RchiOBHm_Chr6g0286161

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
6
OG0000756
Physical Location & Seq
Reverse (-)
49499172 .. 49501888
2717 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ25669

Sequence Viewer

Length: 1329 bp
ATGAATCCAGCTGATGTGCACAAGACTGCTTTTAGGACTCATAATGGCCATTATGAATTTTTGGTGATGCCATTTGGGCTTACCAATGCCCCATCCACTTTTCAGTCTGTGATGAATGATGTACTAAGGGACTATTTACGAAAATTTGCATTGGTGTTTTTTGATGATATTTTGGTCTACAGCCCCTCCATGGAGGCACACCTAGATCACTTGGAGAAGGTATTTCAGAAACTACAACAGCATTCCTTGAAGGTTAAACACAGCAAATGTAGTTTTGGAGTTTCTCAAGTGGAGTATCTAGGCCATGTGATTAGTAGAGCAGGAGTAGCTGTTGACCCTGCCAAAATTGAATGTATCAAAAACTGGGAGAAGCCTCAGACTATCAAAGGCTTGAGAAGGTTCCTAGGGCTGGCAGGCTATTACAGAAAGTATGTTCGAAATTTTGGCATCATTGCCAAGACGTTAACTGACATGCTCAAGGTGGGAGGCTTTCAATGGAGTTCAACTTCTGAAGCAGCATTTGAAGAATTAAAGCAAGCCTTGATGAGTACTCCAGTCCTACCATTACCTGATTTCACCAAGGAATTTGTGGTTGAATATGATGCATCTGGCATTGGTATTGGGGCTATTCTATCCCAAGAAGGCCACCCCATTGCTTACTTAAGCAAAGCTCTTGCTCCTAGACATGTGCATTGGAGGCCTTATTTGCTAGGAAATCATTTCAAGATCTATACTGACCACAGAACCATCCAATATTTTCTTAATCAAAAGATTTCTACACCAAGTCAACAAAGGTGGCTACTAAAGTTGGTTGGATATGATTACTCAATACACTACAAGACAGGTAAGACTAATGTAGCACCAGATGCCTTGTCTAGAAAGGAGGAGCTACATGGAGTTCACTCTGATGTCATTTCTAAGTATGGCAACTTATATGCTAGCACGGGTATCTCTTCTCCTGTTCATAGCTACATTAATGAAATCCAAGCTACTTGTTTGAAGGATATGGAGGCAGGTGAGATCATACGGCAGTTGGAACAGGACCCCACTTCTGAACCTCAATACTCACTAGTCAACTCTCAATTGTTATACAAGGGCATGATTTTTGTACTAAAGTCTGATAATTGGAGGACCAAGATTATTCACGAGTTCCACAATGGGTACTGTGGAGGACATGCAGGTGTTCATCGAACTCAGAAGAGAGTTGCTAGATTTTTTCCTGGCCCGGCATGCACAAGGATATTAAGGCAGTTGTTGCAGCTTGTCATACTTGTCAACAAAATCATTATGAAACCATCAACCCTCCTGGCTTGCTTCAACCAAATGTGA
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
RVP_2 RVT_1 Retrotrans_gag rve

Protein Analysis

442

Amino Acids

50.32

Weight (kDa)

9.32

Isoelectric Point (pI)

