Rorug05G0200300

Tornado 1

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_rugosa
GWHBQTZ00000005
OG0015957
Physical Location & Seq
Forward (+)
19827416 .. 19828831
1416 bp
Loading structure...
UTR
Exon/CDS
Intron
Rorug05G0200300.1

Sequence Viewer

Length: 1164 bp
ATGATTTCACGTTCTACAAAATTACTCACCCATCCAATCCTTCAAAGCCCATCTTTCTCCACACTCCCATCTTCCTTCTCCCAAATCCCAAAAAAGCTCCACCACAAAGACTGGCTATCCCCAAACGAAGTTCTCCAAGTCTTTACATCCCTCCAAGACCCCAGCTCAGTCCTCACAGCCCTCGACCACTACTCCAAGCGCAAGGACTACAAGCCCAATGAAGCCCTCTACACCTTGATCATCGACAAGCTCGCCCGAGCCCACCTCTTCGACGCCGTGGACAATGTCATGAACAGAATCAAATCCGAAAGGAAATGCCGCTTATCCGATGACTTCTTCCGCAGTGTTATCAAGAACTACGGCAATGTGGGTGGTCACATTAAGAAGGCGATACAGACCCTTTACGATATGCCCAGTTTCGGGTGCTGGCCGAGTGTGAAGACCTTCAATTTAGTTCTGCATTTGCTGGTCTCGACCAAGATGTTTGATGTTGTTCATCAGGTTTATTTGATGTCGCCGCAATTGGGTGTCGAGATTGATGCTTGTTGTTTGAATATAATCATCAAAGGGCTGTGCGAAAGTGGGAAGCTGGATAGTGCACTCCAGGTGCTCGACGAATTTCCCCAGCAGAAATGTGAGCCGAATGCGCTGACGTTTTCGACGCTGATGCATGGGCTCTGTGTCAATGGGAAAGTGGATGAGGCTTTTGGGTTGCTGAAGAGGATGGAAAATGAGGGCATTGAGCCGGATTCGGTCACGTTTAATATATTGATAGCAGGGCTGAGGAAACAGAAGAGATATGATGAGGGCATTGAGCTTTTGGAGCAAATGAAGCTCAAGGGGTGTGCTCCAAATCCAGCTTCCTATCAGGAGGTTTTGTATTGTTTGCTTGATGCACAGAGGTTCACTGAGGCGAAACAGTTCATGATTCGGATGGTTTCAGAGCGTGTTGGTCCGAGTTTTGTGTCGTACAAGCAACTGATTCAGGGGTTGTGTAAAGAAAATAGGGTGGAGGATCTGGATTGGGTTTTGAGGCAGATGATGCGACAAGGTTTTGTGCCAAAGATGGGTATGTGGAGGCAGATTATCAGAAGTGTGTTTTCAAAGAAGAGCAACCATTATTGTGTTTCTTGTGAAGAGACTATAGATGATTTGATCACTTGA

Protein Analysis

387

Amino Acids

44.25

Weight (kDa)

8.49

Isoelectric Point (pI)

56.37

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
TPR_24 PF23276 80 - 205 9.7e-06 Fungal tetratrico peptide repeats
PPR_3 PF13812 175 - 224 1e-05 Pentatricopeptide repeat domain
PPR_1 PF12854 176 - 206 8.2e-08 PPR repeat
PPR_2 PF13041 180 - 227 7.4e-13 PPR repeat family
TPR_24 PF23276 200 - 297 2e-06 Fungal tetratrico peptide repeats
PPR_1 PF12854 212 - 243 1.9e-11 PPR repeat
PPR PF01535 218 - 247 7.6e-08 PPR repeat
PPR_3 PF13812 218 - 258 5.3e-06 Pentatricopeptide repeat domain
PPR_2 PF13041 221 - 262 2.6e-13 PPR repeat family
PPR_3 PF13812 238 - 291 1.7e-07 Pentatricopeptide repeat domain
PPR_1 PF12854 246 - 278 9.4e-08 PPR repeat
PPR_2 PF13041 249 - 290 1.1e-10 PPR repeat family
PPR PF01535 252 - 282 4.9e-06 PPR repeat
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Orthologous Genes (Group: OG0015957)

