Rroxscaffold_4G00329910

RNA helicase SDE3

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000004
OG0000595
Physical Location & Seq
Forward (+)
63265885 .. 63267689
1805 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_4G00329910.1

Sequence Viewer

Length: 1296 bp
ATGCATAAATCTTATTACCCTGTTGCATATCTCAAACCATTAGATATATACTTATTGGAAGCTGCAGACCATGCCTTACTGTTCATAGCTTACTTCCCTTACTTTGTGCCTTACTTTGTACATAGGAGTGATATAGAGGGTGTGACATTAGCGTTGGATGAAAGTTCAATTTATAAAAACCGGAAAAAGGAAGCACTTTATAAAAATCGGAAAAAGGAAGATAAGGAAGACAAAACCTTTGGAGCATTTGAGCTTGATTGTGTTCCTGAGAAACGGCCATTCCTCTTATCAAGGGACTTGGTCCTTGCACGACCAGTGGGTAATAGTACTACTGAGCCCTTTAAGGGCCCCATCCATAAAGTTGTTGGGAGCAATCGCGTTTTGGTTGAATTTGAGGATGGCTTTTATTCTTATCATCATTCCAACAAAAAATATGATATCAGCTTCTCATACAATAGAGTTTGTTTGAAAAGAGCCCACCGTGCAGTAAAAGCTGCATCAGATGCCTTGTTTCAGAACTTCCTCTTCCCTGACTGTGACTCACGAGCAAGCATTCCTGCTGCACCAGCTCTGCTTTCTACTACCTATCATAAGCTTGATCAAGAGCAACGTTCTGCAGTCGGACATATCTTAAGGATTCAGGGCTCACCACCTTATGTAGTAACTGGTCCAGACTGTGAAGGCAAATCTTTTGCAAATTTAAGAGAACCTTCAAGAACTGGAGTGGTTGTTAGTGAAGCAGTATACCAATTATGTCGGAAGTCACCAGAGTATCGCATTCTTATCTGTGCGCCTACTAACAGCTGCTGCGATATGCTGATGAGAAGCTTGGTGAAGGTGATTCCAGAGTCTACTATGTTTCGTGCCAATGCAGCATTCCGAGACAGAGATGAGGTACCTGAGGACATCCTACGTTCATCCCTTTACAAAGAGTCTTGTTTTTCTTGTCCTGCAATAGAGAAACTCCGGGAATACAAGGTGATTTTCTCAACTTTCATGAGTAGCTTCCGACTACATGATAAAGGCATAGCTGCTGGACATTTTAGCCATATTTTTCTGGTGGATGCTTCATCTGCTATTGAGCCGGAAACATTGGTCGCCCTGACTAACTTTGCTGTCAAGGCCACTAGTGTTATAGTTACTGGTAATCATGGAAATAGTCCGCTCTGGGTTCGTGCTGACATTGCAAGGAAAAAGGGACTCAAGATTTCATACTTTGAACGACTCTGCAAGCTCAGGCCATATAGAAGCCCCAGTCCAATGTTCATCACACAACTAGACCTGAACCAAAAGTAA
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

431

Amino Acids

48.96

Weight (kDa)

9.05

Isoelectric Point (pI)

