RchiOBHm_Chr4g0397431

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
4
OG0000756
Physical Location & Seq
Reverse (-)
13861140 .. 13863034
1895 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ36973

Sequence Viewer

Length: 1521 bp
ATGGGACACTTGAATGGACCTCAGCACCCATACTGGCATTACCCGGCACAACACCACCCACCACATGATCCTAGCTTACCTACCATGCGTCAAATGAAGCTAGAGTTCTGTACCTTCAGTGGTGGTGACCCAGTTGAGTGGCTCAATAAAGTTGAGCAGTTTTTTGAATTTTACCAGATTCCTGAGGAGAAAAAGTTAGCCATTGCCACAATGCACCTTACAGAGAGAGCTTCTGACAGGTGGTATATGTTTAGGCATGAGTTTCCACCTACTTGGCTGGGCCTAGCTGATTTATTAATGAGAGAGTTTAGTTGTCACAATGTGCTTGACTATCAGGCAGCTTTAGCCAGGATGTCCCAAACTGGAAGTGTTGAGCAATACAAAGAGCAATTCACAAGGCTTTCAAGGAGAGCTCCTGGATTTTCACAACAGGTATTGTTATCATGCTTCTTGGGAGGTTTGAAAAGTGAAATCAGAGTTGATGTGAAAGCACAGAAGCCTAAATCATTGTATGAAGCGTGCGAGTTGGCTAAGATATATGAAGAGAGAGAAGCAAGCCAAAGAAACCAAAATAAGTCCAACAGTAGTGGCAGGCCATTTTCAGCTATCCAAACTAGTCAGTTTAGTAAAGCAACTCTTGCAGCAGGTAGTAGCCAAGCAGGGAGGGGTCAACCAAGCCACATCAGGCCTGCCATGATACAAAACCTTGTAGCTCCCAACATGGGAAAACTCAACAATGGTAACAGGAGGCTTTCTCAAGCAGAGTACCAAGAGAGAAGAGCTAGGAATCAGTGTTTTTTCTGTGAAGAATTGTTTAGGCCGGGGCATAATTGCAGGAAAGGTCAACTCATAGTCATTGAGGTGGTACAGGATGAGGCTGATCAACCAGCCTTGACTGATAATGAAGGAGTAGAGGGGGCTACACATGAAGAGGAAATTCCAGAACCTGAAATACAGTTACAAATCTTGGGTGAACATAATACCTCAGACACAATGCAGTTAAAGGGTGTGTTTAACGACAAACAAGTGCATGTCCTGATTGATACTGGAGCCTCGCACAATTTTATTCATCCTTCCCTGCTCAAGAAGTTCAAGGCAAAAATTGTTGATATTAAACCTTTAAAAGTAAGACTGGCAAGTGGGGCTTTAATGCAGACAAAGGGGCAGGTAACAGTGGCTATGAAATTACAACAATTTACATTTTTAGCTGATTTTTACATTTTACCAATTTCAGGCTGTGAGGTGGTATTAGGAGCGTCCTGGCTTAGAACATTGGGGGATATCACCTGGAATTTTGAAACAATGAAGATGCAGTTCTATCATGAACAAGTGAAGTACACCCTGCAAGGGGAAACTAAGTCTCAAGCTTCTATAATCAGCTGCAAATCAATGACAAGACTTCTCAAAAAGGAAAAAGAAGCAGTGATGGTACAATTGTGCCCCATTACAACAAGGAACAAAACAGCTGAGACCCATCCTAAAATACAGCAACTGTTGCAGCAGTTTGTAGAAGTATTTTAG
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

506

Amino Acids

57.75

Weight (kDa)

8.54

Isoelectric Point (pI)

