Rroxscaffold_4G00329810

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000595
Physical Location & Seq
Forward (+)
63152311 .. 63153381
1071 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00329810.1

Sequence Viewer

Length: 816 bp
ATGGGAGTAAAAGCTGCATCAGATGCCTTGTTTCAGAACTTCCTCTTCCCTGACTGTGACTCACGAGCAAGCATTCCTGCTGCACCAGCTCTGCTTTCTACTACCTATCATAAGCTTGATCAAGAGCAACGTTCTGCAGTTGGACATATCTTAAGGATTCAGGGCTCACCACCTTATGTAGTAACTGGTCCAGACTGTGAAGGCAAATCTTTTGCAAATTTAAGAGAACCTTCAAGAACTGGAGTGGTTGTTAGTGAAGCAGTATACCAATTATGTCGGAAGTCACCAGAGTATCGCATTCTTATCTGTGCGCCTACTAACAGCTGCTGCGATATGCTGATGAGAAGCTTGGTGAAGGTGATTCCAGAGTCTACTATGTTTCGTGCCAATGCAGCATTCCGAGACAGAGATGAGGTACCTGAGGACATCCTACGTTCATCCCTTTACAAAGAGTCTTGTTTTTCTTGTCCTGCAATAGAGAAACTCCGGGAATACAAGGTGATTTTCTCAACTTTCATGAGTAGCTTCCGACTACATGATAAAGGCATAGCTGCTGGACATTTTAGCCATATTTTTCTGGTGGATGCTTCATCTGCTATTGAGCCGGAAACATTGGTCGCCCTGACTAACTTTGCTGTCAAGGCCACTAGTGTTATAGTTACTGGTAATCATGGAAATAGTCCGCTCTGGGTTCGTGCTGACATTGCAAGGAAAAAGGGACTCAAGATTTCATACTTTGAACGACTCTGCAAGCTCAGGCCATATAGAAGCCCCAGTCCAATGTTCATCACACAACTAGACCTGAACCAAAAGTAA
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

271

Amino Acids

30.21

Weight (kDa)

8.94

Isoelectric Point (pI)