51.07

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
MOV-10_beta-barrel PF21634 73 - 149 3.9e-09 Helicase MOV-10, beta-barrel domain
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 2 cut(s) 174, 201
Acc65I GGTACC 1 cut(s) 895
AccB1I GGYRCC 1 cut(s) 895
AccBSI CCGCTC 1 cut(s) 1165
AccI GTMKAC 2 cut(s) 744, 851
AccII CGCG 1 cut(s) 378
AciI CCGC 1 cut(s) 1163
AclI AACGTT 1 cut(s) 610
AcoI YGGCCR 1 cut(s) 275
AcsI RAATTY 2 cut(s) 389, 697
AfaI GTAC 3 cut(s) 120, 328, 897
AfiI CCNNNNNNNGG 2 cut(s) 187, 344
AflII CTTAAG 1 cut(s) 631
AgsI TTSAA 5 cut(s) 168, 389, 469, 714, 1220
AhlI ACTAGT 1 cut(s) 1127
AjuI GAANNNNNNNTTGG 2 cut(s) 860, 892
Alw26I GTCTC 1 cut(s) 876
AlwNI CAGNNNCTG 1 cut(s) 807
AoxI GGCC 4 cut(s) 275, 346, 1122, 1238
ApaI GGGCCC 1 cut(s) 350
ApeKI GCWGC 7 cut(s) 62, 494, 560, 804, 807, 872, 1031
ApoI RAATTY 2 cut(s) 389, 697
ArsI GACNNNNNNTTYG 2 cut(s) 221, 253
Asp718I GGTACC 1 cut(s) 895
AspLEI GCGC 1 cut(s) 793
AspS9I GGNCC 4 cut(s) 301, 346, 347, 668
AsuC2I CCSGG 1 cut(s) 968
AsuHPI GGTGA 5 cut(s) 639, 756, 844, 850, 991
AvaII GGWCC 2 cut(s) 301, 668
AxyI CCTNAGG 1 cut(s) 900
BaeGI GKGCMC 1 cut(s) 350
BaeI ACNNNNGTAYC 2 cut(s) 755, 788
BanI GGYRCC 1 cut(s) 895
BanII GRGCYC 4 cut(s) 339, 350, 478, 647
BauI CACGAG 1 cut(s) 543
BbsI GAAGAC 1 cut(s) 234
BbvI GCAGC 7 cut(s) 49, 481, 547, 791, 794, 884, 1018
BccI CCATC 2 cut(s) 359, 392
BceAI ACGGC 1 cut(s) 290
BclI TGATCA 1 cut(s) 598
BcnI CCSGG 1 cut(s) 968
BcoDI GTCTC 1 cut(s) 876
BcuI ACTAGT 1 cut(s) 1127
BfaI CTAG 2 cut(s) 1128, 1277
BfmI CTRYAG 2 cut(s) 63, 615
BfrI CTTAAG 1 cut(s) 631
BisI GCNGC 7 cut(s) 63, 495, 561, 805, 808, 873, 1032
BlsI GCNGC 7 cut(s) 64, 496, 562, 806, 809, 874, 1033
BmcAI AGTACT 1 cut(s) 328
Bme1390I CCNGG 1 cut(s) 968
Bme18I GGWCC 2 cut(s) 301, 668
BmgT120I GGNCC 4 cut(s) 301, 346, 347, 668
BmiI GGNNCC 3 cut(s) 348, 349, 897
BmrFI CCNGG 1 cut(s) 968
BmrI ACTGGG 1 cut(s) 1248
BmsI GCATC 3 cut(s) 493, 506, 1054
BmuI ACTGGG 1 cut(s) 1248
BpiI GAAGAC 1 cut(s) 234
BpmI CTGGAG 1 cut(s) 741
Bpu10I CCTNAGC 1 cut(s) 1235
BpuEI CTTGAG 1 cut(s) 1187
BpuMI CCSGG 1 cut(s) 968
BsaWI WCCGGW 1 cut(s) 180
BsaXI ACNNNNNCTCC 2 cut(s) 714, 744
Bsc4I CCNNNNNNNGG 2 cut(s) 187, 344
Bse1I ACTGG 5 cut(s) 314, 670, 724, 1147, 1254
Bse21I CCTNAGG 1 cut(s) 900
Bse3DI GCAATG 1 cut(s) 1182
BseGI GGATG 6 cut(s) 163, 351, 403, 906, 917, 1069
BseLI CCNNNNNNNGG 2 cut(s) 187, 344
BseMI GCAATG 1 cut(s) 1182
BseMII CTCAG 4 cut(s) 258, 324, 891, 1249
