RchiOBHm_Chr5g0021471

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0000756
Physical Location & Seq
Reverse (-)
15664953 .. 15667224
2272 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ30152

Sequence Viewer

Length: 1173 bp
ATGACAACCACTCCAATACTTGCACTCCCTGATTTTTCAAAGGAATTCACTGTGGAGTGTGATGCTTCTGGTCATGGTTTGGGAGCAGTTTTGTCTCAAGAGGGACATCCCATTGCTTATCTCAGTAAGACTTTGGCTCCGAAACATCTCGCATTAAGTGTTTACGACAAAGAGATGATGGCAGTGGTGTTTGCGGTTCAGCATTGGAGGCCTTACTTGTTAGGACACCGTTTCAAGATCCTCACTGATCATAGGACTATCCAATACTTTCTCAACCAAAGAATCACTACGCCGGCACAACAAAAGTGGTTGCTCAAATTGTTAGGATATGACTACAGTATTGCTTATAGAGCTGGACCCCAAAATATTGTTCCTGATGCACTTTCAAGACAAGCTGAGCTCAATTCTTTGATGGGAATTTCAAGTCCTGTCATGGACTTCATGAAGGAAATTGCTGCTATATGTCATACTCATCCTGACACCATAAAAGTAGTGAGTGACATTGAGAACGGTACTTCTTCACAAAAGAATTTCACTATCATGAATGGTCAGTTGATGTATAAGAAGAGATTCTTTGTCCCAAATGTTGATGATTGGAGAGTCAAGATAATCAAGGAACTGCATTGTGGGAAAGAAGGGGGTCATTCAGGATGGTTGAGAACCTACAAAAGGATCTCAAGGAGTTTTTTGTGGCCTGGTATTAAGAAACAAGTGAAAACCTTTGTTTCCGAGTGTATGGTTTGTCAACAAGTCCACTATGAAACTATAGCACCTCCTGGCCTACTTCAACCTAATCCCATTCCTTCTGGTTTTTGGACTGACATATCAATGGACTTCATCGATGGTCTTCCTCGAGTTGCAGGTAAGGATTCTATTTTGGTTGTTGTGGACAGATTAACTAAATATGGACATTTTGTTGCTCTTAGCCATCCTTATACTGCAAGGTCTGTGGCTGAATCCTTTATCAAAGAAATATTTAGATTGCATGGAATGCCGGAAAATATCATCAGTGACAGAGATCCTATTTTTCTGAGTGCTTTCTGGAAGGATTTCTTTGAATTGCAGGGTTCTAAGCTTTGTATGAGCACGTCCTACCATCCTCAAACTGATGGCCAGACAGAGTGTCTAAACAGAGTCTTAGAGCAATATCTCAGGTGCGTAATATGTGAGTAG
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

390

Amino Acids

44.39

Weight (kDa)

8.46

Isoelectric Point (pI)

