNGG 3 cut(s) 558, 705, 831
Bme18I GGWCC 4 cut(s) 254, 322, 701, 1088
BmgT120I GGNCC 5 cut(s) 105, 254, 322, 701, 1088
BmiI GGNNCC 7 cut(s) 106, 158, 225, 255, 280, 394, 555
BmrFI CCNGG 3 cut(s) 558, 705, 831
BmsI GCATC 2 cut(s) 471, 729
BpmI CTGGAG 1 cut(s) 201
BpuEI CTTGAG 1 cut(s) 163
BpuMI CCSGG 1 cut(s) 558
BsaHI GRCGYC 1 cut(s) 300
BsaI GGTCTC 1 cut(s) 10
BsaJI CCNNGG 3 cut(s) 12, 294, 388
BsaWI WCCGGW 1 cut(s) 226
BsaXI ACNNNNNCTCC 2 cut(s) 174, 204
Bsc4I CCNNNNNNNGG 5 cut(s) 310, 402, 616, 710, 920
Bse1I ACTGG 2 cut(s) 99, 184
Bse3DI GCAATG 2 cut(s) 244, 648
BseBI CCWGG 2 cut(s) 705, 831
BseDI CCNNGG 3 cut(s) 12, 294, 388
BseGI GGATG 4 cut(s) 462, 606, 929, 1123
BseLI CCNNNNNNNGG 5 cut(s) 310, 402, 616, 710, 920
BseMI GCAATG 2 cut(s) 244, 648
BseMII CTCAG 4 cut(s) 86, 800, 839, 1046
BseNI ACTGG 2 cut(s) 99, 184
BseXI GCAGC 1 cut(s) 1035
BshFI GGCC 2 cut(s) 107, 387
BsiHKAI GWGCWC 1 cut(s) 861
BsiSI CCGG 2 cut(s) 227, 558
BslFI GGGAC 4 cut(s) 223, 267, 552, 653
BslI CCNNNNNNNGG 5 cut(s) 310, 402, 616, 710, 920
BsmAI GTCTC 2 cut(s) 10, 1053
BsmFI GGGAC 4 cut(s) 223, 267, 552, 653
BsnI GGCC 2 cut(s) 107, 387
Bso31I GGTCTC 1 cut(s) 10
Bsp1286I GDGCHC 1 cut(s) 861
Bsp143I GATC 3 cut(s) 330, 898, 916
BspACI CCGC 2 cut(s) 466, 930
BspANI GGCC 2 cut(s) 107, 387
BspCNI CTCAG 4 cut(s) 85, 799, 838, 1047
BspLI GGNNCC 7 cut(s) 106, 158, 225, 255, 280, 394, 555
BspMAI CTGCAG 2 cut(s) 1009, 1025
BspMI ACCTGC 2 cut(s) 259, 1099
BspPI GGATC 1 cut(s) 338
BspTNI GGTCTC 1 cut(s) 10
BsrDI GCAATG 2 cut(s) 244, 648
BsrI ACTGG 2 cut(s) 99, 184
BssECI CCNNGG 3 cut(s) 12, 294, 388
BssMI GATC 3 cut(s) 330, 898, 916
BssNI GRCGYC 1 cut(s) 300
BssSI CACGAG 1 cut(s) 735
BssT1I CCWWGG 2 cut(s) 12, 388
Bst2BI CACGAG 1 cut(s) 735
Bst2UI CCWGG 2 cut(s) 705, 831
Bst4CI ACNGT 3 cut(s) 566, 698, 745
BstACI GRCGYC 1 cut(s) 300
BstAPI GCANNNNNTGC 1 cut(s) 654
BstC8I GCNNGC 2 cut(s) 460, 655
BstDEI CTNAG 5 cut(s) 34, 72, 786, 825, 1055
BstDSI CCRYGG 1 cut(s) 294
BstF5I GGATG 4 cut(s) 462, 606, 929, 1123
BstKTI GATC 3 cut(s) 333, 901, 919
BstMAI GTCTC 2 cut(s) 10, 1053
BstMBI GATC 3 cut(s) 330, 898, 916
BstMWI GCNNNNNNNGC 2 cut(s) 654, 726
BstNI CCWGG 2 cut(s) 705, 831
BstNSI RCATGY 1 cut(s) 519
BstSCI CCNGG 3 cut(s) 556, 703, 829
BstSFI CTRYAG 2 cut(s) 1005, 1021
BstV1I GCAGC 1 cut(s) 1035
BsuRI GGCC 2 cut(s) 107, 387
BtgI CCRYGG 1 cut(s) 294
BtsCI GGATG 4 cut(s) 462, 606, 929, 1123
BtsI GCAGTG 1 cut(s) 526