BseNI ACTGG 5 cut(s) 314, 670, 724, 1147, 1254
BseSI GKGCMC 1 cut(s) 350
BseXI GCAGC 7 cut(s) 49, 481, 547, 791, 794, 884, 1018
BsgI GTGCAG 2 cut(s) 504, 546
Bsh1236I CGCG 1 cut(s) 378
BshFI GGCC 4 cut(s) 277, 348, 1124, 1240
BshNI GGYRCC 1 cut(s) 895
BsiSI CCGG 3 cut(s) 181, 967, 1085
BslFI GGGAC 2 cut(s) 308, 1212
BslI CCNNNNNNNGG 2 cut(s) 187, 344
BsmAI GTCTC 1 cut(s) 876
BsmFI GGGAC 2 cut(s) 308, 1212
BsmI GAATGC 3 cut(s) 552, 777, 875
BsnI GGCC 4 cut(s) 277, 348, 1124, 1240
Bsp120I GGGCCC 1 cut(s) 346
Bsp1286I GDGCHC 4 cut(s) 339, 350, 478, 647
Bsp1407I TGTACA 1 cut(s) 118
Bsp143I GATC 1 cut(s) 598
BspACI CCGC 1 cut(s) 1163
BspANI GGCC 4 cut(s) 277, 348, 1124, 1240
BspCNI CTCAG 4 cut(s) 259, 325, 892, 1248
BspFNI CGCG 1 cut(s) 378
BspHI TCATGA 1 cut(s) 996
BspLI GGNNCC 3 cut(s) 348, 349, 897
BspMAI CTGCAG 2 cut(s) 67, 619
BspT107I GGYRCC 1 cut(s) 895
BspTI CTTAAG 1 cut(s) 631
BsrBI CCGCTC 1 cut(s) 1165
BsrDI GCAATG 1 cut(s) 1182
BsrGI TGTACA 1 cut(s) 118
BsrI ACTGG 5 cut(s) 314, 670, 724, 1147, 1254
BssMI GATC 1 cut(s) 598
BssNAI GTATAC 1 cut(s) 745
BssSI CACGAG 1 cut(s) 543
Bst1107I GTATAC 1 cut(s) 745
Bst2BI CACGAG 1 cut(s) 543
Bst4CI ACNGT 4 cut(s) 81, 482, 536, 677
Bst6I CTCTTC 1 cut(s) 530
BstAFI CTTAAG 1 cut(s) 631
BstAPI GCANNNNNTGC 2 cut(s) 71, 503
BstAUI TGTACA 1 cut(s) 118
BstC8I GCNNGC 2 cut(s) 550, 1232
BstDEI CTNAG 4 cut(s) 267, 333, 900, 1235
BstF5I GGATG 6 cut(s) 163, 351, 403, 906, 917, 1069
BstFNI CGCG 1 cut(s) 378
BstHHI GCGC 1 cut(s) 793
BstKTI GATC 1 cut(s) 601
BstMAI GTCTC 1 cut(s) 876
BstMBI GATC 1 cut(s) 598
BstMWI GCNNNNNNNGC 9 cut(s) 71, 482, 491, 503, 566, 872, 1073, 1121, 1184
BstSCI CCNGG 1 cut(s) 966
BstSFI CTRYAG 2 cut(s) 63, 615
BstSLI GKGCMC 1 cut(s) 350
BstUI CGCG 1 cut(s) 378
BstV1I GCAGC 7 cut(s) 49, 481, 547, 791, 794, 884, 1018
BstV2I GAAGAC 1 cut(s) 234
BstZ17I GTATAC 1 cut(s) 745
Bsu36I CCTNAGG 1 cut(s) 900
BsuRI GGCC 4 cut(s) 277, 348, 1124, 1240
BtsCI GGATG 6 cut(s) 163, 351, 403, 906, 917, 1069
BtsIMutI CAGTG 1 cut(s) 321
Cac8I GCNNGC 2 cut(s) 550, 1232
CaiI CAGNNNCTG 1 cut(s) 807
CciI TCATGA 1 cut(s) 996
CfoI GCGC 1 cut(s) 793
Cfr13I GGNCC 4 cut(s) 301, 346, 347, 668
Csp6I GTAC 3 cut(s) 119, 327, 896
CviAII CATG 4 cut(s) 71, 997, 1016, 1151
CviQI GTAC 3 cut(s) 119, 327, 896
DdeI CTNAG 4 cut(s) 267, 333, 900, 1235
DpnI GATC 1 cut(s) 600
DpnII GATC 1 cut(s) 598
EaeI YGGCCR 1 cut(s) 275
Eam1104I CTCTTC 1 cut(s) 530
EarI CTCTTC 1 cut(s) 530