40.24

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RT_RNaseH_2 PF17919 1 - 80 4.6e-26 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 11 - 110 1.4e-31 RNase H-like domain found in reverse transcriptase
Integrase_H2C2 PF17921 199 - 251 1.3e-16 Integrase zinc binding 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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 851
AciI CCGC 1 cut(s) 194
AclWI GGATC 3 cut(s) 232, 680, 1013
AcoI YGGCCR 1 cut(s) 1111
AcsI RAATTY 3 cut(s) 44, 417, 529
AfaI GTAC 1 cut(s) 514
AfiI CCNNNNNNNGG 1 cut(s) 669
AgsI TTSAA 6 cut(s) 39, 235, 387, 423, 788, 1058
AhdI GACNNNNNGTC 1 cut(s) 1122
AjiI CACGTC 1 cut(s) 1089
AjnI CCWGG 2 cut(s) 694, 775
AjuI GAANNNNNNNTTGG 2 cut(s) 354, 386
AluBI AGCT 4 cut(s) 353, 395, 400, 1075
AluI AGCT 4 cut(s) 353, 395, 400, 1075
Alw21I GWGCWC 2 cut(s) 402, 1088
Alw26I GTCTC 1 cut(s) 99
AlwI GGATC 3 cut(s) 232, 680, 1013
Ama87I CYCGRG 1 cut(s) 852
AoxI GGCC 4 cut(s) 209, 692, 778, 1111
ApeKI GCWGC 1 cut(s) 455
ApoI RAATTY 3 cut(s) 44, 417, 529
Asp700I GAANNNNTTC 2 cut(s) 569, 1049
AspS9I GGNCC 1 cut(s) 356
AvaI CYCGRG 1 cut(s) 852
AvaII GGWCC 1 cut(s) 356
BalI TGGCCA 1 cut(s) 1113
BanII GRGCYC 1 cut(s) 402
BbsI GAAGAC 1 cut(s) 839
Bbv12I GWGCWC 2 cut(s) 402, 1088
BbvI GCAGC 1 cut(s) 442
BccI CCATC 7 cut(s) 172, 406, 645, 836, 936, 1103, 1104
BciT130I CCWGG 2 cut(s) 696, 777
BclI TGATCA 1 cut(s) 247
BcoDI GTCTC 1 cut(s) 99
BfmI CTRYAG 2 cut(s) 334, 765
BfuAI ACCTGC 1 cut(s) 851
BisI GCNGC 1 cut(s) 456
BlpI GCTNAGC 1 cut(s) 396
BlsI GCNGC 1 cut(s) 457
Bme1390I CCNGG 2 cut(s) 696, 777
Bme18I GGWCC 1 cut(s) 356
BmeRI GACNNNNNGTC 1 cut(s) 1122
BmeT110I CYCGRG 1 cut(s) 852
BmgBI CACGTC 1 cut(s) 1089
BmgT120I GGNCC 1 cut(s) 356
BmiI GGNNCC 2 cut(s) 138, 358
BmrFI CCNGG 2 cut(s) 696, 777
BmsI GCATC 2 cut(s) 52, 367
BpiI GAAGAC 1 cut(s) 839
Bpu1102I GCTNAGC 1 cut(s) 396
BpuEI CTTGAG 2 cut(s) 81, 661
Bsa29I ATCGAT 1 cut(s) 840
BsaXI ACNNNNNCTCC 5 cut(s) 9, 25, 39, 121, 151
Bsc4I CCNNNNNNNGG 1 cut(s) 669
Bse118I RCCGGY 1 cut(s) 292
Bse3DI GCAATG 1 cut(s) 111
BseBI CCWGG 2 cut(s) 696, 777
BseCI ATCGAT 1 cut(s) 840
BseGI GGATG 5 cut(s) 106, 472, 656, 928, 1096
BseLI CCNNNNNNNGG 1 cut(s) 669
BseMI GCAATG 1 cut(s) 111
BseMII CTCAG 4 cut(s) 136, 387, 1022, 1165
BseXI GCAGC 1 cut(s) 442
