RchiOBHm_Chr5g0017911

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0009688
Physical Location & Seq
Forward (+)
12446885 .. 12451394
4510 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ29814

Sequence Viewer

Length: 1497 bp
ATGGATGAAGAAATGAAAGCTCTCATTAAGAATGAGACTTGGGATCTTGTTCCAAAACCAGATCATGTGAATCCCATCACATGTAAATGGGTTTACAAGTTGAAAAGAAAAGCTGATGGAAGTGTGGACAGATTTAAAGCTAGATTGGTTGCTCGTGGTTTCTCTCAAAGCTATGGAATAGATTATGAGGAGACTTTCAGTCCCGTTGCAAAGATGACATCTGTTCGTGTTGGGATTTCCTTGGCAGCCTCTCAAGGTTGGAAGCTATGGCAGCTCGATGTGAAAAATGAATTTCTATATGGTGATCTTGACAAGGACATCTATATGGAGCAACCAATAAGCTACACATCAAAAGCTCATCCAAGTTATGTGTTCAAACTCAAGAAAGCTTTATATGGTTTAAAGCAAGCTCCGAGAGCATGGTACGGGAAGATTGCAGAATTTCTACAATTCTGTGGTTATCATTCTACAGATGCAGATTCAAGTCTTTTTGTTAAGAAGGATGGAGACTTGCATATGGTGGTCCTTTTATATGTGGATGATATGATAGTAACCGGAAGTGATGAAGGTGAGATTGCAAAGCTAAGGGCAGAATTATCTACTCGGTTCGATATGAAGATTTTGGGTGAGCTAAGCCATTTTCTTGGTTTAGAAGTGAAAAATATGAAGGATGGTGTTCTGTTATCACAAGAAGGTTATGCTAAGAAGTTGGTTGAGAAATATGGCCTGAAACTTAGCAAGAGACGATCTACTCCACTTGACATAAGTGAGAAATTAAGGCGAGATGTAGGATCTCTCTTGCCAGATCCTAAGTCTTATCGTTCTCTTGTTGGTGGTCTTCTTTATTTGACAATCACAAGGCCAGACATTGCCTTTTCAGTTGGGCTCATAAGCCGGTACTTGCAAGAGCCTCGGAAGCCACATCTAGAAGCAGCAAAGAAGATTCTCAAGTATGTTAATTGTACTCTTGATCTGGGTCTCTTTTACAAAAGAGGTGGTGGTTTCTTGTTAAATGGCTATACAGATGCTGATTTTGGTGGAGATTTAGACGAAAGAAGATCCACTTCTGGTTATGTCTTTCTGTGCAACAATACAAGTGTTTCTTTGTGCAGCAAGAAACAAGATGCAGTGGTTTTATCTACAGCTGAAGCAGAGTACAAGGCTGCTACACTTGCTGCACATGAGTGTGTTTGGCTTCGAAGACTTATTAAGGATGTTTATCATCCAATTCATAAGGCTACTGATCTGTTTGGTGATAATCAGAGTGCCATCAAGCTTGCTTATAATCCAGTGTGCCATGCTAGAACTAAACACATTGAGATTGAGCATCATTTTATTCGAGAGAAGGTTCTTGATGGAACAATTGACAACAAGGAAGTGAGAAGTGATCTTAATGTTGCAGATATCTTTACAAAGACTCTCTCCAAAGGTCCATTCGAGTTTCTTCGTGCAAGGCTGGGGTTGATCTCGAAAAACAACTCTAAGGGGGAGTGTTGA
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
DUF4219 RVT_2 Retrotran_gag_2 Retrotran_gag_3 gag_pre-integrs rve zf-CCHC

Protein Analysis

498

Amino Acids

56.34

Weight (kDa)

8.97

Isoelectric Point (pI)