Eco24I GRGCYC 4 cut(s) 339, 350, 478, 647
Eco32I GATATC 1 cut(s) 439
Eco47I GGWCC 2 cut(s) 301, 668
Eco81I CCTNAGG 1 cut(s) 900
EcoO109I RGGNCCY 2 cut(s) 346, 347
EcoRV GATATC 1 cut(s) 439
EcoT22I ATGCAT 1 cut(s) 6
EcoT38I GRGCYC 4 cut(s) 339, 350, 478, 647
FaeI CATG 4 cut(s) 74, 1000, 1019, 1154
FalI AAGNNNNNCTT 2 cut(s) 694, 726
FaqI GGGAC 2 cut(s) 308, 1212
FatI CATG 4 cut(s) 70, 996, 1015, 1150
FbaI TGATCA 1 cut(s) 598
FblI GTMKAC 2 cut(s) 744, 851
Fnu4HI GCNGC 7 cut(s) 63, 495, 561, 805, 808, 873, 1032
FokI GGATG 6 cut(s) 170, 338, 410, 893, 904, 1076
FriOI GRGCYC 4 cut(s) 339, 350, 478, 647
Fsp4HI GCNGC 7 cut(s) 63, 495, 561, 805, 808, 873, 1032
FspBI CTAG 2 cut(s) 1128, 1277
GlaI GCGC 1 cut(s) 792
GluI GCNGC 7 cut(s) 63, 495, 561, 805, 808, 873, 1032
GsuI CTGGAG 1 cut(s) 741
HaeIII GGCC 4 cut(s) 277, 348, 1124, 1240
HapII CCGG 3 cut(s) 181, 967, 1085
HhaI GCGC 1 cut(s) 793
Hin1II CATG 4 cut(s) 74, 1000, 1019, 1154
Hin6I GCGC 1 cut(s) 791
HinP1I GCGC 1 cut(s) 791
HindIII AAGCTT 2 cut(s) 593, 826
HinfI GANTC 7 cut(s) 539, 637, 841, 848, 932, 1200, 1224
HpaII CCGG 3 cut(s) 181, 967, 1085
HphI GGTGA 5 cut(s) 639, 756, 844, 850, 991
Hpy166II GTNNAC 2 cut(s) 745, 852
Hpy188I TCNGA 7 cut(s) 210, 502, 516, 623, 759, 881, 1010
Hpy188III TCNNGA 8 cut(s) 266, 543, 602, 671, 714, 845, 997, 1204
Hpy8I GTNNAC 2 cut(s) 745, 852
HpyAV CCTTC 3 cut(s) 674, 720, 829
HpyCH4III ACNGT 4 cut(s) 81, 482, 536, 677
HpyCH4IV ACGT 2 cut(s) 610, 913
HpyF10VI GCNNNNNNNGC 9 cut(s) 71, 482, 491, 503, 566, 872, 1073, 1121, 1184
HpyF3I CTNAG 4 cut(s) 267, 333, 900, 1235
HpySE526I ACGT 2 cut(s) 610, 913
Hsp92II CATG 4 cut(s) 74, 1000, 1019, 1154
HspAI GCGC 1 cut(s) 791
KpnI GGTACC 1 cut(s) 899
Ksp22I TGATCA 1 cut(s) 598
Kzo9I GATC 1 cut(s) 598
LmnI GCTCC 2 cut(s) 242, 369
Lsp1109I GCAGC 7 cut(s) 49, 481, 547, 791, 794, 884, 1018
LweI GCATC 3 cut(s) 493, 506, 1054
MaeI CTAG 2 cut(s) 1128, 1277
MaeII ACGT 2 cut(s) 610, 913
MaeIII GTNAC 5 cut(s) 142, 536, 661, 762, 1138
MalI GATC 1 cut(s) 600
MbiI CCGCTC 1 cut(s) 1165
MboI GATC 1 cut(s) 598
MboII GAAGA 3 cut(s) 230, 239, 517
MhlI GDGCHC 4 cut(s) 339, 350, 478, 647
MluCI AATT 4 cut(s) 168, 389, 697, 749
MlyI GAGTC 5 cut(s) 533, 857, 941, 1194, 1218
MmeI TCCRAC 5 cut(s) 135, 447, 601, 737, 1033
MnlI CCTC 6 cut(s) 130, 293, 388, 533, 886, 895
Mph1103I ATGCAT 1 cut(s) 6
MseI TTAA 3 cut(s) 342, 632, 701
MslI CAYNNNNRTG 1 cut(s) 126
MspA1I CMGCKG 1 cut(s) 804
MspCI CTTAAG 1 cut(s) 631
