Rorug04G0375300

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000004
OG0000595
Physical Location & Seq
Forward (+)
54563726 .. 54567675
3950 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug04G0375300.1

Sequence Viewer

Length: 855 bp
ATGGATCGGTACCAGAGAGTGGAGAAGCCAAGAGCAGAGACGCCAATTGATGAGAATGAGATTAGGATTACGAGCCAAGGGAGGATGCGAAACTACATCACTTACGCCATGACTCTGCTTCAGAACAAGGGTTCGAACGAAATTGTTTTCAAGGCTATGGGAAGAGCTATCAACAAGAGTGTGACGATTGTGGAGCTAATTAAGAGAAGAATTGTCGGTCTTCACCAGTATACTACAATTGGATCCACCGACATAACTGATACTTGGGAACCCCTTGAGGAAGGCCTTCTACCTTTGTGTTCTGTGGTGTTGAAAGTTGGAGAGAGATCGATTGATATGGGAATGAAGTTAATTTTGGAACTTGGTCCGTACATTGAGGAGCTCACAAAAACAGGAGGTGCCATAAAGGAGTTTGTTAACCCAAAATACAAGGATGCTAGTAAGACTTCATTCAAGTCCTCAACTCGGTTAGTATATGATGCAAGACTACCCAAAAACTTGGGAAGATCAGAGATGCTTAAGCTTCAATCAAATTTTGTACAATTAAGGAAGACCACAGAGAATAGGAAAGCTATTATTATGACAGTTACCTCCTATTGTCTGATTCACCCATCAGACGGCATTGAGATAGACAACAGCAACGTGCCTTATCAGACGACATGCAAGTCCCCACTTAAGAGGAGTCTTGGCTGGGGTGAGGAGATTGTACTCGCATTTGGCGTTGTGTCGCTATCGCGAATCGGTGGTAGGGTCTCATGCGTCTTTTGGCGCATATGCCGTGCCCTGTCCGGTGTACTGGAGTCCGTAACATGTAATAATGGCGCAGTGGTGAGGAGCCGAGGCGACGGCGCATGA
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

284

Amino Acids

31.79

Weight (kDa)

9.4

Isoelectric Point (pI)