34.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 11 - 253 1.4e-72 Reverse transcriptase (RNA-dependent DNA polymerase)
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 1284
AclWI GGATC 4 cut(s) 51, 799, 800, 1053
AcsI RAATTY 2 cut(s) 290, 440
AcuI CTGAAG 1 cut(s) 1167
AfaI GTAC 4 cut(s) 425, 899, 964, 1157
AflIII ACRYGT 1 cut(s) 80
AgsI TTSAA 3 cut(s) 103, 376, 483
AhdI GACNNNNNGTC 1 cut(s) 198
AjuI GAANNNNNNNTTGG 2 cut(s) 1418, 1450
AleI CACNNNNGTG 1 cut(s) 1183
Alw26I GTCTC 5 cut(s) 29, 185, 501, 736, 983
AlwI GGATC 4 cut(s) 51, 799, 800, 1053
AlwNI CAGNNNCTG 1 cut(s) 1028
AoxI GGCC 2 cut(s) 724, 860
ApeKI GCWGC 6 cut(s) 245, 271, 932, 1110, 1163, 1175
ApoI RAATTY 2 cut(s) 290, 440
AspS9I GGNCC 2 cut(s) 523, 1430
AsuHPI GGTGA 4 cut(s) 314, 581, 638, 1265
AsuII TTCGAA 1 cut(s) 1198
AvaII GGWCC 2 cut(s) 523, 1430
BanII GRGCYC 1 cut(s) 888
BauI CACGAG 1 cut(s) 153
BbsI GAAGAC 2 cut(s) 830, 1207
BbvI GCAGC 6 cut(s) 257, 283, 944, 1122, 1150, 1162
BccI CCATC 6 cut(s) 83, 110, 497, 665, 1277, 1349
BcgI CGANNNNNNTGC 2 cut(s) 893, 927
BcoDI GTCTC 5 cut(s) 29, 185, 501, 736, 983
BfaI CTAG 3 cut(s) 141, 926, 1302
BfmI CTRYAG 2 cut(s) 468, 1140
BisI GCNGC 6 cut(s) 246, 272, 933, 1111, 1164, 1176
BlpI GCTNAGC 1 cut(s) 632
BlsI GCNGC 6 cut(s) 247, 273, 934, 1112, 1165, 1177
Bme18I GGWCC 2 cut(s) 523, 1430
BmeRI GACNNNNNGTC 1 cut(s) 198
BmgT120I GGNCC 2 cut(s) 523, 1430
BmsI GCATC 4 cut(s) 463, 1015, 1114, 1336
BpiI GAAGAC 2 cut(s) 830, 1207
Bpu10I CCTNAGC 1 cut(s) 584
Bpu1102I GCTNAGC 1 cut(s) 632
Bpu14I TTCGAA 1 cut(s) 1198
BpuEI CTTGAG 3 cut(s) 237, 365, 932
BsaBI GATNNNNATC 1 cut(s) 1218
BsaI GGTCTC 1 cut(s) 983
BsaJI CCNNGG 2 cut(s) 240, 911
BsaWI WCCGGW 1 cut(s) 554
Bse118I RCCGGY 1 cut(s) 894
Bse1I ACTGG 1 cut(s) 1289
Bse3DI GCAATG 1 cut(s) 867
Bse8I GATNNNNATC 1 cut(s) 1218
BseDI CCNNGG 2 cut(s) 240, 911
BseGI GGATG 7 cut(s) 10, 358, 508, 544, 676, 1219, 1222
BseJI GATNNNNATC 1 cut(s) 1218
BseMI GCAATG 1 cut(s) 867
BseNI ACTGG 1 cut(s) 1289
BseRI GAGGAG 1 cut(s) 203
BseXI GCAGC 6 cut(s) 257, 283, 944, 1122, 1150, 1162
BseYI CCCAGC 1 cut(s) 1456
BsgI GTGCAG 2 cut(s) 1129, 1161
BshFI GGCC 2 cut(s) 726, 862
BsiSI CCGG 2 cut(s) 555, 895
BslFI GGGAC 1 cut(s) 186
BsmAI GTCTC 5 cut(s) 29, 185, 501, 736, 983
BsmBI CGTCTC 1 cut(s) 736
BsmFI GGGAC 1 cut(s) 186
BsnI GGCC 2 cut(s) 726, 862
Bso31I GGTCTC 1 cut(s) 983
Bsp119I TTCGAA 1 cut(s) 1198
Bsp1286I GDGCHC 1 cut(s) 888
Bsp1720I GCTNAGC 1 cut(s) 632
BspANI GGCC 2 cut(s) 726, 862
BspPI GGATC 4 cut(s) 51, 799, 800, 1053
BspT104I TTCGAA 1 cut(s) 1198
BspTNI GGTCTC 1 cut(s) 983
BsrDI GCAATG 1 cut(s) 867
BsrFI RCCGGY 1 cut(s) 894