Species Orthologous Gene IDs
arabidopsis_thaliana AT5G55540 AT5G55540
fragaria_vesca FvH4_3g23950
malus_domestica MD03G1189500.v1.1
prunus_persica Prupe.4G231800_v2.0.a1
pyrus_communis pycom03g14240
rosa_chinensis RchiOBHm_Chr5g0042451
rosa_laevigata RLG00000034127
rosa_multiflora Rmu_sc0002779.1_g000005 Rmu_sc0016438.1_g000001
rosa_roxburghii Rroxscaffold_1G00038240
rosa_rugosa Rorug05G0200300
rosa_samantha Rh5AG286400 Rh5CG323200
rosa_wichuraiana Rw5G026610

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AciI CCGC 3 cut(s) 319, 340, 518
AclWI GGATC 1 cut(s) 1023
AcoI YGGCCR 1 cut(s) 428
AcsI RAATTY 1 cut(s) 617
AcuI CTGAAG 1 cut(s) 737
AcyI GRCGYC 1 cut(s) 273
AfaI GTAC 1 cut(s) 971
AfiI CCNNNNNNNGG 4 cut(s) 419, 420, 524, 1067
AgsI TTSAA 4 cut(s) 44, 448, 553, 1104
AjnI CCWGG 1 cut(s) 603
AjuI GAANNNNNNNTTGG 2 cut(s) 844, 876
AluBI AGCT 7 cut(s) 97, 165, 250, 589, 817, 835, 860
AluI AGCT 7 cut(s) 97, 165, 250, 589, 817, 835, 860
Alw21I GWGCWC 3 cut(s) 601, 612, 850
Alw26I GTCTC 2 cut(s) 475, 1133
Alw44I GTGCAC 1 cut(s) 597
AlwI GGATC 1 cut(s) 1023
Ama87I CYCGRG 1 cut(s) 255
AoxI GGCC 1 cut(s) 428
ApaLI GTGCAC 1 cut(s) 597
ApoI RAATTY 1 cut(s) 617
Asp700I GAANNNNTTC 2 cut(s) 443, 920
AspLEI GCGC 2 cut(s) 201, 649
AspS9I GGNCC 1 cut(s) 953
AsuHPI GGTGA 1 cut(s) 19
AvaI CYCGRG 1 cut(s) 255
AvaII GGWCC 1 cut(s) 953
BaeGI GKGCMC 1 cut(s) 601
BanII GRGCYC 2 cut(s) 262, 678
BbsI GAAGAC 1 cut(s) 446
Bbv12I GWGCWC 3 cut(s) 601, 612, 850
BbvCI CCTCAGC 1 cut(s) 782
BccI CCATC 6 cut(s) 39, 58, 76, 718, 928, 1060
BceAI ACGGC 2 cut(s) 260, 376
BcgI CGANNNNNNTGC 4 cut(s) 521, 555, 649, 683
BciT130I CCWGG 1 cut(s) 605
BclI TGATCA 2 cut(s) 237, 1155
BcoDI GTCTC 2 cut(s) 475, 1133
BfmI CTRYAG 1 cut(s) 1143
BisI GCNGC 2 cut(s) 319, 518
BlsI GCNGC 2 cut(s) 320, 519
Bme1390I CCNGG 1 cut(s) 605
Bme18I GGWCC 1 cut(s) 953
BmeT110I CYCGRG 1 cut(s) 255
BmgT120I GGNCC 1 cut(s) 953
BmrFI CCNGG 1 cut(s) 605
BmrI ACTGGG 1 cut(s) 408
BmsI GCATC 4 cut(s) 529, 657, 883, 1032
BmuI ACTGGG 1 cut(s) 408
BpiI GAAGAC 1 cut(s) 446
BplI GAGNNNNNCTC 2 cut(s) 249, 281
BpmI CTGGAG 1 cut(s) 587
Bpu10I CCTNAGC 1 cut(s) 782
BpuEI CTTGAG 1 cut(s) 821
BsaHI GRCGYC 1 cut(s) 273
BsaI GGTCTC 1 cut(s) 475