37.86

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Alba PF01918 19 - 83 2.4e-21 Alba
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)
AasI GACNNNNNNGTC 1 cut(s) 664
Acc65I GGTACC 1 cut(s) 9
AccB1I GGYRCC 2 cut(s) 9, 398
AccB7I CCANNNNNTGG 1 cut(s) 19
AccI GTMKAC 1 cut(s) 230
AccII CGCG 1 cut(s) 736
AclWI GGATC 3 cut(s) 12, 237, 250
AcsI RAATTY 1 cut(s) 532
AcuI CTGAAG 1 cut(s) 104
AcyI GRCGYC 1 cut(s) 41
AfaI GTAC 5 cut(s) 11, 371, 540, 708, 795
AfiI CCNNNNNNNGG 3 cut(s) 19, 465, 617
AflII CTTAAG 2 cut(s) 518, 674
AflIII ACRYGT 1 cut(s) 809
AgsI TTSAA 4 cut(s) 151, 313, 454, 527
AjuI GAANNNNNNNTTGG 2 cut(s) 338, 370
AluBI AGCT 5 cut(s) 167, 196, 382, 523, 572
AluI AGCT 5 cut(s) 167, 196, 382, 523, 572
Alw21I GWGCWC 1 cut(s) 384
Alw26I GTCTC 2 cut(s) 32, 757
AlwI GGATC 3 cut(s) 12, 237, 250
AoxI GGCC 1 cut(s) 283
ApoI RAATTY 1 cut(s) 532
Asp700I GAANNNNTTC 1 cut(s) 285
Asp718I GGTACC 1 cut(s) 9
AspLEI GCGC 3 cut(s) 771, 824, 851
AspS9I GGNCC 1 cut(s) 365
AsuHPI GGTGA 4 cut(s) 215, 599, 707, 841
AsuII TTCGAA 1 cut(s) 134
AvaII GGWCC 1 cut(s) 365
BaeGI GKGCMC 1 cut(s) 784
BamHI GGATCC 1 cut(s) 242
BanI GGYRCC 2 cut(s) 9, 398
BanII GRGCYC 1 cut(s) 384
BarI GAAGNNNNNNTAC 2 cut(s) 273, 305
BbsI GAAGAC 2 cut(s) 212, 557
Bbv12I GWGCWC 1 cut(s) 384
BccI CCATC 1 cut(s) 619
BceAI ACGGC 2 cut(s) 634, 762
BcoDI GTCTC 2 cut(s) 32, 757
BfaI CTAG 1 cut(s) 438
BfrI CTTAAG 2 cut(s) 518, 674
Bme18I GGWCC 1 cut(s) 365
BmgT120I GGNCC 1 cut(s) 365
BmiI GGNNCC 5 cut(s) 11, 244, 270, 400, 836
BmsI GCATC 4 cut(s) 75, 424, 469, 504
BpiI GAAGAC 2 cut(s) 212, 557
BpmI CTGGAG 1 cut(s) 818
Bpu14I TTCGAA 1 cut(s) 134
BpuEI CTTGAG 1 cut(s) 296
Bsa29I ATCGAT 1 cut(s) 329
BsaHI GRCGYC 1 cut(s) 41
BsaI GGTCTC 1 cut(s) 757
BsaJI CCNNGG 2 cut(s) 76, 838
BsaWI WCCGGW 1 cut(s) 788
Bsc4I CCNNNNNNNGG 3 cut(s) 19, 465, 617
Bse1I ACTGG 2 cut(s) 226, 801
BseCI ATCGAT 1 cut(s) 329
BseDI CCNNGG 2 cut(s) 76, 838
BseGI GGATG 2 cut(s) 90, 439
BseLI CCNNNNNNNGG 3 cut(s) 19, 465, 617
BseNI ACTGG 2 cut(s) 226, 801
BseRI GAGGAG 4 cut(s) 392, 694, 713, 847
BseSI GKGCMC 1 cut(s) 784
BseYI CCCAGC 1 cut(s) 690
Bsh1236I CGCG 1 cut(s) 736
BshFI GGCC 1 cut(s) 285
BshNI GGYRCC 2 cut(s) 9, 398
BshVI ATCGAT 1 cut(s) 329
BsiHKAI GWGCWC 1 cut(s) 384
