Rroxscaffold_5G00343610

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0000595
Physical Location & Seq
Forward (+)
13132260 .. 13133721
1462 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00343610.1

Sequence Viewer

Length: 912 bp
ATGGAGTTGCGAGAAGAAGAAATTTATAATTACAAAACTCAAGAGAAGGCAAGAGAAACCTTTGCTGCATTTGCGATTGATTCTGTTCCTGAGAGACGACCATTTCTCTATTCGAGGGACTTGGTGTATGTACGACCATCAGATATGGATACTGAGCACTTCCAGATTCATGATGTCAGCTTCTCATTCAATAGAGACTGTTTAAAAAGACCTCACCAGGCAGTTAGAGCTGCATCAGAAGCTTTGTTTCGGAACTTCCTCTTTCCTGATTGTGTCTCCCGTCCAAGCATTCCCATTGCACCAGCACTGGTCTCTACCTTTCATAAACTTGACGAAGGTGAACTTTCTGCAGTTCGTCATATCATAAACAGTCAGGGCTCACCACCTTACCTAGTAGCTGGCGAACTCTTTGTTGAACTGAAAAACCTTTCTGATCGAACCATATATCGAGGACTGGACTGGGGTTGTGATGTGCTTCTGAGAAGCTTGATGGAAGTGATTCCAGAGTCGGATATGTTTCGAGCCGACGCGGCAATCCGTGAGATAGAAGAGGTACTTGAGGACATCCTGCCGTCATGCCAGTACACCGTGCCATCATGCCTTCACAAAGACCCTTATTTCTCTCGTCCTCCAACCCAGCAACTCCGAAAATTCAGGGTGATTTCATCAACTTTCATGAGTAGCTATCGGCTACATGATCAAGGCATTACTAGTGGACACCTTAGCCATATTTTTCTGGCGGATGCTTCATCCGCTACTGAGCCGGAAACAATGGTGATCCTGACTAATTTTGTGGACGAAAGTACTACTGTTATAGTTACTGGTAAACCCGGACATACATTCACGTTGGGTTCACGCCAACATTGCAAGGGAGAAGGGAATGTACGTTTCATACTTTTGAAAGACTTTTGA
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

303

Amino Acids

34.57

Weight (kDa)

5.68

Isoelectric Point (pI)