MspI CCGG 3 cut(s) 181, 967, 1085
MspR9I CCNGG 1 cut(s) 968
Mva1269I GAATGC 3 cut(s) 552, 777, 875
MvnI CGCG 1 cut(s) 378
MwoI GCNNNNNNNGC 9 cut(s) 71, 482, 491, 503, 566, 872, 1073, 1121, 1184
NciI CCSGG 1 cut(s) 968
NdeII GATC 1 cut(s) 598
NlaIII CATG 4 cut(s) 74, 1000, 1019, 1154
NlaIV GGNNCC 3 cut(s) 348, 349, 897
NmuCI GTSAC 3 cut(s) 142, 536, 762
NsiI ATGCAT 1 cut(s) 6
PagI TCATGA 1 cut(s) 996
PctI GAATGC 3 cut(s) 552, 777, 875
PfeI GAWTC 2 cut(s) 637, 841
PflFI GACNNNGTC 1 cut(s) 299
PfoI TCCNGGA 1 cut(s) 966
PkrI GCNGC 7 cut(s) 64, 496, 562, 806, 809, 874, 1033
PleI GAGTC 5 cut(s) 533, 856, 940, 1194, 1218
PpsI GAGTC 5 cut(s) 533, 856, 940, 1194, 1218
PsiI TTATAA 2 cut(s) 174, 201
Psp1406I AACGTT 1 cut(s) 610
PspN4I GGNNCC 3 cut(s) 348, 349, 897
PspOMI GGGCCC 1 cut(s) 346
PspPI GGNCC 4 cut(s) 301, 346, 347, 668
PstI CTGCAG 2 cut(s) 67, 619
PstNI CAGNNNCTG 1 cut(s) 807
PsyI GACNNNGTC 1 cut(s) 299
PvuII CAGCTG 1 cut(s) 804
RsaI GTAC 3 cut(s) 120, 328, 897
RsaNI GTAC 3 cut(s) 119, 327, 896
RseI CAYNNNNRTG 1 cut(s) 126
SaqAI TTAA 3 cut(s) 342, 632, 701
SatI GCNGC 7 cut(s) 63, 495, 561, 805, 808, 873, 1032
Sau3AI GATC 1 cut(s) 598
Sau96I GGNCC 4 cut(s) 301, 346, 347, 668
ScaI AGTACT 1 cut(s) 328
SchI GAGTC 5 cut(s) 533, 857, 941, 1194, 1218
ScrFI CCNGG 1 cut(s) 968
SduI GDGCHC 4 cut(s) 339, 350, 478, 647
SfaNI GCATC 3 cut(s) 493, 506, 1054
SfcI CTRYAG 2 cut(s) 63, 615
SinI GGWCC 2 cut(s) 301, 668
SmiMI CAYNNNNRTG 1 cut(s) 126
SmlI CTYRAG 2 cut(s) 631, 1202
SmoI CTYRAG 2 cut(s) 631, 1202
SpeI ACTAGT 1 cut(s) 1127
Sse9I AATT 4 cut(s) 168, 389, 697, 749
SsiI CCGC 1 cut(s) 1163
SspMI CTAG 2 cut(s) 1128, 1277
StyD4I CCNGG 1 cut(s) 966
TaaI ACNGT 4 cut(s) 81, 482, 536, 677
TaiI ACGT 2 cut(s) 613, 916
TasI AATT 4 cut(s) 168, 389, 697, 749
TatI WGTACW 2 cut(s) 118, 326
TfiI GAWTC 2 cut(s) 637, 841
Tru1I TTAA 3 cut(s) 342, 632, 701
Tru9I TTAA 3 cut(s) 342, 632, 701
TscAI CASTG 1 cut(s) 321
TseFI GTSAC 3 cut(s) 142, 536, 762
TseI GCWGC 7 cut(s) 62, 494, 560, 804, 807, 872, 1031
Tsp45I GTSAC 3 cut(s) 142, 536, 762
TspDTI ATGAA 7 cut(s) 73, 174, 906, 985, 1059, 1200, 1255
TspRI CASTG 1 cut(s) 321
Tth111I GACNNNGTC 1 cut(s) 299
Vha464I CTTAAG 1 cut(s) 631
VpaK11BI GGWCC 2 cut(s) 301, 668
XapI RAATTY 2 cut(s) 389, 697
XcmI CCANNNNNNNNNTGG 1 cut(s) 362
XmiI GTMKAC 2 cut(s) 744, 851
XspI CTAG 2 cut(s) 1128, 1277
ZrmI AGTACT 1 cut(s) 328
Zsp2I ATGCAT 1 cut(s) 6
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.