42.07

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_1 PF00078 8 - 104 5.7e-25 Reverse transcriptase (RNA-dependent DNA polymerase)
RT_RNaseH_2 PF17919 166 - 234 1.5e-18 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 191 - 227 1.6e-07 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 231 - 273 1.2e-09 RNase H-like domain found in reverse transcriptase
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 2 cut(s) 1004, 1169
Acc36I ACCTGC 2 cut(s) 1004, 1169
AccI GTMKAC 1 cut(s) 177
AcoI YGGCCR 1 cut(s) 46
AcsI RAATTY 4 cut(s) 56, 143, 439, 584
AcuI CTGAAG 1 cut(s) 531
AfaI GTAC 4 cut(s) 123, 550, 1110, 1163
AfiI CCNNNNNNNGG 2 cut(s) 190, 409
AflII CTTAAG 1 cut(s) 661
AflIII ACRYGT 1 cut(s) 685
AgsI TTSAA 9 cut(s) 250, 350, 494, 504, 524, 596, 724, 1000, 1318
AhlI ACTAGT 1 cut(s) 1069
AjnI CCWGG 2 cut(s) 1219, 1305
AluBI AGCT 7 cut(s) 11, 329, 671, 889, 969, 989, 1261
AluI AGCT 7 cut(s) 11, 329, 671, 889, 969, 989, 1261
Alw21I GWGCWC 1 cut(s) 21
Alw44I GTGCAC 1 cut(s) 17
AoxI GGCC 5 cut(s) 46, 301, 643, 698, 1222
ApaLI GTGCAC 1 cut(s) 17
ApeKI GCWGC 2 cut(s) 515, 1258
ApoI RAATTY 4 cut(s) 56, 143, 439, 584
AseI ATTAAT 1 cut(s) 975
AspA2I CCTAGG 1 cut(s) 403
AspS9I GGNCC 3 cut(s) 1042, 1131, 1223
AsuC2I CCSGG 1 cut(s) 1226
AsuHPI GGTGA 3 cut(s) 76, 568, 1028
AsuII TTCGAA 1 cut(s) 436
AsuNHI GCTAGC 1 cut(s) 938
AvaII GGWCC 2 cut(s) 1042, 1131
AvrII CCTAGG 1 cut(s) 403
BaeGI GKGCMC 1 cut(s) 21
BalI TGGCCA 1 cut(s) 48
BauI CACGAG 1 cut(s) 1145
Bbv12I GWGCWC 1 cut(s) 21
BbvI GCAGC 2 cut(s) 527, 1270
BccI CCATC 3 cut(s) 100, 755, 1303
BceAI ACGGC 1 cut(s) 1043
BciT130I CCWGG 2 cut(s) 1221, 1307
BcnI CCSGG 1 cut(s) 1226
BcuI ACTAGT 1 cut(s) 1069
BfaI CTAG 9 cut(s) 203, 299, 404, 681, 710, 876, 939, 1070, 1209
BfmI CTRYAG 1 cut(s) 178
BfrI CTTAAG 1 cut(s) 661
BfuAI ACCTGC 2 cut(s) 1004, 1169
BglI GCCNNNNNGGC 1 cut(s) 76
BglII AGATCT 1 cut(s) 726
BisI GCNGC 2 cut(s) 516, 1259
BlnI CCTAGG 1 cut(s) 403
BlsI GCNGC 2 cut(s) 517, 1260
BmcAI AGTACT 1 cut(s) 550
Bme1390I CCNGG 3 cut(s) 1221, 1226, 1307
Bme18I GGWCC 2 cut(s) 1042, 1131
BmgT120I GGNCC 3 cut(s) 1042, 1131, 1223
BmiI GGNNCC 2 cut(s) 401, 1044
BmrFI CCNGG 3 cut(s) 1221, 1226, 1307
BmrI ACTGGG 1 cut(s) 373
BmsI GCATC 5 cut(s) 57, 456, 592, 614, 856
BmtI GCTAGC 1 cut(s) 942
BmuI ACTGGG 1 cut(s) 373
BpmI CTGGAG 1 cut(s) 537
Bpu14I TTCGAA 1 cut(s) 436
BpuEI CTTGAG 3 cut(s) 270, 412, 461
BpuMI CCSGG 1 cut(s) 1226
BsaJI CCNNGG 3 cut(s) 189, 403, 579
BsaXI ACNNNNNCTCC 4 cut(s) 170, 200, 315, 345
Bsc4I CCNNNNNNNGG 2 cut(s) 190, 409
Bse1I ACTGG 2 cut(s) 368, 554
Bse3DI GCAATG 2 cut(s) 450, 651