51.48

Instability Index
Protein Domains (Pfam)
No Pfam domains detected for this protein.
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: 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)
AanI TTATAA 1 cut(s) 27
AccII CGCG 1 cut(s) 530
AciI CCGC 3 cut(s) 530, 740, 753
AclWI GGATC 1 cut(s) 772
AcsI RAATTY 2 cut(s) 21, 650
AfaI GTAC 5 cut(s) 132, 555, 584, 805, 885
AgsI TTSAA 3 cut(s) 190, 416, 901
AhlI ACTAGT 1 cut(s) 710
AjnI CCWGG 1 cut(s) 216
AluBI AGCT 6 cut(s) 180, 230, 242, 398, 486, 684
AluI AGCT 6 cut(s) 180, 230, 242, 398, 486, 684
Alw21I GWGCWC 1 cut(s) 159
Alw26I GTCTC 4 cut(s) 88, 189, 280, 316
AlwI GGATC 1 cut(s) 772
ApeKI GCWGC 2 cut(s) 65, 230
ApoI RAATTY 2 cut(s) 21, 650
Asp700I GAANNNNTTC 1 cut(s) 498
AsuC2I CCSGG 1 cut(s) 831
AsuHPI GGTGA 5 cut(s) 206, 350, 372, 670, 787
BanII GRGCYC 1 cut(s) 380
BarI GAAGNNNNNNTAC 2 cut(s) 867, 899
Bbv12I GWGCWC 1 cut(s) 159
BbvI GCAGC 2 cut(s) 52, 217
BccI CCATC 3 cut(s) 145, 484, 601
BceAI ACGGC 1 cut(s) 556
BciT130I CCWGG 1 cut(s) 218
BciVI GTATCC 1 cut(s) 142
BclI TGATCA 1 cut(s) 697
BcnI CCSGG 1 cut(s) 831
BcoDI GTCTC 4 cut(s) 88, 189, 280, 316
BcuI ACTAGT 1 cut(s) 710
BfaI CTAG 2 cut(s) 392, 711
BfmI CTRYAG 1 cut(s) 348
BfuI GTATCC 1 cut(s) 142
BglI GCCNNNNNGGC 1 cut(s) 530
BisI GCNGC 3 cut(s) 66, 231, 531
BlsI GCNGC 3 cut(s) 67, 232, 532
BmcAI AGTACT 1 cut(s) 805
Bme1390I CCNGG 2 cut(s) 218, 831
BmrFI CCNGG 2 cut(s) 218, 831
BmrI ACTGGG 1 cut(s) 469
BmsI GCATC 2 cut(s) 242, 733
BmuI ACTGGG 1 cut(s) 469
Bpu10I CCTNAGC 1 cut(s) 722
BpuEI CTTGAG 2 cut(s) 24, 578
BpuMI CCSGG 1 cut(s) 831
BsaI GGTCTC 1 cut(s) 316
Bse1I ACTGG 5 cut(s) 312, 459, 464, 580, 826
Bse3DI GCAATG 2 cut(s) 294, 862
BseBI CCWGG 1 cut(s) 218
BseGI GGATG 3 cut(s) 564, 748, 749
BseMI GCAATG 2 cut(s) 294, 862
BseMII CTCAG 4 cut(s) 81, 144, 470, 750
BseNI ACTGG 5 cut(s) 312, 459, 464, 580, 826
BseXI GCAGC 2 cut(s) 52, 217
BseYI CCCAGC 1 cut(s) 636
Bsh1236I CGCG 1 cut(s) 530
BsiHKAI GWGCWC 1 cut(s) 159
BsiSI CCGG 2 cut(s) 764, 831
BslFI GGGAC 1 cut(s) 131
BsmAI GTCTC 4 cut(s) 88, 189, 280, 316
BsmBI CGTCTC 1 cut(s) 88
BsmFI GGGAC 1 cut(s) 131
BsmI GAATGC 1 cut(s) 288
Bso31I GGTCTC 1 cut(s) 316
Bsp1286I GDGCHC 2 cut(s) 159, 380
Bsp143I GATC 3 cut(s) 433, 697, 777
BspACI CCGC 3 cut(s) 530, 740, 753
BspCNI CTCAG 4 cut(s) 82, 145, 471, 751
BspFNI CGCG 1 cut(s) 530
BspHI TCATGA 2 cut(s) 169, 675
BspMAI CTGCAG 1 cut(s) 352
BspPI GGATC 1 cut(s) 772