BsaJI CCNNGG 1 cut(s) 276
BsaXI ACNNNNNCTCC 4 cut(s) 176, 206, 863, 893
Bsc4I CCNNNNNNNGG 4 cut(s) 419, 420, 524, 1067
Bse1I ACTGG 2 cut(s) 116, 414
Bse3DI GCAATG 1 cut(s) 370
BseBI CCWGG 1 cut(s) 605
BseDI CCNNGG 1 cut(s) 276
BseGI GGATG 5 cut(s) 31, 146, 703, 729, 939
BseLI CCNNNNNNNGG 4 cut(s) 419, 420, 524, 1067
BseMI GCAATG 1 cut(s) 370
BseMII CTCAG 3 cut(s) 180, 773, 900
BseNI ACTGG 2 cut(s) 116, 414
BseSI GKGCMC 1 cut(s) 601
BseYI CCCAGC 2 cut(s) 161, 624
BshFI GGCC 1 cut(s) 430
BsiHKAI GWGCWC 3 cut(s) 601, 612, 850
BsiHKCI CYCGRG 1 cut(s) 255
BsiSI CCGG 1 cut(s) 746
BslI CCNNNNNNNGG 4 cut(s) 419, 420, 524, 1067
BsmAI GTCTC 2 cut(s) 475, 1133
BsmI GAATGC 1 cut(s) 649
BsnI GGCC 1 cut(s) 430
Bso31I GGTCTC 1 cut(s) 475
BsoBI CYCGRG 1 cut(s) 255
Bsp1286I GDGCHC 5 cut(s) 262, 601, 612, 678, 850
Bsp143I GATC 3 cut(s) 237, 1015, 1155
BspACI CCGC 3 cut(s) 319, 340, 518
BspANI GGCC 1 cut(s) 430
BspCNI CTCAG 3 cut(s) 179, 774, 901
BspHI TCATGA 2 cut(s) 288, 924
BspPI GGATC 1 cut(s) 1023
BspQI GCTCTTC 1 cut(s) 1103
BspTNI GGTCTC 1 cut(s) 475
BsrDI GCAATG 1 cut(s) 370
BsrI ACTGG 2 cut(s) 116, 414
BssECI CCNNGG 1 cut(s) 276
BssMI GATC 3 cut(s) 237, 1015, 1155
BssNI GRCGYC 1 cut(s) 273
Bst2UI CCWGG 1 cut(s) 605
Bst4CI ACNGT 1 cut(s) 921
Bst6I CTCTTC 5 cut(s) 272, 713, 788, 1103, 1131
BstACI GRCGYC 1 cut(s) 273
BstAPI GCANNNNNTGC 1 cut(s) 1042
BstC8I GCNNGC 2 cut(s) 252, 428
BstDEI CTNAG 3 cut(s) 166, 782, 909
BstDSI CCRYGG 1 cut(s) 276
BstF5I GGATG 5 cut(s) 31, 146, 703, 729, 939
BstHHI GCGC 2 cut(s) 201, 649
BstKTI GATC 3 cut(s) 240, 1018, 1158
BstMAI GTCTC 2 cut(s) 475, 1133
BstMBI GATC 3 cut(s) 237, 1015, 1155
BstMWI GCNNNNNNNGC 4 cut(s) 646, 823, 832, 1042
BstNI CCWGG 1 cut(s) 605
BstSCI CCNGG 1 cut(s) 603
BstSFI CTRYAG 1 cut(s) 1143
BstSLI GKGCMC 1 cut(s) 601
BstV2I GAAGAC 1 cut(s) 446
BstX2I RGATCY 1 cut(s) 1015
BstYI RGATCY 1 cut(s) 1015
BsuRI GGCC 1 cut(s) 430
BtgI CCRYGG 1 cut(s) 276
BtsCI GGATG 5 cut(s) 31, 146, 703, 729, 939
BtsI GCAGTG 1 cut(s) 349
BtsIMutI CAGTG 2 cut(s) 349, 906
Cac8I GCNNGC 2 cut(s) 252, 428
CciI TCATGA 2 cut(s) 288, 924
CfoI GCGC 2 cut(s) 201, 649
Cfr13I GGNCC 1 cut(s) 953
CseI GACGC 2 cut(s) 281, 670
Csp6I GTAC 1 cut(s) 970
CspCI CAANNNNNGTGG 2 cut(s) 352, 387