BshFI GGCC 4 cut(s) 211, 694, 780, 1113
BshVI ATCGAT 1 cut(s) 840
BsiHKAI GWGCWC 2 cut(s) 402, 1088
BsiHKCI CYCGRG 1 cut(s) 852
BsiSI CCGG 2 cut(s) 293, 995
BslFI GGGAC 2 cut(s) 117, 563
BslI CCNNNNNNNGG 1 cut(s) 669
BsmAI GTCTC 1 cut(s) 99
BsmFI GGGAC 2 cut(s) 117, 563
BsmI GAATGC 1 cut(s) 996
BsnI GGCC 4 cut(s) 211, 694, 780, 1113
BsoBI CYCGRG 1 cut(s) 852
Bsp1286I GDGCHC 2 cut(s) 402, 1088
Bsp143I GATC 4 cut(s) 237, 247, 672, 1018
Bsp1720I GCTNAGC 1 cut(s) 396
BspACI CCGC 1 cut(s) 194
BspANI GGCC 4 cut(s) 211, 694, 780, 1113
BspCNI CTCAG 4 cut(s) 135, 388, 1023, 1164
BspDI ATCGAT 1 cut(s) 840
BspHI TCATGA 2 cut(s) 441, 540
BspLI GGNNCC 2 cut(s) 138, 358
BspMI ACCTGC 1 cut(s) 851
BspPI GGATC 3 cut(s) 232, 680, 1013
BsrDI GCAATG 1 cut(s) 111
BsrFI RCCGGY 1 cut(s) 292
BssAI RCCGGY 1 cut(s) 292
BssMI GATC 4 cut(s) 237, 247, 672, 1018
Bst2UI CCWGG 2 cut(s) 696, 777
Bst4CI ACNGT 4 cut(s) 52, 230, 338, 512
Bst6I CTCTTC 1 cut(s) 560
BstAPI GCANNNNNTGC 1 cut(s) 991
BstC8I GCNNGC 1 cut(s) 294
BstDEI CTNAG 7 cut(s) 122, 396, 923, 1031, 1071, 1138, 1151
BstENI CCTNNNNNAGG 1 cut(s) 667
BstF5I GGATG 5 cut(s) 106, 472, 656, 928, 1096
BstKTI GATC 4 cut(s) 240, 250, 675, 1021
BstMAI GTCTC 1 cut(s) 99
BstMBI GATC 4 cut(s) 237, 247, 672, 1018
BstMWI GCNNNNNNNGC 3 cut(s) 208, 350, 991
BstNI CCWGG 2 cut(s) 696, 777
BstSCI CCNGG 2 cut(s) 694, 775
BstSFI CTRYAG 2 cut(s) 334, 765
BstV1I GCAGC 1 cut(s) 442
BstV2I GAAGAC 1 cut(s) 839
BstX2I RGATCY 3 cut(s) 237, 672, 1018
BstYI RGATCY 3 cut(s) 237, 672, 1018
Bsu15I ATCGAT 1 cut(s) 840
BsuRI GGCC 4 cut(s) 211, 694, 780, 1113
BsuTUI ATCGAT 1 cut(s) 840
BtrI CACGTC 1 cut(s) 1089
BtsCI GGATG 5 cut(s) 106, 472, 656, 928, 1096
BtsI GCAGTG 1 cut(s) 189
BtsIMutI CAGTG 4 cut(s) 48, 189, 243, 1015
BveI ACCTGC 1 cut(s) 851
Cac8I GCNNGC 1 cut(s) 294
CciI TCATGA 2 cut(s) 441, 540
Cfr10I RCCGGY 1 cut(s) 292
Cfr13I GGNCC 1 cut(s) 356
ClaI ATCGAT 1 cut(s) 840
Csp6I GTAC 1 cut(s) 513
CspCI CAANNNNNGTGG 4 cut(s) 287, 322, 930, 965
CviAII CATG 5 cut(s) 74, 433, 442, 541, 986
CviQI GTAC 1 cut(s) 513
DdeI CTNAG 7 cut(s) 122, 396, 923, 1031, 1071, 1138, 1151
DpnI GATC 4 cut(s) 239, 249, 674, 1020
DpnII GATC 4 cut(s) 237, 247, 672, 1018
DriI GACNNNNNGTC 1 cut(s) 1122
EaeI YGGCCR 1 cut(s) 1111
Eam1104I CTCTTC 1 cut(s) 560