52.33

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)
Acc65I GGTACC 1 cut(s) 415
AccB1I GGYRCC 1 cut(s) 415
AccBSI CCGCTC 1 cut(s) 685
AccI GTMKAC 2 cut(s) 264, 371
AciI CCGC 1 cut(s) 683
AclI AACGTT 1 cut(s) 130
AcsI RAATTY 1 cut(s) 217
AfaI GTAC 1 cut(s) 417
AflII CTTAAG 1 cut(s) 151
AgsI TTSAA 2 cut(s) 234, 740
AhlI ACTAGT 1 cut(s) 647
AjuI GAANNNNNNNTTGG 2 cut(s) 380, 412
AluBI AGCT 8 cut(s) 14, 89, 115, 324, 348, 525, 551, 754
AluI AGCT 8 cut(s) 14, 89, 115, 324, 348, 525, 551, 754
Alw26I GTCTC 1 cut(s) 396
AlwNI CAGNNNCTG 1 cut(s) 327
AoxI GGCC 2 cut(s) 642, 758
ApeKI GCWGC 6 cut(s) 14, 80, 324, 327, 392, 551
ApoI RAATTY 1 cut(s) 217
Asp718I GGTACC 1 cut(s) 415
AspLEI GCGC 1 cut(s) 313
AspS9I GGNCC 1 cut(s) 188
AsuC2I CCSGG 1 cut(s) 488
AsuHPI GGTGA 5 cut(s) 159, 276, 364, 370, 511
AvaII GGWCC 1 cut(s) 188
AxyI CCTNAGG 1 cut(s) 420
BaeI ACNNNNGTAYC 2 cut(s) 275, 308
BanI GGYRCC 1 cut(s) 415
BanII GRGCYC 1 cut(s) 167
BauI CACGAG 1 cut(s) 63
BbvI GCAGC 5 cut(s) 67, 311, 314, 404, 538
BclI TGATCA 1 cut(s) 118
BcnI CCSGG 1 cut(s) 488
BcoDI GTCTC 1 cut(s) 396
BcuI ACTAGT 1 cut(s) 647
BfaI CTAG 2 cut(s) 648, 797
BfmI CTRYAG 1 cut(s) 135
BfrI CTTAAG 1 cut(s) 151
BisI GCNGC 6 cut(s) 15, 81, 325, 328, 393, 552
BlsI GCNGC 6 cut(s) 16, 82, 326, 329, 394, 553
Bme1390I CCNGG 1 cut(s) 488
Bme18I GGWCC 1 cut(s) 188
BmgT120I GGNCC 1 cut(s) 188
BmiI GGNNCC 1 cut(s) 417
BmrFI CCNGG 1 cut(s) 488
BmrI ACTGGG 1 cut(s) 768
BmsI GCATC 3 cut(s) 13, 26, 574
BmuI ACTGGG 1 cut(s) 768
BpmI CTGGAG 1 cut(s) 261
Bpu10I CCTNAGC 1 cut(s) 755
BpuEI CTTGAG 1 cut(s) 707
BpuMI CCSGG 1 cut(s) 488
BsaXI ACNNNNNCTCC 2 cut(s) 234, 264
Bse1I ACTGG 4 cut(s) 190, 244, 667, 774
Bse21I CCTNAGG 1 cut(s) 420
Bse3DI GCAATG 1 cut(s) 702
BseGI GGATG 3 cut(s) 426, 437, 589
BseMI GCAATG 1 cut(s) 702
BseMII CTCAG 2 cut(s) 411, 769
BseNI ACTGG 4 cut(s) 190, 244, 667, 774
BseXI GCAGC 5 cut(s) 67, 311, 314, 404, 538
BsgI GTGCAG 1 cut(s) 66
BshFI GGCC 2 cut(s) 644, 760
BshNI GGYRCC 1 cut(s) 415
BsiSI CCGG 2 cut(s) 487, 605
BslFI GGGAC 1 cut(s) 732
BsmAI GTCTC 1 cut(s) 396
BsmFI GGGAC 1 cut(s) 732
BsmI GAATGC 3 cut(s) 72, 297, 395
BsnI GGCC 2 cut(s) 644, 760
Bsp1286I GDGCHC 1 cut(s) 167
Bsp143I GATC 1 cut(s) 118
BspACI CCGC 1 cut(s) 683
BspANI GGCC 2 cut(s) 644, 760
BspCNI CTCAG 2 cut(s) 412, 768
BspHI TCATGA 1 cut(s) 516
BspLI GGNNCC 1 cut(s) 417
BspMAI CTGCAG 1 cut(s) 139
BspT107I GGYRCC 1 cut(s) 415
BspTI CTTAAG 1 cut(s) 151
BsrBI CCGCTC 1 cut(s) 685