CviAII CATG 3 cut(s) 289, 671, 925
CviQI GTAC 1 cut(s) 970
DdeI CTNAG 3 cut(s) 166, 782, 909
DpnI GATC 3 cut(s) 239, 1017, 1157
DpnII GATC 3 cut(s) 237, 1015, 1155
EaeI YGGCCR 1 cut(s) 428
Eam1104I CTCTTC 5 cut(s) 272, 713, 788, 1103, 1131
EarI CTCTTC 5 cut(s) 272, 713, 788, 1103, 1131
Eco24I GRGCYC 2 cut(s) 262, 678
Eco31I GGTCTC 1 cut(s) 475
Eco47I GGWCC 1 cut(s) 953
Eco57I CTGAAG 1 cut(s) 737
Eco88I CYCGRG 1 cut(s) 255
EcoRII CCWGG 1 cut(s) 603
EcoT22I ATGCAT 1 cut(s) 672
EcoT38I GRGCYC 2 cut(s) 262, 678
FaeI CATG 3 cut(s) 292, 674, 928
FaiI YATR 9 cut(s) 290, 410, 557, 672, 767, 801, 926, 1073, 1145
FalI AAGNNNNNCTT 2 cut(s) 37, 69
FatI CATG 3 cut(s) 288, 670, 924
FbaI TGATCA 2 cut(s) 237, 1155
Fnu4HI GCNGC 2 cut(s) 319, 518
FokI GGATG 5 cut(s) 18, 133, 710, 736, 946
FriOI GRGCYC 2 cut(s) 262, 678
Fsp4HI GCNGC 2 cut(s) 319, 518
GlaI GCGC 2 cut(s) 200, 648
GluI GCNGC 2 cut(s) 319, 518
GsaI CCCAGC 2 cut(s) 165, 628
GsuI CTGGAG 1 cut(s) 587
HaeIII GGCC 1 cut(s) 430
HapII CCGG 1 cut(s) 746
HgaI GACGC 2 cut(s) 281, 670
HhaI GCGC 2 cut(s) 201, 649
Hin1I GRCGYC 1 cut(s) 273
Hin1II CATG 3 cut(s) 292, 674, 928
Hin6I GCGC 2 cut(s) 199, 647
HinP1I GCGC 2 cut(s) 199, 647
HinfI GANTC 4 cut(s) 297, 749, 928, 982
HpaII CCGG 1 cut(s) 746
HphI GGTGA 1 cut(s) 19
Hpy166II GTNNAC 3 cut(s) 280, 599, 906
Hpy188I TCNGA 6 cut(s) 307, 328, 933, 943, 957, 1091
Hpy188III TCNNGA 7 cut(s) 289, 352, 472, 532, 869, 925, 1019
Hpy8I GTNNAC 3 cut(s) 280, 599, 906
Hpy99I CGWCG 3 cut(s) 275, 617, 664
HpyAV CCTTC 4 cut(s) 50, 85, 379, 454
HpyCH4III ACNGT 1 cut(s) 921
HpyCH4IV ACGT 3 cut(s) 10, 653, 758
HpyCH4V TGCA 4 cut(s) 460, 599, 670, 896
HpyF10VI GCNNNNNNNGC 4 cut(s) 646, 823, 832, 1042
HpyF3I CTNAG 3 cut(s) 166, 782, 909
HpySE526I ACGT 3 cut(s) 10, 653, 758
Hsp92I GRCGYC 1 cut(s) 273
Hsp92II CATG 3 cut(s) 292, 674, 928
HspAI GCGC 2 cut(s) 199, 647
Ksp22I TGATCA 2 cut(s) 237, 1155
Kzo9I GATC 3 cut(s) 237, 1015, 1155
LguI GCTCTTC 1 cut(s) 1103
LmnI GCTCC 3 cut(s) 102, 823, 853
LweI GCATC 4 cut(s) 529, 657, 883, 1032
MaeII ACGT 3 cut(s) 10, 653, 758
MaeIII GTNAC 2 cut(s) 374, 754
MalI GATC 3 cut(s) 239, 1017, 1157
MboI GATC 3 cut(s) 237, 1015, 1155
MboII GAAGA 8 cut(s) 63, 259, 328, 451, 730, 805, 1120, 1148