BspTNI GGTCTC 1 cut(s) 316
BsrDI GCAATG 2 cut(s) 294, 862
BsrI ACTGG 5 cut(s) 312, 459, 464, 580, 826
BssMI GATC 3 cut(s) 433, 697, 777
Bst2UI CCWGG 1 cut(s) 218
Bst4CI ACNGT 4 cut(s) 200, 371, 589, 811
Bst6I CTCTTC 1 cut(s) 543
BstC8I GCNNGC 1 cut(s) 400
BstDEI CTNAG 5 cut(s) 90, 153, 479, 722, 759
BstF5I GGATG 3 cut(s) 564, 748, 749
BstFNI CGCG 1 cut(s) 530
BstKTI GATC 3 cut(s) 436, 700, 780
BstMAI GTCTC 4 cut(s) 88, 189, 280, 316
BstMBI GATC 3 cut(s) 433, 697, 777
BstMWI GCNNNNNNNGC 6 cut(s) 71, 227, 239, 530, 752, 864
BstNI CCWGG 1 cut(s) 218
BstSCI CCNGG 2 cut(s) 216, 829
BstSFI CTRYAG 1 cut(s) 348
BstUI CGCG 1 cut(s) 530
BstV1I GCAGC 2 cut(s) 52, 217
BsuI GTATCC 1 cut(s) 142
BtsCI GGATG 3 cut(s) 564, 748, 749
BtsIMutI CAGTG 1 cut(s) 305
Cac8I GCNNGC 1 cut(s) 400
CciI TCATGA 2 cut(s) 169, 675
CseI GACGC 1 cut(s) 536
Csp6I GTAC 5 cut(s) 131, 554, 583, 804, 884
CviAII CATG 5 cut(s) 170, 576, 597, 676, 695
CviQI GTAC 5 cut(s) 131, 554, 583, 804, 884
DdeI CTNAG 5 cut(s) 90, 153, 479, 722, 759
DpnI GATC 3 cut(s) 435, 699, 779
DpnII GATC 3 cut(s) 433, 697, 777
DraI TTTAAA 1 cut(s) 204
Eam1104I CTCTTC 1 cut(s) 543
EarI CTCTTC 1 cut(s) 543
EciI GGCGGA 1 cut(s) 755
Eco24I GRGCYC 1 cut(s) 380
Eco31I GGTCTC 1 cut(s) 316
EcoRII CCWGG 1 cut(s) 216
EcoT38I GRGCYC 1 cut(s) 380
Esp3I CGTCTC 1 cut(s) 88
FaeI CATG 5 cut(s) 173, 579, 600, 679, 698
FalI AAGNNNNNCTT 4 cut(s) 327, 359, 540, 572
FaqI GGGAC 1 cut(s) 131
FatI CATG 5 cut(s) 169, 575, 596, 675, 694
FbaI TGATCA 1 cut(s) 697
Fnu4HI GCNGC 3 cut(s) 66, 231, 531
FokI GGATG 3 cut(s) 551, 736, 755
FriOI GRGCYC 1 cut(s) 380
Fsp4HI GCNGC 3 cut(s) 66, 231, 531
FspBI CTAG 2 cut(s) 392, 711
GluI GCNGC 3 cut(s) 66, 231, 531
GsaI CCCAGC 1 cut(s) 640
HapII CCGG 2 cut(s) 764, 831
HgaI GACGC 1 cut(s) 536
Hin1II CATG 5 cut(s) 173, 579, 600, 679, 698
HindIII AAGCTT 2 cut(s) 240, 484
HinfI GANTC 4 cut(s) 80, 166, 499, 506
HpaII CCGG 2 cut(s) 764, 831
HphI GGTGA 5 cut(s) 206, 350, 372, 670, 787
Hpy166II GTNNAC 6 cut(s) 341, 585, 716, 796, 827, 854
Hpy188I TCNGA 7 cut(s) 142, 238, 252, 433, 480, 511, 647
Hpy188III TCNNGA 8 cut(s) 41, 89, 163, 170, 266, 503, 676, 781
Hpy8I GTNNAC 6 cut(s) 341, 585, 716, 796, 827, 854
Hpy99I CGWCG 1 cut(s) 530
HpyAV CCTTC 4 cut(s) 40, 329, 611, 869
HpyCH4III ACNGT 4 cut(s) 200, 371, 589, 811
HpyCH4IV ACGT 2 cut(s) 845, 886
HpyCH4V TGCA 5 cut(s) 68, 233, 299, 350, 867
HpyF10VI GCNNNNNNNGC 6 cut(s) 71, 227, 239, 530, 752, 864