BseBI CCWGG 2 cut(s) 1221, 1307
BseDI CCNNGG 3 cut(s) 189, 403, 579
BseGI GGATG 2 cut(s) 92, 747
BseLI CCNNNNNNNGG 2 cut(s) 190, 409
BseMI GCAATG 2 cut(s) 450, 651
BseMII CTCAG 2 cut(s) 389, 1208
BseNI ACTGG 2 cut(s) 368, 554
BseRI GAGGAG 1 cut(s) 899
BseSI GKGCMC 1 cut(s) 21
BseXI GCAGC 2 cut(s) 527, 1270
BshFI GGCC 5 cut(s) 48, 303, 645, 700, 1224
BsiHKAI GWGCWC 1 cut(s) 21
BsiSI CCGG 1 cut(s) 1226
BslFI GGGAC 1 cut(s) 143
BslI CCNNNNNNNGG 2 cut(s) 190, 409
BsmFI GGGAC 1 cut(s) 143
BsmI GAATGC 1 cut(s) 241
BsnI GGCC 5 cut(s) 48, 303, 645, 700, 1224
Bsp119I TTCGAA 1 cut(s) 436
Bsp1286I GDGCHC 1 cut(s) 21
Bsp143I GATC 3 cut(s) 205, 726, 1020
Bsp19I CCATGG 1 cut(s) 189
BspANI GGCC 5 cut(s) 48, 303, 645, 700, 1224
BspCNI CTCAG 2 cut(s) 388, 1207
BspLI GGNNCC 2 cut(s) 401, 1044
BspMI ACCTGC 2 cut(s) 1004, 1169
BspOI GCTAGC 1 cut(s) 942
BspT104I TTCGAA 1 cut(s) 436
BspTI CTTAAG 1 cut(s) 661
BsrDI GCAATG 2 cut(s) 450, 651
BsrI ACTGG 2 cut(s) 368, 554
BssECI CCNNGG 3 cut(s) 189, 403, 579
BssMI GATC 3 cut(s) 205, 726, 1020
BssSI CACGAG 1 cut(s) 1145
BssT1I CCWWGG 3 cut(s) 189, 403, 579
Bst2BI CACGAG 1 cut(s) 1145
Bst2UI CCWGG 2 cut(s) 1221, 1307
Bst4CI ACNGT 1 cut(s) 1166
Bst6I CTCTTC 2 cut(s) 958, 1193
BstAFI CTTAAG 1 cut(s) 661
BstAPI GCANNNNNTGC 2 cut(s) 866, 1255
BstBI TTCGAA 1 cut(s) 436
BstC8I GCNNGC 6 cut(s) 411, 415, 537, 940, 1231, 1312
BstDEI CTNAG 4 cut(s) 125, 375, 918, 1194
BstDSI CCRYGG 1 cut(s) 189
BstF5I GGATG 2 cut(s) 92, 747
BstKTI GATC 3 cut(s) 208, 729, 1023
BstMBI GATC 3 cut(s) 205, 726, 1020
BstMWI GCNNNNNNNGC 7 cut(s) 76, 326, 697, 706, 866, 1230, 1255
BstNI CCWGG 2 cut(s) 1221, 1307
BstNSI RCATGY 4 cut(s) 475, 689, 1178, 1233
BstSCI CCNGG 3 cut(s) 1219, 1224, 1305
BstSFI CTRYAG 1 cut(s) 178
BstSLI GKGCMC 1 cut(s) 21
BstV1I GCAGC 2 cut(s) 527, 1270
BstX2I RGATCY 1 cut(s) 726
BstYI RGATCY 1 cut(s) 726
BsuRI GGCC 5 cut(s) 48, 303, 645, 700, 1224
BtgI CCRYGG 1 cut(s) 189
BtsCI GGATG 2 cut(s) 92, 747
BveI ACCTGC 2 cut(s) 1004, 1169
Cac8I GCNNGC 6 cut(s) 411, 415, 537, 940, 1231, 1312
Cfr13I GGNCC 3 cut(s) 1042, 1131, 1223
Csp6I GTAC 4 cut(s) 122, 549, 1109, 1162
CspCI CAANNNNNGTGG 2 cut(s) 776, 811
CviAII CATG 8 cut(s) 190, 305, 472, 686, 893, 1099, 1175, 1230
CviQI GTAC 4 cut(s) 122, 549, 1109, 1162
DdeI CTNAG 4 cut(s) 125, 375, 918, 1194
DpnI GATC 3 cut(s) 207, 728, 1022
DpnII GATC 3 cut(s) 205, 726, 1020
EaeI YGGCCR 1 cut(s) 46
Eam1104I CTCTTC 2 cut(s) 958, 1193
EarI CTCTTC 2 cut(s) 958, 1193
Eco130I CCWWGG 3 cut(s) 189, 403, 579
Eco147I AGGCCT 1 cut(s) 700
Eco47I GGWCC 2 cut(s) 1042, 1131
Eco57I CTGAAG 1 cut(s) 531
EcoO109I RGGNCCY 1 cut(s) 1042