BtsIMutI CAGTG 5 cut(s) 177, 526, 573, 630, 694
BveI ACCTGC 2 cut(s) 259, 1099
Cac8I GCNNGC 2 cut(s) 460, 655
Cfr13I GGNCC 5 cut(s) 105, 254, 322, 701, 1088
Csp6I GTAC 4 cut(s) 92, 272, 741, 783
CviAII CATG 7 cut(s) 217, 365, 455, 516, 710, 1043, 1104
CviQI GTAC 4 cut(s) 92, 272, 741, 783
DdeI CTNAG 5 cut(s) 34, 72, 786, 825, 1055
DpnI GATC 3 cut(s) 332, 900, 918
DpnII GATC 3 cut(s) 330, 898, 916
EaeI YGGCCR 1 cut(s) 385
EciI GGCGGA 1 cut(s) 455
Eco130I CCWWGG 2 cut(s) 12, 388
Eco31I GGTCTC 1 cut(s) 10
Eco32I GATATC 1 cut(s) 630
Eco47I GGWCC 4 cut(s) 254, 322, 701, 1088
Eco57I CTGAAG 1 cut(s) 322
EcoO109I RGGNCCY 1 cut(s) 1088
EcoRI GAATTC 1 cut(s) 1096
EcoRII CCWGG 2 cut(s) 703, 829
EcoRV GATATC 1 cut(s) 630
EcoT14I CCWWGG 2 cut(s) 12, 388
ErhI CCWWGG 2 cut(s) 12, 388
FaeI CATG 7 cut(s) 220, 368, 458, 519, 713, 1046, 1107
FalI AAGNNNNNCTT 2 cut(s) 1021, 1053
FaqI GGGAC 4 cut(s) 223, 267, 552, 653
FatI CATG 7 cut(s) 216, 364, 454, 515, 709, 1042, 1103
FauNDI CATATG 2 cut(s) 844, 1111
FbaI TGATCA 2 cut(s) 898, 916
Fnu4HI GCNGC 1 cut(s) 1024
FokI GGATG 4 cut(s) 449, 593, 936, 1130
Fsp4HI GCNGC 1 cut(s) 1024
FspBI CTAG 1 cut(s) 687
GluI GCNGC 1 cut(s) 1024
GsuI CTGGAG 1 cut(s) 201
HaeIII GGCC 2 cut(s) 107, 387
HapII CCGG 2 cut(s) 227, 558
Hin1I GRCGYC 1 cut(s) 300
Hin1II CATG 7 cut(s) 220, 368, 458, 519, 713, 1046, 1107
HindIII AAGCTT 1 cut(s) 1125
HinfI GANTC 4 cut(s) 582, 620, 801, 938
HpaII CCGG 2 cut(s) 227, 558
HphI GGTGA 1 cut(s) 572
Hpy166II GTNNAC 7 cut(s) 85, 298, 322, 694, 701, 776, 1034
Hpy188I TCNGA 4 cut(s) 341, 725, 789, 954
Hpy188III TCNNGA 4 cut(s) 7, 142, 805, 993
Hpy8I GTNNAC 7 cut(s) 85, 298, 322, 694, 701, 776, 1034
HpyAV CCTTC 2 cut(s) 668, 1158
HpyCH4III ACNGT 3 cut(s) 566, 698, 745
HpyCH4IV ACGT 3 cut(s) 212, 300, 837
HpyCH4V TGCA 9 cut(s) 113, 249, 268, 458, 519, 648, 842, 1007, 1023
HpyF10VI GCNNNNNNNGC 2 cut(s) 654, 726
HpyF3I CTNAG 5 cut(s) 34, 72, 786, 825, 1055
HpySE526I ACGT 3 cut(s) 212, 300, 837
Hsp92I GRCGYC 1 cut(s) 300
Hsp92II CATG 7 cut(s) 220, 368, 458, 519, 713, 1046, 1107
Ksp22I TGATCA 2 cut(s) 898, 916
Kzo9I GATC 3 cut(s) 330, 898, 916
LmnI GCTCC 4 cut(s) 229, 295, 392, 559
Lsp1109I GCAGC 1 cut(s) 1035
LweI GCATC 2 cut(s) 471, 729
MaeI CTAG 1 cut(s) 687
MaeII ACGT 3 cut(s) 212, 300, 837
MaeIII GTNAC 4 cut(s) 49, 560, 745, 847
MalI GATC 3 cut(s) 332, 900, 918
MboI GATC 3 cut(s) 330, 898, 916
MboII GAAGA 1 cut(s) 300
MhlI GDGCHC 1 cut(s) 861