BsiSI CCGG 1 cut(s) 789
BslFI GGGAC 1 cut(s) 652
BslI CCNNNNNNNGG 3 cut(s) 19, 465, 617
BsmAI GTCTC 2 cut(s) 32, 757
BsmBI CGTCTC 1 cut(s) 32
BsmFI GGGAC 1 cut(s) 652
BsnI GGCC 1 cut(s) 285
Bso31I GGTCTC 1 cut(s) 757
Bsp119I TTCGAA 1 cut(s) 134
Bsp1286I GDGCHC 2 cut(s) 384, 784
Bsp1407I TGTACA 1 cut(s) 538
Bsp143I GATC 4 cut(s) 4, 242, 326, 506
Bsp68I TCGCGA 1 cut(s) 736
BspANI GGCC 1 cut(s) 285
BspDI ATCGAT 1 cut(s) 329
BspFNI CGCG 1 cut(s) 736
BspLI GGNNCC 5 cut(s) 11, 244, 270, 400, 836
BspPI GGATC 3 cut(s) 12, 237, 250
BspQI GCTCTTC 1 cut(s) 157
BspT104I TTCGAA 1 cut(s) 134
BspT107I GGYRCC 2 cut(s) 9, 398
BspTI CTTAAG 2 cut(s) 518, 674
BspTNI GGTCTC 1 cut(s) 757
BsrGI TGTACA 1 cut(s) 538
BsrI ACTGG 2 cut(s) 226, 801
BssECI CCNNGG 2 cut(s) 76, 838
BssMI GATC 4 cut(s) 4, 242, 326, 506
BssNAI GTATAC 1 cut(s) 231
BssNI GRCGYC 1 cut(s) 41
BssT1I CCWWGG 1 cut(s) 76
Bst1107I GTATAC 1 cut(s) 231
Bst4CI ACNGT 1 cut(s) 586
Bst6I CTCTTC 1 cut(s) 157
BstACI GRCGYC 1 cut(s) 41
BstAFI CTTAAG 2 cut(s) 518, 674
BstAUI TGTACA 1 cut(s) 538
BstBI TTCGAA 1 cut(s) 134
BstF5I GGATG 2 cut(s) 90, 439
BstFNI CGCG 1 cut(s) 736
BstHHI GCGC 3 cut(s) 771, 824, 851
BstKTI GATC 4 cut(s) 7, 245, 329, 509
BstMAI GTCTC 2 cut(s) 32, 757
BstMBI GATC 4 cut(s) 4, 242, 326, 506
BstNSI RCATGY 2 cut(s) 663, 813
BstSLI GKGCMC 1 cut(s) 784
BstUI CGCG 1 cut(s) 736
BstV2I GAAGAC 2 cut(s) 212, 557
BstX2I RGATCY 1 cut(s) 242
BstXI CCANNNNNNTGG 1 cut(s) 499
BstYI RGATCY 1 cut(s) 242
BstZ17I GTATAC 1 cut(s) 231
Bsu15I ATCGAT 1 cut(s) 329
BsuRI GGCC 1 cut(s) 285
BsuTUI ATCGAT 1 cut(s) 329
BtsCI GGATG 2 cut(s) 90, 439
BtsI GCAGTG 1 cut(s) 831
BtsIMutI CAGTG 1 cut(s) 831
BtuMI TCGCGA 1 cut(s) 736
CfoI GCGC 3 cut(s) 771, 824, 851
Cfr13I GGNCC 1 cut(s) 365
ClaI ATCGAT 1 cut(s) 329
CseI GACGC 2 cut(s) 49, 748
Csp6I GTAC 5 cut(s) 10, 370, 539, 707, 794
CviAII CATG 5 cut(s) 109, 660, 756, 810, 852
CviQI GTAC 5 cut(s) 10, 370, 539, 707, 794
DpnI GATC 4 cut(s) 6, 244, 328, 508
DpnII GATC 4 cut(s) 4, 242, 326, 506
DrdI GACNNNNNNGTC 1 cut(s) 664
DseDI GACNNNNNNGTC 1 cut(s) 664
Eam1104I CTCTTC 1 cut(s) 157
EarI CTCTTC 1 cut(s) 157
Ecl136II GAGCTC 1 cut(s) 382
Eco130I CCWWGG 1 cut(s) 76
Eco147I AGGCCT 1 cut(s) 285
Eco24I GRGCYC 1 cut(s) 384