BsrDI GCAATG 1 cut(s) 702
BsrI ACTGG 4 cut(s) 190, 244, 667, 774
BssMI GATC 1 cut(s) 118
BssNAI GTATAC 1 cut(s) 265
BssSI CACGAG 1 cut(s) 63
Bst1107I GTATAC 1 cut(s) 265
Bst2BI CACGAG 1 cut(s) 63
Bst4CI ACNGT 2 cut(s) 56, 197
Bst6I CTCTTC 1 cut(s) 50
BstAFI CTTAAG 1 cut(s) 151
BstAPI GCANNNNNTGC 1 cut(s) 23
BstC8I GCNNGC 2 cut(s) 70, 752
BstDEI CTNAG 2 cut(s) 420, 755
BstF5I GGATG 3 cut(s) 426, 437, 589
BstHHI GCGC 1 cut(s) 313
BstKTI GATC 1 cut(s) 121
BstMAI GTCTC 1 cut(s) 396
BstMBI GATC 1 cut(s) 118
BstMWI GCNNNNNNNGC 6 cut(s) 23, 86, 392, 593, 641, 704
BstSCI CCNGG 1 cut(s) 486
BstSFI CTRYAG 1 cut(s) 135
BstV1I GCAGC 5 cut(s) 67, 311, 314, 404, 538
BstZ17I GTATAC 1 cut(s) 265
Bsu36I CCTNAGG 1 cut(s) 420
BsuRI GGCC 2 cut(s) 644, 760
BtsCI GGATG 3 cut(s) 426, 437, 589
Cac8I GCNNGC 2 cut(s) 70, 752
CaiI CAGNNNCTG 1 cut(s) 327
CciI TCATGA 1 cut(s) 516
CfoI GCGC 1 cut(s) 313
Cfr13I GGNCC 1 cut(s) 188
Csp6I GTAC 1 cut(s) 416
CviAII CATG 3 cut(s) 517, 536, 671
CviQI GTAC 1 cut(s) 416
DdeI CTNAG 2 cut(s) 420, 755
DpnI GATC 1 cut(s) 120
DpnII GATC 1 cut(s) 118
Eam1104I CTCTTC 1 cut(s) 50
EarI CTCTTC 1 cut(s) 50
Eco24I GRGCYC 1 cut(s) 167
Eco47I GGWCC 1 cut(s) 188
Eco81I CCTNAGG 1 cut(s) 420
EcoT38I GRGCYC 1 cut(s) 167
FaeI CATG 3 cut(s) 520, 539, 674
FalI AAGNNNNNCTT 2 cut(s) 214, 246
FaqI GGGAC 1 cut(s) 732
FatI CATG 3 cut(s) 516, 535, 670
FbaI TGATCA 1 cut(s) 118
FblI GTMKAC 2 cut(s) 264, 371
Fnu4HI GCNGC 6 cut(s) 15, 81, 325, 328, 393, 552
FokI GGATG 3 cut(s) 413, 424, 596
FriOI GRGCYC 1 cut(s) 167
Fsp4HI GCNGC 6 cut(s) 15, 81, 325, 328, 393, 552
FspBI CTAG 2 cut(s) 648, 797
GlaI GCGC 1 cut(s) 312
GluI GCNGC 6 cut(s) 15, 81, 325, 328, 393, 552
GsuI CTGGAG 1 cut(s) 261
HaeIII GGCC 2 cut(s) 644, 760
HapII CCGG 2 cut(s) 487, 605
HhaI GCGC 1 cut(s) 313
Hin1II CATG 3 cut(s) 520, 539, 674
Hin6I GCGC 1 cut(s) 311
HinP1I GCGC 1 cut(s) 311
HindIII AAGCTT 2 cut(s) 113, 346
HinfI GANTC 7 cut(s) 59, 157, 361, 368, 452, 720, 744
HpaII CCGG 2 cut(s) 487, 605
HphI GGTGA 5 cut(s) 159, 276, 364, 370, 511
Hpy166II GTNNAC 2 cut(s) 265, 372
Hpy188I TCNGA 5 cut(s) 22, 36, 279, 401, 530
Hpy188III TCNNGA 7 cut(s) 63, 122, 191, 234, 365, 517, 724
Hpy8I GTNNAC 2 cut(s) 265, 372
HpyAV CCTTC 3 cut(s) 194, 240, 349
HpyCH4III ACNGT 2 cut(s) 56, 197
HpyCH4IV ACGT 2 cut(s) 130, 433
HpyCH4V TGCA 8 cut(s) 17, 83, 137, 215, 392, 473, 707, 750
HpyF10VI GCNNNNNNNGC 6 cut(s) 23, 86, 392, 593, 641, 704
HpyF3I CTNAG 2 cut(s) 420, 755