MmeI TCCRAC 1 cut(s) 360
MnlI CCTC 6 cut(s) 176, 406, 429, 952, 1079, 1155
MroXI GAANNNNTTC 1 cut(s) 730
MseI TTAA 5 cut(s) 57, 957, 966, 972, 1011
MslI CAYNNNNRTG 2 cut(s) 369, 866
MspI CCGG 2 cut(s) 227, 558
MspR9I CCNGG 3 cut(s) 558, 705, 831
MvaI CCWGG 2 cut(s) 705, 831
MwoI GCNNNNNNNGC 2 cut(s) 654, 726
NciI CCSGG 1 cut(s) 558
NdeI CATATG 2 cut(s) 844, 1111
NdeII GATC 3 cut(s) 330, 898, 916
NlaIII CATG 7 cut(s) 220, 368, 458, 519, 713, 1046, 1107
NlaIV GGNNCC 7 cut(s) 106, 158, 225, 255, 280, 394, 555
NmuCI GTSAC 1 cut(s) 560
NspI RCATGY 1 cut(s) 519
PdmI GAANNNNTTC 1 cut(s) 730
PfeI GAWTC 4 cut(s) 582, 620, 801, 938
PflMI CCANNNNNTGG 1 cut(s) 616
PkrI GCNGC 1 cut(s) 1025
PpuMI RGGWCCY 1 cut(s) 1088
Psp1406I AACGTT 1 cut(s) 837
Psp5II RGGWCCY 1 cut(s) 1088
Psp6I CCWGG 2 cut(s) 703, 829
PspGI CCWGG 2 cut(s) 703, 829
PspN4I GGNNCC 7 cut(s) 106, 158, 225, 255, 280, 394, 555
PspPI GGNCC 5 cut(s) 105, 254, 322, 701, 1088
PspPPI RGGWCCY 1 cut(s) 1088
PstI CTGCAG 2 cut(s) 1009, 1025
RsaI GTAC 4 cut(s) 93, 273, 742, 784
RsaNI GTAC 4 cut(s) 92, 272, 741, 783
RseI CAYNNNNRTG 2 cut(s) 369, 866
SaqAI TTAA 5 cut(s) 57, 957, 966, 972, 1011
SatI GCNGC 1 cut(s) 1024
Sau3AI GATC 3 cut(s) 330, 898, 916
Sau96I GGNCC 5 cut(s) 105, 254, 322, 701, 1088
ScrFI CCNGG 3 cut(s) 558, 705, 831
SduI GDGCHC 1 cut(s) 861
SfaNI GCATC 2 cut(s) 471, 729
SfcI CTRYAG 2 cut(s) 1005, 1021
SinI GGWCC 4 cut(s) 254, 322, 701, 1088
SmiMI CAYNNNNRTG 2 cut(s) 369, 866
SmlI CTYRAG 1 cut(s) 142
SmoI CTYRAG 1 cut(s) 142
SsiI CCGC 2 cut(s) 466, 930
SspMI CTAG 1 cut(s) 687
StyD4I CCNGG 3 cut(s) 556, 703, 829
StyI CCWWGG 2 cut(s) 12, 388
TaaI ACNGT 3 cut(s) 566, 698, 745
TaiI ACGT 3 cut(s) 215, 303, 840
TaqI TCGA 1 cut(s) 8
TatI WGTACW 1 cut(s) 91
TfiI GAWTC 4 cut(s) 582, 620, 801, 938
Tru1I TTAA 5 cut(s) 57, 957, 966, 972, 1011
Tru9I TTAA 5 cut(s) 57, 957, 966, 972, 1011
TscAI CASTG 5 cut(s) 184, 526, 580, 630, 701
TseFI GTSAC 1 cut(s) 560
TseI GCWGC 1 cut(s) 1023
Tsp45I GTSAC 1 cut(s) 560
TspDTI ATGAA 4 cut(s) 205, 353, 810, 1098
TspGWI ACGGA 3 cut(s) 594, 622, 936
TspRI CASTG 5 cut(s) 184, 526, 580, 630, 701
Van91I CCANNNNNTGG 1 cut(s) 616
VpaK11BI GGWCC 4 cut(s) 254, 322, 701, 1088
XapI RAATTY 3 cut(s) 122, 507, 1096
XceI RCATGY 1 cut(s) 519
XcmI CCANNNNNNNNNTGG 1 cut(s) 311
XmnI GAANNNNTTC 1 cut(s) 730
XspI CTAG 1 cut(s) 687
ZraI GACGTC 1 cut(s) 301
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.