Eco31I GGTCTC 1 cut(s) 757
Eco47I GGWCC 1 cut(s) 365
Eco53kI GAGCTC 1 cut(s) 382
Eco57I CTGAAG 1 cut(s) 104
EcoICRI GAGCTC 1 cut(s) 382
EcoT14I CCWWGG 1 cut(s) 76
EcoT38I GRGCYC 1 cut(s) 384
ErhI CCWWGG 1 cut(s) 76
Esp3I CGTCTC 1 cut(s) 32
FaeI CATG 5 cut(s) 112, 663, 759, 813, 855
FaqI GGGAC 1 cut(s) 652
FatI CATG 5 cut(s) 108, 659, 755, 809, 851
FauNDI CATATG 1 cut(s) 773
FblI GTMKAC 1 cut(s) 230
FokI GGATG 2 cut(s) 97, 446
FriOI GRGCYC 1 cut(s) 384
FspBI CTAG 1 cut(s) 438
GlaI GCGC 3 cut(s) 770, 823, 850
GsaI CCCAGC 1 cut(s) 694
GsuI CTGGAG 1 cut(s) 818
HaeIII GGCC 1 cut(s) 285
HapII CCGG 1 cut(s) 789
HgaI GACGC 2 cut(s) 49, 748
HhaI GCGC 3 cut(s) 771, 824, 851
Hin1I GRCGYC 1 cut(s) 41
Hin1II CATG 5 cut(s) 112, 663, 759, 813, 855
Hin6I GCGC 3 cut(s) 769, 822, 849
HinP1I GCGC 3 cut(s) 769, 822, 849
HincII GTYRAC 1 cut(s) 418
HindII GTYRAC 1 cut(s) 418
HindIII AAGCTT 1 cut(s) 521
HinfI GANTC 5 cut(s) 112, 604, 682, 738, 800
HpaI GTTAAC 1 cut(s) 418
HpaII CCGG 1 cut(s) 789
HphI GGTGA 4 cut(s) 215, 599, 707, 841
Hpy166II GTNNAC 3 cut(s) 231, 418, 794
Hpy188I TCNGA 5 cut(s) 123, 511, 603, 616, 654
Hpy188III TCNNGA 1 cut(s) 735
Hpy8I GTNNAC 3 cut(s) 231, 418, 794
Hpy99I CGWCG 1 cut(s) 848
HpyAV CCTTC 2 cut(s) 275, 296
HpyCH4III ACNGT 1 cut(s) 586
HpyCH4IV ACGT 1 cut(s) 642
HpyCH4V TGCA 2 cut(s) 482, 663
HpySE526I ACGT 1 cut(s) 642
Hsp92I GRCGYC 1 cut(s) 41
Hsp92II CATG 5 cut(s) 112, 663, 759, 813, 855
HspAI GCGC 3 cut(s) 769, 822, 849
KpnI GGTACC 1 cut(s) 13
KspAI GTTAAC 1 cut(s) 418
Kzo9I GATC 4 cut(s) 4, 242, 326, 506
LguI GCTCTTC 1 cut(s) 157
LmnI GCTCC 3 cut(s) 193, 379, 834
LpnPI CCDG 7 cut(s) 26, 239, 378, 676, 782, 797, 802
LweI GCATC 4 cut(s) 75, 424, 469, 504
MaeI CTAG 1 cut(s) 438
MaeII ACGT 1 cut(s) 642
MaeIII GTNAC 3 cut(s) 181, 586, 805
MalI GATC 4 cut(s) 6, 244, 328, 508
MboI GATC 4 cut(s) 4, 242, 326, 506
MboII GAAGA 5 cut(s) 174, 212, 219, 516, 562
MfeI CAATTG 2 cut(s) 45, 237
MflI RGATCY 1 cut(s) 242
MhlI GDGCHC 2 cut(s) 384, 784
MluCI AATT 8 cut(s) 45, 141, 198, 210, 237, 351, 532, 542
MlyI GAGTC 3 cut(s) 106, 691, 809
MmeI TCCRAC 1 cut(s) 298
MroXI GAANNNNTTC 1 cut(s) 285
MseI TTAA 6 cut(s) 201, 350, 417, 519, 545, 675
MspCI CTTAAG 2 cut(s) 518, 674
MspI CCGG 1 cut(s) 789
MunI CAATTG 2 cut(s) 45, 237