MfeI CAATTG 1 cut(s) 521
MflI RGATCY 1 cut(s) 1015
MhlI GDGCHC 5 cut(s) 262, 601, 612, 678, 850
MluCI AATT 4 cut(s) 20, 448, 521, 617
Mph1103I ATGCAT 1 cut(s) 672
MroXI GAANNNNTTC 2 cut(s) 443, 920
MseI TTAA 2 cut(s) 381, 762
MslI CAYNNNNRTG 1 cut(s) 1122
MspI CCGG 1 cut(s) 746
MspR9I CCNGG 1 cut(s) 605
MunI CAATTG 1 cut(s) 521
Mva1269I GAATGC 1 cut(s) 649
MvaI CCWGG 1 cut(s) 605
MwoI GCNNNNNNNGC 4 cut(s) 646, 823, 832, 1042
NdeII GATC 3 cut(s) 237, 1015, 1155
NlaIII CATG 3 cut(s) 292, 674, 928
NmeAIII GCCGAG 1 cut(s) 456
NmuCI GTSAC 2 cut(s) 374, 754
NsiI ATGCAT 1 cut(s) 672
PagI TCATGA 2 cut(s) 288, 924
PciSI GCTCTTC 1 cut(s) 1103
PctI GAATGC 1 cut(s) 649
PdmI GAANNNNTTC 2 cut(s) 443, 920
PfeI GAWTC 4 cut(s) 297, 749, 928, 982
PflFI GACNNNGTC 1 cut(s) 284
PkrI GCNGC 2 cut(s) 320, 519
Psp6I CCWGG 1 cut(s) 603
PspFI CCCAGC 2 cut(s) 161, 624
PspGI CCWGG 1 cut(s) 603
PspPI GGNCC 1 cut(s) 953
PsuI RGATCY 1 cut(s) 1015
PsyI GACNNNGTC 1 cut(s) 284
RsaI GTAC 1 cut(s) 971
RsaNI GTAC 1 cut(s) 970
RseI CAYNNNNRTG 1 cut(s) 1122
SapI GCTCTTC 1 cut(s) 1103
SaqAI TTAA 2 cut(s) 381, 762
SatI GCNGC 2 cut(s) 319, 518
Sau3AI GATC 3 cut(s) 237, 1015, 1155
Sau96I GGNCC 1 cut(s) 953
ScrFI CCNGG 1 cut(s) 605
SduI GDGCHC 5 cut(s) 262, 601, 612, 678, 850
SfaNI GCATC 4 cut(s) 529, 657, 883, 1032
SfcI CTRYAG 1 cut(s) 1143
SinI GGWCC 1 cut(s) 953
SmiMI CAYNNNNRTG 1 cut(s) 1122
SmlI CTYRAG 1 cut(s) 836
SmoI CTYRAG 1 cut(s) 836
Sse9I AATT 4 cut(s) 20, 448, 521, 617
SsiI CCGC 3 cut(s) 319, 340, 518
StyD4I CCNGG 1 cut(s) 603
TaaI ACNGT 1 cut(s) 921
TaiI ACGT 3 cut(s) 13, 656, 761
TaqI TCGA 7 cut(s) 183, 243, 270, 473, 531, 612, 659
TaqII GACCGA 1 cut(s) 742
TasI AATT 4 cut(s) 20, 448, 521, 617
TauI GCSGC 2 cut(s) 321, 520
TfiI GAWTC 4 cut(s) 297, 749, 928, 982
Tru1I TTAA 2 cut(s) 381, 762
Tru9I TTAA 2 cut(s) 381, 762
TscAI CASTG 2 cut(s) 349, 913
TseFI GTSAC 2 cut(s) 374, 754
Tsp45I GTSAC 2 cut(s) 374, 754
TspDTI ATGAA 5 cut(s) 234, 305, 485, 845, 913
TspRI CASTG 2 cut(s) 349, 913
Tth111I GACNNNGTC 1 cut(s) 284
VneI GTGCAC 1 cut(s) 597
VpaK11BI GGWCC 1 cut(s) 953
XapI RAATTY 1 cut(s) 617
XmnI GAANNNNTTC 2 cut(s) 443, 920
Zsp2I ATGCAT 1 cut(s) 672
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.