BsrI ACTGG 1 cut(s) 1289
BssAI RCCGGY 1 cut(s) 894
BssECI CCNNGG 2 cut(s) 240, 911
BssSI CACGAG 1 cut(s) 153
BssT1I CCWWGG 1 cut(s) 240
Bst2BI CACGAG 1 cut(s) 153
BstBI TTCGAA 1 cut(s) 1198
BstC8I GCNNGC 2 cut(s) 408, 1278
BstDEI CTNAG 6 cut(s) 584, 632, 702, 734, 810, 1482
BstF5I GGATG 7 cut(s) 10, 358, 508, 544, 676, 1219, 1222
BstMAI GTCTC 5 cut(s) 29, 185, 501, 736, 983
BstMWI GCNNNNNNNGC 4 cut(s) 271, 416, 916, 1172
BstNSI RCATGY 1 cut(s) 84
BstSFI CTRYAG 2 cut(s) 468, 1140
BstV1I GCAGC 6 cut(s) 257, 283, 944, 1122, 1150, 1162
BstV2I GAAGAC 2 cut(s) 830, 1207
BstX2I RGATCY 4 cut(s) 43, 791, 805, 1058
BstXI CCANNNNNNTGG 1 cut(s) 644
BstYI RGATCY 4 cut(s) 43, 791, 805, 1058
BsuRI GGCC 2 cut(s) 726, 862
BtsCI GGATG 7 cut(s) 10, 358, 508, 544, 676, 1219, 1222
BtsI GCAGTG 1 cut(s) 1134
BtsIMutI CAGTG 2 cut(s) 1134, 1296
Cac8I GCNNGC 2 cut(s) 408, 1278
CaiI CAGNNNCTG 1 cut(s) 1028
Cfr10I RCCGGY 1 cut(s) 894
Cfr13I GGNCC 2 cut(s) 523, 1430
Csp6I GTAC 4 cut(s) 424, 898, 963, 1156
CspCI CAANNNNNGTGG 2 cut(s) 976, 1011
CviAII CATG 5 cut(s) 65, 81, 420, 1181, 1298
CviQI GTAC 4 cut(s) 424, 898, 963, 1156
DdeI CTNAG 6 cut(s) 584, 632, 702, 734, 810, 1482
DraI TTTAAA 2 cut(s) 136, 402
DriI GACNNNNNGTC 1 cut(s) 198
Eam1105I GACNNNNNGTC 1 cut(s) 198
Eco130I CCWWGG 1 cut(s) 240
Eco24I GRGCYC 1 cut(s) 888
Eco31I GGTCTC 1 cut(s) 983
Eco32I GATATC 1 cut(s) 1405
Eco47I GGWCC 2 cut(s) 523, 1430
Eco57I CTGAAG 1 cut(s) 1167
EcoRV GATATC 1 cut(s) 1405
EcoT14I CCWWGG 1 cut(s) 240
EcoT38I GRGCYC 1 cut(s) 888
ErhI CCWWGG 1 cut(s) 240
Esp3I CGTCTC 1 cut(s) 736
FaeI CATG 5 cut(s) 68, 84, 423, 1184, 1301
FalI AAGNNNNNCTT 4 cut(s) 1048, 1080, 1087, 1119
FaqI GGGAC 1 cut(s) 186
FatI CATG 5 cut(s) 64, 80, 419, 1180, 1297
FauNDI CATATG 1 cut(s) 516
Fnu4HI GCNGC 6 cut(s) 246, 272, 933, 1111, 1164, 1176
FokI GGATG 7 cut(s) 17, 345, 515, 551, 683, 1209, 1226
FriOI GRGCYC 1 cut(s) 888
Fsp4HI GCNGC 6 cut(s) 246, 272, 933, 1111, 1164, 1176
FspBI CTAG 3 cut(s) 141, 926, 1302
GluI GCNGC 6 cut(s) 246, 272, 933, 1111, 1164, 1176
GsaI CCCAGC 1 cut(s) 1460
HaeIII GGCC 2 cut(s) 726, 862
HapII CCGG 2 cut(s) 555, 895
Hin1II CATG 5 cut(s) 68, 84, 423, 1184, 1301
HindIII AAGCTT 2 cut(s) 387, 1274
HinfI GANTC 4 cut(s) 70, 479, 943, 1417
HpaII CCGG 2 cut(s) 555, 895
HphI GGTGA 4 cut(s) 314, 581, 638, 1265
Hpy166II GTNNAC 2 cut(s) 94, 127
Hpy188I TCNGA 3 cut(s) 414, 915, 1263
Hpy188III TCNNGA 7 cut(s) 308, 382, 926, 968, 1340, 1352, 1468
Hpy8I GTNNAC 2 cut(s) 94, 127
HpyAV CCTTC 5 cut(s) 493, 560, 661, 686, 1339
HpyF10VI GCNNNNNNNGC 4 cut(s) 271, 416, 916, 1172
HpyF3I CTNAG 6 cut(s) 584, 632, 702, 734, 810, 1482
Hsp92II CATG 5 cut(s) 68, 84, 423, 1184, 1301