EcoRII CCWGG 2 cut(s) 1219, 1305
EcoT14I CCWWGG 3 cut(s) 189, 403, 579
EcoT22I ATGCAT 1 cut(s) 607
ErhI CCWWGG 3 cut(s) 189, 403, 579
FaeI CATG 8 cut(s) 193, 308, 475, 689, 896, 1102, 1178, 1233
FalI AAGNNNNNCTT 2 cut(s) 524, 556
FaqI GGGAC 1 cut(s) 143
FatI CATG 8 cut(s) 189, 304, 471, 685, 892, 1098, 1174, 1229
FblI GTMKAC 1 cut(s) 177
Fnu4HI GCNGC 2 cut(s) 516, 1259
FokI GGATG 2 cut(s) 79, 734
Fsp4HI GCNGC 2 cut(s) 516, 1259
FspBI CTAG 9 cut(s) 203, 299, 404, 681, 710, 876, 939, 1070, 1209
GluI GCNGC 2 cut(s) 516, 1259
GsuI CTGGAG 1 cut(s) 537
HaeIII GGCC 5 cut(s) 48, 303, 645, 700, 1224
HapII CCGG 1 cut(s) 1226
Hin1II CATG 8 cut(s) 193, 308, 475, 689, 896, 1102, 1178, 1233
HincII GTYRAC 5 cut(s) 334, 465, 788, 1075, 1276
HindII GTYRAC 5 cut(s) 334, 465, 788, 1075, 1276
HinfI GANTC 2 cut(s) 4, 37
HpaI GTTAAC 1 cut(s) 465
HpaII CCGG 1 cut(s) 1226
HphI GGTGA 3 cut(s) 76, 568, 1028
Hpy166II GTNNAC 8 cut(s) 19, 178, 334, 465, 788, 901, 1075, 1276
Hpy188I TCNGA 7 cut(s) 228, 378, 511, 907, 1054, 1120, 1197
Hpy188III TCNNGA 3 cut(s) 724, 876, 1145
Hpy8I GTNNAC 8 cut(s) 19, 178, 334, 465, 788, 901, 1075, 1276
HpyAV CCTTC 5 cut(s) 211, 244, 390, 635, 994
HpyCH4III ACNGT 1 cut(s) 1166
HpyCH4IV ACGT 1 cut(s) 461
HpyCH4V TGCA 7 cut(s) 19, 149, 605, 691, 1178, 1233, 1258
HpyF10VI GCNNNNNNNGC 7 cut(s) 76, 326, 697, 706, 866, 1230, 1255
HpyF3I CTNAG 4 cut(s) 125, 375, 918, 1194
HpySE526I ACGT 1 cut(s) 461
Hsp92II CATG 8 cut(s) 193, 308, 475, 689, 896, 1102, 1178, 1233
KspAI GTTAAC 1 cut(s) 465
Kzo9I GATC 3 cut(s) 205, 726, 1020
LmnI GCTCC 2 cut(s) 682, 886
Lsp1109I GCAGC 2 cut(s) 527, 1270
LweI GCATC 5 cut(s) 57, 456, 592, 614, 856
MaeI CTAG 9 cut(s) 203, 299, 404, 681, 710, 876, 939, 1070, 1209
MaeII ACGT 1 cut(s) 461
MalI GATC 3 cut(s) 207, 728, 1022
MboI GATC 3 cut(s) 205, 726, 1020
MboII GAAGA 3 cut(s) 536, 945, 1210
MfeI CAATTG 1 cut(s) 1082
MflI RGATCY 1 cut(s) 726
MhlI GDGCHC 1 cut(s) 21
MlsI TGGCCA 1 cut(s) 48
MluCI AATT 8 cut(s) 56, 143, 345, 439, 527, 584, 1082, 1123
MluNI TGGCCA 1 cut(s) 48
MlyI GAGTC 1 cut(s) 31
MmeI TCCRAC 2 cut(s) 793, 1014
Mox20I TGGCCA 1 cut(s) 48
Mph1103I ATGCAT 1 cut(s) 607
MscI TGGCCA 1 cut(s) 48
MseI TTAA 7 cut(s) 255, 464, 530, 662, 762, 975, 1244
MslI CAYNNNNRTG 2 cut(s) 906, 1179
Msp20I TGGCCA 1 cut(s) 48
MspA1I CMGCKG 1 cut(s) 11
MspCI CTTAAG 1 cut(s) 661
MspI CCGG 1 cut(s) 1226
MspR9I CCNGG 3 cut(s) 1221, 1226, 1307
MunI CAATTG 1 cut(s) 1082
Mva1269I GAATGC 1 cut(s) 241
MvaI CCWGG 2 cut(s) 1221, 1307
MwoI GCNNNNNNNGC 7 cut(s) 76, 326, 697, 706, 866, 1230, 1255
NciI CCSGG 1 cut(s) 1226
NcoI CCATGG 1 cut(s) 189
NdeII GATC 3 cut(s) 205, 726, 1020