46.73

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 37 - 197 6.2e-11 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 68 - 155 2.1e-09 Retrotransposon gag protein
gag-asp_proteas PF13975 335 - 423 2.4e-09 gag-polyprotein putative aspartyl protease
RVP_2 PF08284 336 - 423 2.6e-08 Retroviral aspartyl protease
Asp_protease_2 PF13650 336 - 420 1.2e-07 Aspartyl protease
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)
Acc36I ACCTGC 2 cut(s) 635, 1156
AclWI GGATC 1 cut(s) 62
AcsI RAATTY 3 cut(s) 167, 936, 1291
AcuI CTGAAG 1 cut(s) 100
AdeI CACNNNGTG 1 cut(s) 322
AfaI GTAC 5 cut(s) 112, 767, 867, 1337, 1431
AfiI CCNNNNNNNGG 4 cut(s) 722, 1232, 1347, 1348
AgsI TTSAA 6 cut(s) 13, 167, 405, 463, 1093, 1298
AhlI ACTAGT 1 cut(s) 614
AjnI CCWGG 4 cut(s) 347, 415, 1259, 1286
Alw21I GWGCWC 1 cut(s) 415
Alw26I GTCTC 2 cut(s) 1365, 1463
AlwI GGATC 1 cut(s) 62
AlwNI CAGNNNCTG 2 cut(s) 947, 1492
AoxI GGCC 4 cut(s) 280, 593, 686, 818
ApeKI GCWGC 4 cut(s) 338, 641, 1380, 1498
ApoI RAATTY 3 cut(s) 167, 936, 1291
AseI ATTAAT 1 cut(s) 296
AspS9I GGNCC 2 cut(s) 17, 280
AsuC2I CCSGG 2 cut(s) 44, 822
AsuHPI GGTGA 3 cut(s) 137, 983, 1276
AvaII GGWCC 1 cut(s) 17
AxyI CCTNAGG 1 cut(s) 183
BaeGI GKGCMC 1 cut(s) 1442
BaeI ACNNNNGTAYC 2 cut(s) 1421, 1454
BanII GRGCYC 1 cut(s) 415
Bbv12I GWGCWC 1 cut(s) 415
BbvCI CCTCAGC 1 cut(s) 21
BbvI GCAGC 4 cut(s) 350, 653, 1367, 1510
BccI CCATC 2 cut(s) 1420, 1482
BciT130I CCWGG 4 cut(s) 349, 417, 1261, 1288
BclI TGATCA 1 cut(s) 880
BcnI CCSGG 2 cut(s) 44, 822
BcoDI GTCTC 2 cut(s) 1365, 1463
BcuI ACTAGT 1 cut(s) 614
BfaI CTAG 5 cut(s) 72, 101, 284, 615, 783
BfuAI ACCTGC 2 cut(s) 635, 1156
BisI GCNGC 4 cut(s) 339, 642, 1381, 1499
BlsI GCNGC 4 cut(s) 340, 643, 1382, 1500
Bme1390I CCNGG 6 cut(s) 44, 349, 417, 822, 1261, 1288
Bme18I GGWCC 1 cut(s) 17
BmgT120I GGNCC 2 cut(s) 17, 280
BmiI GGNNCC 1 cut(s) 1051
BmrFI CCNGG 6 cut(s) 44, 349, 417, 822, 1261, 1288
BmrI ACTGGG 1 cut(s) 125
BmsI GCATC 1 cut(s) 1299
BmuI ACTGGG 1 cut(s) 125
BplI GAGNNNNNCTC 2 cut(s) 739, 771
BpmI CTGGAG 1 cut(s) 1068
Bpu10I CCTNAGC 1 cut(s) 21
BpuEI CTTGAG 3 cut(s) 741, 1067, 1347
BpuMI CCSGG 2 cut(s) 44, 822
BsaI GGTCTC 1 cut(s) 1463
BsaJI CCNNGG 1 cut(s) 821
BsaXI ACNNNNNCTCC 2 cut(s) 179, 209
Bsc4I CCNNNNNNNGG 4 cut(s) 722, 1232, 1347, 1348
Bse1I ACTGG 5 cut(s) 38, 131, 367, 1051, 1137
Bse21I CCTNAGG 1 cut(s) 183
Bse3DI GCAATG 1 cut(s) 201
BseBI CCWGG 4 cut(s) 349, 417, 1261, 1288