LmnI GCTCC 2 cut(s) 328, 415
Lsp1109I GCAGC 6 cut(s) 257, 283, 944, 1122, 1150, 1162
LweI GCATC 4 cut(s) 463, 1015, 1114, 1336
MaeI CTAG 3 cut(s) 141, 926, 1302
MaeIII GTNAC 1 cut(s) 550
MboII GAAGA 8 cut(s) 20, 442, 628, 830, 952, 1068, 1212, 1436
MfeI CAATTG 1 cut(s) 1362
MflI RGATCY 4 cut(s) 43, 791, 805, 1058
MhlI GDGCHC 1 cut(s) 888
MluCI AATT 8 cut(s) 290, 440, 449, 593, 773, 958, 1227, 1362
MlyI GAGTC 1 cut(s) 1411
MmeI TCCRAC 1 cut(s) 239
MnlI CCTC 4 cut(s) 181, 259, 921, 986
MseI TTAA 9 cut(s) 27, 135, 401, 495, 776, 957, 1010, 1209, 1392
MslI CAYNNNNRTG 4 cut(s) 85, 323, 1183, 1185
MspA1I CMGCKG 1 cut(s) 1145
MspI CCGG 2 cut(s) 555, 895
MunI CAATTG 1 cut(s) 1362
MwoI GCNNNNNNNGC 4 cut(s) 271, 416, 916, 1172
NdeI CATATG 1 cut(s) 516
NlaIII CATG 5 cut(s) 68, 84, 423, 1184, 1301
NspI RCATGY 1 cut(s) 84
NspV TTCGAA 1 cut(s) 1198
OliI CACNNNNGTG 1 cut(s) 1183
PciI ACATGT 1 cut(s) 80
PfeI GAWTC 3 cut(s) 70, 479, 943
PkrI GCNGC 6 cut(s) 247, 273, 934, 1112, 1165, 1177
PleI GAGTC 1 cut(s) 1411
PpsI GAGTC 1 cut(s) 1411
PscI ACATGT 1 cut(s) 80
PsiI TTATAA 1 cut(s) 1284
PspFI CCCAGC 1 cut(s) 1456
PspPI GGNCC 2 cut(s) 523, 1430
PstNI CAGNNNCTG 1 cut(s) 1028
PsuI RGATCY 4 cut(s) 43, 791, 805, 1058
PvuII CAGCTG 1 cut(s) 1145
RsaI GTAC 4 cut(s) 425, 899, 964, 1157
RsaNI GTAC 4 cut(s) 424, 898, 963, 1156
RseI CAYNNNNRTG 4 cut(s) 85, 323, 1183, 1185
SaqAI TTAA 9 cut(s) 27, 135, 401, 495, 776, 957, 1010, 1209, 1392
SatI GCNGC 6 cut(s) 246, 272, 933, 1111, 1164, 1176
Sau96I GGNCC 2 cut(s) 523, 1430
SchI GAGTC 1 cut(s) 1411
SduI GDGCHC 1 cut(s) 888
SfaNI GCATC 4 cut(s) 463, 1015, 1114, 1336
SfcI CTRYAG 2 cut(s) 468, 1140
SfuI TTCGAA 1 cut(s) 1198
SinI GGWCC 2 cut(s) 523, 1430
SmiMI CAYNNNNRTG 4 cut(s) 85, 323, 1183, 1185
SmlI CTYRAG 3 cut(s) 252, 380, 947
SmoI CTYRAG 3 cut(s) 252, 380, 947
Sse9I AATT 8 cut(s) 290, 440, 449, 593, 773, 958, 1227, 1362
SspMI CTAG 3 cut(s) 141, 926, 1302
StyI CCWWGG 1 cut(s) 240
TaqI TCGA 6 cut(s) 276, 609, 1198, 1339, 1437, 1469
TasI AATT 8 cut(s) 290, 440, 449, 593, 773, 958, 1227, 1362
TatI WGTACW 2 cut(s) 962, 1155
TfiI GAWTC 3 cut(s) 70, 479, 943
Tru1I TTAA 9 cut(s) 27, 135, 401, 495, 776, 957, 1010, 1209, 1392
Tru9I TTAA 9 cut(s) 27, 135, 401, 495, 776, 957, 1010, 1209, 1392
TscAI CASTG 2 cut(s) 1134, 1296
TseI GCWGC 6 cut(s) 245, 271, 932, 1110, 1163, 1175
TspDTI ATGAA 7 cut(s) 21, 29, 303, 579, 629, 680, 1220
TspRI CASTG 2 cut(s) 1134, 1296
VpaK11BI GGWCC 2 cut(s) 523, 1430
XapI RAATTY 2 cut(s) 290, 440
XbaI TCTAGA 1 cut(s) 925
XceI RCATGY 1 cut(s) 84
XspI CTAG 3 cut(s) 141, 926, 1302
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.