HpyF3I CTNAG 5 cut(s) 90, 153, 479, 722, 759
HpySE526I ACGT 2 cut(s) 845, 886
Hsp92II CATG 5 cut(s) 173, 579, 600, 679, 698
Ksp22I TGATCA 1 cut(s) 697
Kzo9I GATC 3 cut(s) 433, 697, 777
Lsp1109I GCAGC 2 cut(s) 52, 217
LweI GCATC 2 cut(s) 242, 733
MaeI CTAG 2 cut(s) 392, 711
MaeII ACGT 2 cut(s) 845, 886
MaeIII GTNAC 1 cut(s) 817
MalI GATC 3 cut(s) 435, 699, 779
MboI GATC 3 cut(s) 433, 697, 777
MboII GAAGA 3 cut(s) 26, 29, 560
MhlI GDGCHC 2 cut(s) 159, 380
MluCI AATT 4 cut(s) 21, 28, 650, 787
MlyI GAGTC 1 cut(s) 515
MmeI TCCRAC 2 cut(s) 489, 656
MnlI CCTC 7 cut(s) 108, 222, 269, 443, 544, 553, 639
MroXI GAANNNNTTC 1 cut(s) 498
MseI TTAA 1 cut(s) 203
MspI CCGG 2 cut(s) 764, 831
MspR9I CCNGG 2 cut(s) 218, 831
Mva1269I GAATGC 1 cut(s) 288
MvaI CCWGG 1 cut(s) 218
MvnI CGCG 1 cut(s) 530
MwoI GCNNNNNNNGC 6 cut(s) 71, 227, 239, 530, 752, 864
NciI CCSGG 1 cut(s) 831
NdeII GATC 3 cut(s) 433, 697, 777
NlaIII CATG 5 cut(s) 173, 579, 600, 679, 698
PagI TCATGA 2 cut(s) 169, 675
PctI GAATGC 1 cut(s) 288
PdmI GAANNNNTTC 1 cut(s) 498
PfeI GAWTC 3 cut(s) 80, 166, 499
PkrI GCNGC 3 cut(s) 67, 232, 532
PleI GAGTC 1 cut(s) 514
PpsI GAGTC 1 cut(s) 514
PsiI TTATAA 1 cut(s) 27
Psp6I CCWGG 1 cut(s) 216
PspFI CCCAGC 1 cut(s) 636
PspGI CCWGG 1 cut(s) 216
PstI CTGCAG 1 cut(s) 352
RsaI GTAC 5 cut(s) 132, 555, 584, 805, 885
RsaNI GTAC 5 cut(s) 131, 554, 583, 804, 884
SaqAI TTAA 1 cut(s) 203
SatI GCNGC 3 cut(s) 66, 231, 531
Sau3AI GATC 3 cut(s) 433, 697, 777
ScaI AGTACT 1 cut(s) 805
SchI GAGTC 1 cut(s) 515
ScrFI CCNGG 2 cut(s) 218, 831
SduI GDGCHC 2 cut(s) 159, 380
SfaNI GCATC 2 cut(s) 242, 733
SfcI CTRYAG 1 cut(s) 348
SmlI CTYRAG 2 cut(s) 39, 557
SmoI CTYRAG 2 cut(s) 39, 557
SpeI ACTAGT 1 cut(s) 710
Sse9I AATT 4 cut(s) 21, 28, 650, 787
SsiI CCGC 3 cut(s) 530, 740, 753
SspMI CTAG 2 cut(s) 392, 711
StyD4I CCNGG 2 cut(s) 216, 829
TaaI ACNGT 4 cut(s) 200, 371, 589, 811
TaiI ACGT 2 cut(s) 848, 889
TaqI TCGA 4 cut(s) 113, 436, 448, 520
TasI AATT 4 cut(s) 21, 28, 650, 787
TatI WGTACW 2 cut(s) 582, 803
TauI GCSGC 1 cut(s) 533
TfiI GAWTC 3 cut(s) 80, 166, 499
Tru1I TTAA 1 cut(s) 203
Tru9I TTAA 1 cut(s) 203
TscAI CASTG 1 cut(s) 312
TseI GCWGC 2 cut(s) 65, 230
TspDTI ATGAA 6 cut(s) 158, 311, 654, 664, 738, 880
TspGWI ACGGA 1 cut(s) 527
TspRI CASTG 1 cut(s) 312
XapI RAATTY 2 cut(s) 21, 650
XmnI GAANNNNTTC 1 cut(s) 498
XspI CTAG 2 cut(s) 392, 711
ZrmI AGTACT 1 cut(s) 805
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.