BseDI CCNNGG 1 cut(s) 821
BseGI GGATG 4 cut(s) 357, 877, 1069, 1474
BseLI CCNNNNNNNGG 4 cut(s) 722, 1232, 1347, 1348
BseMI GCAATG 1 cut(s) 201
BseMII CTCAG 4 cut(s) 35, 174, 999, 1458
BseNI ACTGG 5 cut(s) 38, 131, 367, 1051, 1137
BseRI GAGGAG 1 cut(s) 200
BseSI GKGCMC 1 cut(s) 1442
BseXI GCAGC 4 cut(s) 350, 653, 1367, 1510
BseYI CCCAGC 1 cut(s) 277
BshFI GGCC 4 cut(s) 282, 595, 688, 820
BsiHKAI GWGCWC 1 cut(s) 415
BsiSI CCGG 2 cut(s) 44, 821
BslFI GGGAC 2 cut(s) 18, 340
BslI CCNNNNNNNGG 4 cut(s) 722, 1232, 1347, 1348
BsmAI GTCTC 2 cut(s) 1365, 1463
BsmFI GGGAC 2 cut(s) 18, 340
BsnI GGCC 4 cut(s) 282, 595, 688, 820
Bso31I GGTCTC 1 cut(s) 1463
Bsp1286I GDGCHC 2 cut(s) 415, 1442
Bsp143I GATC 2 cut(s) 67, 880
BspANI GGCC 4 cut(s) 282, 595, 688, 820
BspCNI CTCAG 4 cut(s) 34, 175, 998, 1459
BspHI TCATGA 1 cut(s) 1321
BspLI GGNNCC 1 cut(s) 1051
BspMI ACCTGC 2 cut(s) 635, 1156
BspPI GGATC 1 cut(s) 62
BspQI GCTCTTC 1 cut(s) 772
BspTNI GGTCTC 1 cut(s) 1463
BsrDI GCAATG 1 cut(s) 201
BsrI ACTGG 5 cut(s) 38, 131, 367, 1051, 1137
BssECI CCNNGG 1 cut(s) 821
BssMI GATC 2 cut(s) 67, 880
Bst2UI CCWGG 4 cut(s) 349, 417, 1261, 1288
Bst4CI ACNGT 4 cut(s) 584, 957, 1174, 1494
Bst6I CTCTTC 3 cut(s) 537, 772, 924
BstAPI GCANNNNNTGC 2 cut(s) 638, 1495
BstC8I GCNNGC 4 cut(s) 520, 556, 593, 690
BstDEI CTNAG 7 cut(s) 21, 183, 531, 985, 1265, 1356, 1467
BstEII GGTNACC 1 cut(s) 125
BstF5I GGATG 4 cut(s) 357, 877, 1069, 1474
BstKTI GATC 2 cut(s) 70, 883
BstMAI GTCTC 2 cut(s) 1365, 1463
BstMBI GATC 2 cut(s) 67, 880
BstMWI GCNNNNNNNGC 4 cut(s) 344, 638, 1142, 1495
BstNI CCWGG 4 cut(s) 349, 417, 1261, 1288
BstNSI RCATGY 1 cut(s) 1034
BstPI GGTNACC 1 cut(s) 125
BstSCI CCNGG 6 cut(s) 42, 347, 415, 820, 1259, 1286
BstSLI GKGCMC 1 cut(s) 1442
BstV1I GCAGC 4 cut(s) 350, 653, 1367, 1510
BstXI CCANNNNNNTGG 2 cut(s) 138, 273
Bsu36I CCTNAGG 1 cut(s) 183
BsuRI GGCC 4 cut(s) 282, 595, 688, 820
BtsCI GGATG 4 cut(s) 357, 877, 1069, 1474
BtsI GCAGTG 1 cut(s) 1428
BtsIMutI CAGTG 4 cut(s) 124, 797, 1179, 1428
BveI ACCTGC 2 cut(s) 635, 1156
Cac8I GCNNGC 4 cut(s) 520, 556, 593, 690
CaiI CAGNNNCTG 2 cut(s) 947, 1492
CciI TCATGA 1 cut(s) 1321
Cfr13I GGNCC 2 cut(s) 17, 280
CseI GACGC 2 cut(s) 77, 1245
Csp6I GTAC 5 cut(s) 111, 766, 866, 1336, 1430
CspCI CAANNNNNGTGG 2 cut(s) 568, 603
CviAII CATG 9 cut(s) 65, 85, 257, 444, 694, 721, 926, 1031, 1322
CviQI GTAC 5 cut(s) 111, 766, 866, 1336, 1430
DdeI CTNAG 7 cut(s) 21, 183, 531, 985, 1265, 1356, 1467