NheI GCTAGC 1 cut(s) 938
NlaIII CATG 8 cut(s) 193, 308, 475, 689, 896, 1102, 1178, 1233
NlaIV GGNNCC 2 cut(s) 401, 1044
NsiI ATGCAT 1 cut(s) 607
NspI RCATGY 4 cut(s) 475, 689, 1178, 1233
NspV TTCGAA 1 cut(s) 436
PaeI GCATGC 1 cut(s) 1233
PaqCI CACCTGC 2 cut(s) 1004, 1169
PceI AGGCCT 1 cut(s) 700
PciI ACATGT 1 cut(s) 685
PctI GAATGC 1 cut(s) 241
PfeI GAWTC 1 cut(s) 4
PkrI GCNGC 2 cut(s) 517, 1260
PleI GAGTC 1 cut(s) 31
PpsI GAGTC 1 cut(s) 31
PpuMI RGGWCCY 1 cut(s) 1042
PscI ACATGT 1 cut(s) 685
PshBI ATTAAT 1 cut(s) 975
Psp5II RGGWCCY 1 cut(s) 1042
Psp6I CCWGG 2 cut(s) 1219, 1305
PspGI CCWGG 2 cut(s) 1219, 1305
PspN4I GGNNCC 2 cut(s) 401, 1044
PspPI GGNCC 3 cut(s) 1042, 1131, 1223
PspPPI RGGWCCY 1 cut(s) 1042
PsuI RGATCY 1 cut(s) 726
PvuII CAGCTG 1 cut(s) 11
RsaI GTAC 4 cut(s) 123, 550, 1110, 1163
RsaNI GTAC 4 cut(s) 122, 549, 1109, 1162
RseI CAYNNNNRTG 2 cut(s) 906, 1179
SaqAI TTAA 7 cut(s) 255, 464, 530, 662, 762, 975, 1244
SatI GCNGC 2 cut(s) 516, 1259
Sau3AI GATC 3 cut(s) 205, 726, 1020
Sau96I GGNCC 3 cut(s) 1042, 1131, 1223
ScaI AGTACT 1 cut(s) 550
SchI GAGTC 1 cut(s) 31
ScrFI CCNGG 3 cut(s) 1221, 1226, 1307
SduI GDGCHC 1 cut(s) 21
SfaNI GCATC 5 cut(s) 57, 456, 592, 614, 856
SfcI CTRYAG 1 cut(s) 178
SfuI TTCGAA 1 cut(s) 436
SinI GGWCC 2 cut(s) 1042, 1131
SmiMI CAYNNNNRTG 2 cut(s) 906, 1179
SmlI CTYRAG 4 cut(s) 285, 391, 476, 661
SmoI CTYRAG 4 cut(s) 285, 391, 476, 661
SpeI ACTAGT 1 cut(s) 1069
SphI GCATGC 1 cut(s) 1233
Sse9I AATT 8 cut(s) 56, 143, 345, 439, 527, 584, 1082, 1123
SseBI AGGCCT 1 cut(s) 700
SspI AATATT 1 cut(s) 755
SspMI CTAG 9 cut(s) 203, 299, 404, 681, 710, 876, 939, 1070, 1209
StuI AGGCCT 1 cut(s) 700
StyD4I CCNGG 3 cut(s) 1219, 1224, 1305
StyI CCWWGG 3 cut(s) 189, 403, 579
TaaI ACNGT 1 cut(s) 1166
TaiI ACGT 1 cut(s) 464
TaqI TCGA 2 cut(s) 436, 1189
TasI AATT 8 cut(s) 56, 143, 345, 439, 527, 584, 1082, 1123
TatI WGTACW 3 cut(s) 121, 548, 1108
TfiI GAWTC 1 cut(s) 4
Tru1I TTAA 7 cut(s) 255, 464, 530, 662, 762, 975, 1244
Tru9I TTAA 7 cut(s) 255, 464, 530, 662, 762, 975, 1244
TseI GCWGC 2 cut(s) 515, 1258
TspDTI ATGAA 7 cut(s) 17, 69, 128, 953, 993, 1175, 1304
Vha464I CTTAAG 1 cut(s) 661
VneI GTGCAC 1 cut(s) 17
VpaK11BI GGWCC 2 cut(s) 1042, 1131
VspI ATTAAT 1 cut(s) 975
XapI RAATTY 4 cut(s) 56, 143, 439, 584
XbaI TCTAGA 1 cut(s) 875
XceI RCATGY 4 cut(s) 475, 689, 1178, 1233
XcmI CCANNNNNNNNNTGG 1 cut(s) 586
XmaJI CCTAGG 1 cut(s) 403
XmiI GTMKAC 1 cut(s) 177
XspI CTAG 9 cut(s) 203, 299, 404, 681, 710, 876, 939, 1070, 1209
ZrmI AGTACT 1 cut(s) 550
Zsp2I ATGCAT 1 cut(s) 607
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.