Eam1105I GACNNNNNGTC 1 cut(s) 1122
EarI CTCTTC 1 cut(s) 560
Ecl136II GAGCTC 1 cut(s) 400
Eco147I AGGCCT 1 cut(s) 211
Eco24I GRGCYC 1 cut(s) 402
Eco47I GGWCC 1 cut(s) 356
Eco53kI GAGCTC 1 cut(s) 400
Eco88I CYCGRG 1 cut(s) 852
EcoICRI GAGCTC 1 cut(s) 400
EcoNI CCTNNNNNAGG 1 cut(s) 667
EcoRI GAATTC 1 cut(s) 44
EcoRII CCWGG 2 cut(s) 694, 775
EcoT38I GRGCYC 1 cut(s) 402
FaeI CATG 5 cut(s) 77, 436, 445, 544, 989
FalI AAGNNNNNCTT 4 cut(s) 557, 589, 1037, 1069
FaqI GGGAC 2 cut(s) 117, 563
FatI CATG 5 cut(s) 73, 432, 441, 540, 985
FbaI TGATCA 1 cut(s) 247
Fnu4HI GCNGC 1 cut(s) 456
FokI GGATG 5 cut(s) 93, 459, 663, 915, 1083
FriOI GRGCYC 1 cut(s) 402
Fsp4HI GCNGC 1 cut(s) 456
GluI GCNGC 1 cut(s) 456
HaeIII GGCC 4 cut(s) 211, 694, 780, 1113
HapII CCGG 2 cut(s) 293, 995
Hin1II CATG 5 cut(s) 77, 436, 445, 544, 989
HincII GTYRAC 1 cut(s) 746
HindII GTYRAC 1 cut(s) 746
HindIII AAGCTT 1 cut(s) 1073
HinfI GANTC 6 cut(s) 282, 570, 600, 869, 956, 1134
HpaII CCGG 2 cut(s) 293, 995
Hpy166II GTNNAC 4 cut(s) 163, 746, 754, 889
Hpy188I TCNGA 3 cut(s) 141, 730, 1032
Hpy8I GTNNAC 4 cut(s) 163, 746, 754, 889
HpyAV CCTTC 4 cut(s) 439, 629, 813, 1039
HpyCH4III ACNGT 4 cut(s) 52, 230, 338, 512
HpyCH4IV ACGT 1 cut(s) 1088
HpyCH4V TGCA 7 cut(s) 23, 380, 622, 860, 941, 985, 1063
HpyF10VI GCNNNNNNNGC 3 cut(s) 208, 350, 991
HpyF3I CTNAG 7 cut(s) 122, 396, 923, 1031, 1071, 1138, 1151
HpySE526I ACGT 1 cut(s) 1088
Hsp92II CATG 5 cut(s) 77, 436, 445, 544, 989
KroI GCCGGC 1 cut(s) 292
KroNI GCCGGC 1 cut(s) 294
Ksp22I TGATCA 1 cut(s) 247
Kzo9I GATC 4 cut(s) 237, 247, 672, 1018
LmnI GCTCC 2 cut(s) 83, 142
Lsp1109I GCAGC 1 cut(s) 442
LweI GCATC 2 cut(s) 52, 367
MaeII ACGT 1 cut(s) 1088
MaeIII GTNAC 2 cut(s) 497, 1010
MalI GATC 4 cut(s) 239, 249, 674, 1020
MboI GATC 4 cut(s) 237, 247, 672, 1018
MboII GAAGA 3 cut(s) 510, 577, 839
MflI RGATCY 3 cut(s) 237, 672, 1018
MhlI GDGCHC 2 cut(s) 402, 1088
MlsI TGGCCA 1 cut(s) 1113
MluCI AATT 7 cut(s) 44, 317, 403, 417, 450, 529, 1058
MluNI TGGCCA 1 cut(s) 1113
MlyI GAGTC 2 cut(s) 609, 1143
MnlI CCTC 6 cut(s) 94, 201, 251, 783, 861, 1110
Mox20I TGGCCA 1 cut(s) 1113
MroNI GCCGGC 1 cut(s) 292
MroXI GAANNNNTTC 2 cut(s) 569, 1049
MscI TGGCCA 1 cut(s) 1113
MseI TTAA 3 cut(s) 155, 702, 896
MslI CAYNNNNRTG 2 cut(s) 539, 827
Msp20I TGGCCA 1 cut(s) 1113
MspI CCGG 2 cut(s) 293, 995