DpnI GATC 2 cut(s) 69, 882
DpnII GATC 2 cut(s) 67, 880
DraI TTTAAA 1 cut(s) 1122
DraIII CACNNNGTG 1 cut(s) 322
Eam1104I CTCTTC 3 cut(s) 537, 772, 924
EarI CTCTTC 3 cut(s) 537, 772, 924
Ecl136II GAGCTC 1 cut(s) 413
Eco147I AGGCCT 1 cut(s) 688
Eco24I GRGCYC 1 cut(s) 415
Eco31I GGTCTC 1 cut(s) 1463
Eco32I GATATC 1 cut(s) 1282
Eco47I GGWCC 1 cut(s) 17
Eco53kI GAGCTC 1 cut(s) 413
Eco57I CTGAAG 1 cut(s) 100
Eco81I CCTNAGG 1 cut(s) 183
Eco91I GGTNACC 1 cut(s) 125
EcoICRI GAGCTC 1 cut(s) 413
EcoO65I GGTNACC 1 cut(s) 125
EcoRII CCWGG 4 cut(s) 347, 415, 1259, 1286
EcoRV GATATC 1 cut(s) 1282
EcoT38I GRGCYC 1 cut(s) 415
FaeI CATG 9 cut(s) 68, 88, 260, 447, 697, 724, 929, 1034, 1325
FalI AAGNNNNNCTT 4 cut(s) 621, 653, 1129, 1161
FaqI GGGAC 2 cut(s) 18, 340
FatI CATG 9 cut(s) 64, 84, 256, 443, 693, 720, 925, 1030, 1321
FbaI TGATCA 1 cut(s) 880
Fnu4HI GCNGC 4 cut(s) 339, 642, 1381, 1499
FokI GGATG 4 cut(s) 364, 884, 1056, 1461
FriOI GRGCYC 1 cut(s) 415
Fsp4HI GCNGC 4 cut(s) 339, 642, 1381, 1499
FspBI CTAG 5 cut(s) 72, 101, 284, 615, 783
GluI GCNGC 4 cut(s) 339, 642, 1381, 1499
GsaI CCCAGC 1 cut(s) 281
GsuI CTGGAG 1 cut(s) 1068
HaeIII GGCC 4 cut(s) 282, 595, 688, 820
HapII CCGG 2 cut(s) 44, 821
HgaI GACGC 2 cut(s) 77, 1245
Hin1II CATG 9 cut(s) 68, 88, 260, 447, 697, 724, 929, 1034, 1325
HincII GTYRAC 2 cut(s) 671, 845
HindII GTYRAC 2 cut(s) 671, 845
HindIII AAGCTT 1 cut(s) 1365
HinfI GANTC 2 cut(s) 178, 787
HpaII CCGG 2 cut(s) 44, 821
HphI GGTGA 3 cut(s) 137, 983, 1276
Hpy166II GTNNAC 4 cut(s) 671, 845, 974, 1338
Hpy188I TCNGA 3 cut(s) 235, 476, 988
Hpy188III TCNNGA 5 cut(s) 182, 941, 1036, 1084, 1322
Hpy8I GTNNAC 4 cut(s) 671, 845, 974, 1338
HpyAV CCTTC 3 cut(s) 124, 899, 1083
HpyCH4III ACNGT 4 cut(s) 584, 957, 1174, 1494
HpyF10VI GCNNNNNNNGC 4 cut(s) 344, 638, 1142, 1495
HpyF3I CTNAG 7 cut(s) 21, 183, 531, 985, 1265, 1356, 1467
Hsp92II CATG 9 cut(s) 68, 88, 260, 447, 697, 724, 929, 1034, 1325
Ksp22I TGATCA 1 cut(s) 880
Kzo9I GATC 2 cut(s) 67, 880
LguI GCTCTTC 1 cut(s) 772
LmnI GCTCC 4 cut(s) 418, 718, 1049, 1253
Lsp1109I GCAGC 4 cut(s) 350, 653, 1367, 1510
LweI GCATC 1 cut(s) 1299
MaeI CTAG 5 cut(s) 72, 101, 284, 615, 783
MaeIII GTNAC 5 cut(s) 125, 314, 740, 957, 1168
MalI GATC 2 cut(s) 69, 882
MboI GATC 2 cut(s) 67, 880
MboII GAAGA 5 cut(s) 554, 789, 818, 941, 1318
MfeI CAATTG 1 cut(s) 1433
MhlI GDGCHC 2 cut(s) 415, 1442
MmeI TCCRAC 1 cut(s) 603
MseI TTAA 6 cut(s) 296, 1001, 1014, 1113, 1121, 1148