HpySE526I ACGT 2 cut(s) 130, 433
Hsp92II CATG 3 cut(s) 520, 539, 674
HspAI GCGC 1 cut(s) 311
KpnI GGTACC 1 cut(s) 419
Ksp22I TGATCA 1 cut(s) 118
Kzo9I GATC 1 cut(s) 118
Lsp1109I GCAGC 5 cut(s) 67, 311, 314, 404, 538
LweI GCATC 3 cut(s) 13, 26, 574
MaeI CTAG 2 cut(s) 648, 797
MaeII ACGT 2 cut(s) 130, 433
MaeIII GTNAC 4 cut(s) 56, 181, 282, 658
MalI GATC 1 cut(s) 120
MbiI CCGCTC 1 cut(s) 685
MboI GATC 1 cut(s) 118
MboII GAAGA 1 cut(s) 37
MhlI GDGCHC 1 cut(s) 167
MluCI AATT 2 cut(s) 217, 269
MlyI GAGTC 5 cut(s) 53, 377, 461, 714, 738
MmeI TCCRAC 3 cut(s) 121, 257, 553
MnlI CCTC 3 cut(s) 53, 406, 415
MseI TTAA 2 cut(s) 152, 221
MspA1I CMGCKG 1 cut(s) 324
MspCI CTTAAG 1 cut(s) 151
MspI CCGG 2 cut(s) 487, 605
MspR9I CCNGG 1 cut(s) 488
Mva1269I GAATGC 3 cut(s) 72, 297, 395
MwoI GCNNNNNNNGC 6 cut(s) 23, 86, 392, 593, 641, 704
NciI CCSGG 1 cut(s) 488
NdeII GATC 1 cut(s) 118
NlaIII CATG 3 cut(s) 520, 539, 674
NlaIV GGNNCC 1 cut(s) 417
NmuCI GTSAC 2 cut(s) 56, 282
PagI TCATGA 1 cut(s) 516
PctI GAATGC 3 cut(s) 72, 297, 395
PfeI GAWTC 2 cut(s) 157, 361
PfoI TCCNGGA 1 cut(s) 486
PkrI GCNGC 6 cut(s) 16, 82, 326, 329, 394, 553
PleI GAGTC 5 cut(s) 53, 376, 460, 714, 738
PpsI GAGTC 5 cut(s) 53, 376, 460, 714, 738
Psp1406I AACGTT 1 cut(s) 130
PspN4I GGNNCC 1 cut(s) 417
PspPI GGNCC 1 cut(s) 188
PstI CTGCAG 1 cut(s) 139
PstNI CAGNNNCTG 1 cut(s) 327
PvuII CAGCTG 1 cut(s) 324
RsaI GTAC 1 cut(s) 417
RsaNI GTAC 1 cut(s) 416
SaqAI TTAA 2 cut(s) 152, 221
SatI GCNGC 6 cut(s) 15, 81, 325, 328, 393, 552
Sau3AI GATC 1 cut(s) 118
Sau96I GGNCC 1 cut(s) 188
SchI GAGTC 5 cut(s) 53, 377, 461, 714, 738
ScrFI CCNGG 1 cut(s) 488
SduI GDGCHC 1 cut(s) 167
SfaNI GCATC 3 cut(s) 13, 26, 574
SfcI CTRYAG 1 cut(s) 135
SinI GGWCC 1 cut(s) 188
SmlI CTYRAG 2 cut(s) 151, 722
SmoI CTYRAG 2 cut(s) 151, 722
SpeI ACTAGT 1 cut(s) 647
Sse9I AATT 2 cut(s) 217, 269
SsiI CCGC 1 cut(s) 683
SspMI CTAG 2 cut(s) 648, 797
StyD4I CCNGG 1 cut(s) 486
TaaI ACNGT 2 cut(s) 56, 197
TaiI ACGT 2 cut(s) 133, 436
TasI AATT 2 cut(s) 217, 269
TfiI GAWTC 2 cut(s) 157, 361
Tru1I TTAA 2 cut(s) 152, 221
Tru9I TTAA 2 cut(s) 152, 221
TseFI GTSAC 2 cut(s) 56, 282
TseI GCWGC 6 cut(s) 14, 80, 324, 327, 392, 551
Tsp45I GTSAC 2 cut(s) 56, 282
TspDTI ATGAA 5 cut(s) 426, 505, 579, 720, 775
Vha464I CTTAAG 1 cut(s) 151
VpaK11BI GGWCC 1 cut(s) 188
XapI RAATTY 1 cut(s) 217
XmiI GTMKAC 2 cut(s) 264, 371
XspI CTAG 2 cut(s) 648, 797
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.