MvnI CGCG 1 cut(s) 736
NdeI CATATG 1 cut(s) 773
NdeII GATC 4 cut(s) 4, 242, 326, 506
NlaIII CATG 5 cut(s) 112, 663, 759, 813, 855
NlaIV GGNNCC 5 cut(s) 11, 244, 270, 400, 836
NmuCI GTSAC 1 cut(s) 181
NruI TCGCGA 1 cut(s) 736
NspI RCATGY 2 cut(s) 663, 813
NspV TTCGAA 1 cut(s) 134
PceI AGGCCT 1 cut(s) 285
PciI ACATGT 1 cut(s) 809
PciSI GCTCTTC 1 cut(s) 157
PcsI WCGNNNNNNNCGW 1 cut(s) 717
PdmI GAANNNNTTC 1 cut(s) 285
PfeI GAWTC 2 cut(s) 604, 738
PflMI CCANNNNNTGG 1 cut(s) 19
PleI GAGTC 3 cut(s) 106, 690, 808
PpsI GAGTC 3 cut(s) 106, 690, 808
PscI ACATGT 1 cut(s) 809
Psp124BI GAGCTC 1 cut(s) 384
PspFI CCCAGC 1 cut(s) 690
PspN4I GGNNCC 5 cut(s) 11, 244, 270, 400, 836
PspPI GGNCC 1 cut(s) 365
PsuI RGATCY 1 cut(s) 242
RruI TCGCGA 1 cut(s) 736
RsaI GTAC 5 cut(s) 11, 371, 540, 708, 795
RsaNI GTAC 5 cut(s) 10, 370, 539, 707, 794
SacI GAGCTC 1 cut(s) 384
SapI GCTCTTC 1 cut(s) 157
SaqAI TTAA 6 cut(s) 201, 350, 417, 519, 545, 675
Sau3AI GATC 4 cut(s) 4, 242, 326, 506
Sau96I GGNCC 1 cut(s) 365
SchI GAGTC 3 cut(s) 106, 691, 809
SduI GDGCHC 2 cut(s) 384, 784
SetI ASST 9 cut(s) 169, 198, 295, 384, 400, 525, 574, 593, 645
SfaNI GCATC 4 cut(s) 75, 424, 469, 504
SfuI TTCGAA 1 cut(s) 134
SinI GGWCC 1 cut(s) 365
SmlI CTYRAG 3 cut(s) 275, 518, 674
SmoI CTYRAG 3 cut(s) 275, 518, 674
Sse9I AATT 8 cut(s) 45, 141, 198, 210, 237, 351, 532, 542
SseBI AGGCCT 1 cut(s) 285
SspMI CTAG 1 cut(s) 438
SstI GAGCTC 1 cut(s) 384
StuI AGGCCT 1 cut(s) 285
StyI CCWWGG 1 cut(s) 76
TaaI ACNGT 1 cut(s) 586
TaiI ACGT 1 cut(s) 645
TaqI TCGA 2 cut(s) 134, 329
TaqII GACCGA 1 cut(s) 206
TasI AATT 8 cut(s) 45, 141, 198, 210, 237, 351, 532, 542
TatI WGTACW 3 cut(s) 538, 706, 793
TfiI GAWTC 2 cut(s) 604, 738
Tru1I TTAA 6 cut(s) 201, 350, 417, 519, 545, 675
Tru9I TTAA 6 cut(s) 201, 350, 417, 519, 545, 675
TscAI CASTG 1 cut(s) 831
TseFI GTSAC 1 cut(s) 181
Tsp45I GTSAC 1 cut(s) 181
TspDTI ATGAA 2 cut(s) 359, 438
TspGWI ACGGA 2 cut(s) 357, 793
TspRI CASTG 1 cut(s) 831
Van91I CCANNNNNTGG 1 cut(s) 19
Vha464I CTTAAG 2 cut(s) 518, 674
VpaK11BI GGWCC 1 cut(s) 365
XapI RAATTY 1 cut(s) 532
XceI RCATGY 2 cut(s) 663, 813
XmiI GTMKAC 1 cut(s) 230
XmnI GAANNNNTTC 1 cut(s) 285
XspI CTAG 1 cut(s) 438
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.