MspR9I CCNGG 2 cut(s) 696, 777
Mva1269I GAATGC 1 cut(s) 996
MvaI CCWGG 2 cut(s) 696, 777
MwoI GCNNNNNNNGC 3 cut(s) 208, 350, 991
NaeI GCCGGC 1 cut(s) 294
NdeII GATC 4 cut(s) 237, 247, 672, 1018
NgoMIV GCCGGC 1 cut(s) 292
NlaIII CATG 5 cut(s) 77, 436, 445, 544, 989
NlaIV GGNNCC 2 cut(s) 138, 358
NmuCI GTSAC 2 cut(s) 497, 1010
PaeR7I CTCGAG 1 cut(s) 852
PagI TCATGA 2 cut(s) 441, 540
PceI AGGCCT 1 cut(s) 211
PctI GAATGC 1 cut(s) 996
PdiI GCCGGC 1 cut(s) 294
PdmI GAANNNNTTC 2 cut(s) 569, 1049
PfeI GAWTC 4 cut(s) 282, 570, 869, 956
PkrI GCNGC 1 cut(s) 457
PleI GAGTC 2 cut(s) 608, 1142
PpsI GAGTC 2 cut(s) 608, 1142
Psp124BI GAGCTC 1 cut(s) 402
Psp6I CCWGG 2 cut(s) 694, 775
PspGI CCWGG 2 cut(s) 694, 775
PspN4I GGNNCC 2 cut(s) 138, 358
PspPI GGNCC 1 cut(s) 356
PspXI VCTCGAGB 1 cut(s) 852
PsuI RGATCY 3 cut(s) 237, 672, 1018
RsaI GTAC 1 cut(s) 514
RsaNI GTAC 1 cut(s) 513
RseI CAYNNNNRTG 2 cut(s) 539, 827
SacI GAGCTC 1 cut(s) 402
SaqAI TTAA 3 cut(s) 155, 702, 896
SatI GCNGC 1 cut(s) 456
Sau3AI GATC 4 cut(s) 237, 247, 672, 1018
Sau96I GGNCC 1 cut(s) 356
SchI GAGTC 2 cut(s) 609, 1143
ScrFI CCNGG 2 cut(s) 696, 777
SduI GDGCHC 2 cut(s) 402, 1088
SfaNI GCATC 2 cut(s) 52, 367
SfcI CTRYAG 2 cut(s) 334, 765
Sfr274I CTCGAG 1 cut(s) 852
SinI GGWCC 1 cut(s) 356
SlaI CTCGAG 1 cut(s) 852
SmiMI CAYNNNNRTG 2 cut(s) 539, 827
SmlI CTYRAG 3 cut(s) 96, 676, 852
SmoI CTYRAG 3 cut(s) 96, 676, 852
Sse9I AATT 7 cut(s) 44, 317, 403, 417, 450, 529, 1058
SseBI AGGCCT 1 cut(s) 211
SsiI CCGC 1 cut(s) 194
SspI AATATT 2 cut(s) 367, 975
SstI GAGCTC 1 cut(s) 402
StuI AGGCCT 1 cut(s) 211
StyD4I CCNGG 2 cut(s) 694, 775
TaaI ACNGT 4 cut(s) 52, 230, 338, 512
TaiI ACGT 1 cut(s) 1091
TaqI TCGA 2 cut(s) 840, 853
TasI AATT 7 cut(s) 44, 317, 403, 417, 450, 529, 1058
TfiI GAWTC 4 cut(s) 282, 570, 869, 956
Tru1I TTAA 3 cut(s) 155, 702, 896
Tru9I TTAA 3 cut(s) 155, 702, 896
TscAI CASTG 4 cut(s) 55, 189, 250, 1015
TseFI GTSAC 2 cut(s) 497, 1010
TseI GCWGC 1 cut(s) 455
Tsp45I GTSAC 2 cut(s) 497, 1010
TspDTI ATGAA 5 cut(s) 430, 458, 557, 774, 826
TspRI CASTG 4 cut(s) 55, 189, 250, 1015
VpaK11BI GGWCC 1 cut(s) 356
XagI CCTNNNNNAGG 1 cut(s) 667
XapI RAATTY 3 cut(s) 44, 417, 529
XhoI CTCGAG 1 cut(s) 852
XmnI GAANNNNTTC 2 cut(s) 569, 1049
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.