MslI CAYNNNNRTG 2 cut(s) 12, 860
MspA1I CMGCKG 2 cut(s) 1380, 1466
MspI CCGG 2 cut(s) 44, 821
MspR9I CCNGG 6 cut(s) 44, 349, 417, 822, 1261, 1288
MunI CAATTG 1 cut(s) 1433
MvaI CCWGG 4 cut(s) 349, 417, 1261, 1288
MwoI GCNNNNNNNGC 4 cut(s) 344, 638, 1142, 1495
NciI CCSGG 2 cut(s) 44, 822
NdeII GATC 2 cut(s) 67, 880
NlaIII CATG 9 cut(s) 68, 88, 260, 447, 697, 724, 929, 1034, 1325
NlaIV GGNNCC 1 cut(s) 1051
NmuCI GTSAC 2 cut(s) 125, 314
NspI RCATGY 1 cut(s) 1034
PagI TCATGA 1 cut(s) 1321
PceI AGGCCT 1 cut(s) 688
PciSI GCTCTTC 1 cut(s) 772
PfeI GAWTC 2 cut(s) 178, 787
PfoI TCCNGGA 1 cut(s) 415
PkrI GCNGC 4 cut(s) 340, 643, 1382, 1500
PshBI ATTAAT 1 cut(s) 296
Psp124BI GAGCTC 1 cut(s) 415
Psp6I CCWGG 4 cut(s) 347, 415, 1259, 1286
PspEI GGTNACC 1 cut(s) 125
PspFI CCCAGC 1 cut(s) 277
PspGI CCWGG 4 cut(s) 347, 415, 1259, 1286
PspN4I GGNNCC 1 cut(s) 1051
PspPI GGNCC 2 cut(s) 17, 280
PsrI GAACNNNNNNTAC 2 cut(s) 936, 968
PstNI CAGNNNCTG 2 cut(s) 947, 1492
PvuII CAGCTG 2 cut(s) 1380, 1466
RsaI GTAC 5 cut(s) 112, 767, 867, 1337, 1431
RsaNI GTAC 5 cut(s) 111, 766, 866, 1336, 1430
RseI CAYNNNNRTG 2 cut(s) 12, 860
SacI GAGCTC 1 cut(s) 415
SapI GCTCTTC 1 cut(s) 772
SaqAI TTAA 6 cut(s) 296, 1001, 1014, 1113, 1121, 1148
SatI GCNGC 4 cut(s) 339, 642, 1381, 1499
Sau3AI GATC 2 cut(s) 67, 880
Sau96I GGNCC 2 cut(s) 17, 280
ScrFI CCNGG 6 cut(s) 44, 349, 417, 822, 1261, 1288
SduI GDGCHC 2 cut(s) 415, 1442
SfaNI GCATC 1 cut(s) 1299
SinI GGWCC 1 cut(s) 17
SmiMI CAYNNNNRTG 2 cut(s) 12, 860
SmlI CTYRAG 3 cut(s) 756, 1082, 1362
SmoI CTYRAG 3 cut(s) 756, 1082, 1362
SpeI ACTAGT 1 cut(s) 614
SseBI AGGCCT 1 cut(s) 688
SspMI CTAG 5 cut(s) 72, 101, 284, 615, 783
SstI GAGCTC 1 cut(s) 415
StuI AGGCCT 1 cut(s) 688
StyD4I CCNGG 6 cut(s) 42, 347, 415, 820, 1259, 1286
TaaI ACNGT 4 cut(s) 584, 957, 1174, 1494
TatI WGTACW 1 cut(s) 1335
TfiI GAWTC 2 cut(s) 178, 787
Tru1I TTAA 6 cut(s) 296, 1001, 1014, 1113, 1121, 1148
Tru9I TTAA 6 cut(s) 296, 1001, 1014, 1113, 1121, 1148
TscAI CASTG 4 cut(s) 124, 797, 1179, 1428
TseFI GTSAC 2 cut(s) 125, 314
TseI GCWGC 4 cut(s) 338, 641, 1380, 1498
Tsp45I GTSAC 2 cut(s) 125, 314
TspDTI ATGAA 9 cut(s) 110, 528, 555, 918, 942, 1058, 1196, 1319, 1338
TspRI CASTG 4 cut(s) 124, 797, 1179, 1428
VpaK11BI GGWCC 1 cut(s) 17
VspI ATTAAT 1 cut(s) 296
XapI RAATTY 3 cut(s) 167, 936, 1291
XceI RCATGY 1 cut(s) 1034
XspI CTAG 5 cut(s) 72, 101, 284, 615, 783
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.