Rroxscaffold_6G00402930

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000006
OG0000756
Physical Location & Seq
Forward (+)
25398445 .. 25403939
5495 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_6G00402930.1

Sequence Viewer

Length: 1170 bp
ATGAATTATCCATCACCTCAACCATACCCTTTCCACATTTTGCCTCTAAACATGTATCACACCATGCCTTACCTGACACCTTACCCATCACAAATGCCTCATGTGGATCCCAACCTTCCAACTATGAAGCAGATGCGGCGGCTTGAATTCAGTGTGTTCAGTGGAGGGGATCCAGTTGAATGGTTAAACAAGGCTGAACAGTACTTTGAGTTCTATCAAATTCCGGAGGAAAGAAAACTGTCCATAGCTACCATGCATCTGTCCGACAAGGCCTCAGATCGATGGTATATATTCCGGCACGAGTTTCCCCATACTTGGCAAGGGTTAGCAAACCTACTCATGAGGGAATTTAATGGATACAATCGGTCAGAGTATCAGGCAGCCTTGGCAAGAATGTCACAAACCGGCAGTGTGGAGAACTACAAGGAACAATTCACCAAGTTATCAAGGAGAGCCCCTGGTTTTCCTCCTGAGGTGCTACTATCTTGCTTCATCGGGGGACTCAAGGAGGACATCCTGGTATATGTTCAAGCTCAAAAGCCTCGGACACTATATGAGGCTTGTGAATTAGCCAGAGTATATGAGACCAGGAATGAAAGTCATAGGCACTTTGCTAGGCCTTCTAACCATCCCAGGCCTACTAGTGGTTTCCATTCTACTACACCACAGAAAGTTTCAAACCAGGGTCAACGATTTCAGAACCATTCTACTGCAAGAACTCTGCATGCTCCAACTCCTCATGGGGGCAGACGATTATCTCAAGTTGAGTACCAAGATCGGCGAGCCAAGATTCAGTGCTTCTTTTGTGAGGAGCCCTATAAACCAGGACATAATTGCCGGAAGGGCCAGTTGATGATTATGGAGGTCACACAAGATGAGGAGGACTTCTTGAGTATAAAAGAGTCCCTTGATCAAGAGGTTCCTCCAATCACTGATATTGAGGAGCCACTGATCCGGTTACACGTCCTGGGAGATGGAAGCTCTAGTCCAGTGACCATGCAATTAAAAGGGATGTTCAATAACAAGATTGTTCATGTGCTCATTGATTCGGGAGCAACACACAACTTCATTCATCCACAGTTATTGAAGAATACGAAAGTACAAGTTTACCAACTTTCACCACTCAATGTCATCCTGGCAAGTGGTGCAAAGATGAAAACCCGAGGGTGA
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

389

Amino Acids

44.98

Weight (kDa)

8.79

Isoelectric Point (pI)

53.75

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 69 - 198 1e-08 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 82 - 170 5.5e-11 Retrotransposon gag protein
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)
AccIII TCCGGA 1 cut(s) 223
AciI CCGC 2 cut(s) 136, 139
AclWI GGATC 5 cut(s) 101, 114, 164, 177, 946
AcsI RAATTY 3 cut(s) 146, 219, 347
AfaI GTAC 3 cut(s) 203, 770, 1101
AfiI CCNNNNNNNGG 3 cut(s) 315, 644, 743
AflIII ACRYGT 2 cut(s) 51, 961
AgsI TTSAA 6 cut(s) 146, 179, 530, 678, 1018, 1087
AhlI ACTAGT 1 cut(s) 641
AjiI CACGTC 1 cut(s) 964
AjnI CCWGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
AluBI AGCT 3 cut(s) 248, 533, 981
AluI AGCT 3 cut(s) 248, 533, 981
Alw21I GWGCWC 1 cut(s) 1041
Alw26I GTCTC 1 cut(s) 578
AlwI GGATC 5 cut(s) 101, 114, 164, 177, 946
Ama87I CYCGRG 1 cut(s) 1161
Aor13HI TCCGGA 1 cut(s) 223
AoxI GGCC 4 cut(s) 270, 617, 635, 844
ApeKI GCWGC 1 cut(s) 380
ApoI RAATTY 3 cut(s) 146, 219, 347
AspS9I GGNCC 1 cut(s) 844
AsuHPI GGTGA 3 cut(s) 6, 427, 1110
AvaI CYCGRG 1 cut(s) 1161
AxyI CCTNAGG 1 cut(s) 471
BamHI GGATCC 2 cut(s) 106, 169
BanII GRGCYC 2 cut(s) 457, 816
BauI CACGAG 1 cut(s) 299
Bbv12I GWGCWC 1 cut(s) 1041
BbvI GCAGC 1 cut(s) 392
BccI CCATC 5 cut(s) 19, 94, 276, 636, 968
BciT130I CCWGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
BciVI GTATCC 1 cut(s) 350
BclI TGATCA 1 cut(s) 910
BcoDI GTCTC 1 cut(s) 578
BcuI ACTAGT 1 cut(s) 641
BfaI CTAG 3 cut(s) 615, 642, 984
BfuI GTATCC 1 cut(s) 350
BglI GCCNNNNNGGC 1 cut(s) 843
BisI GCNGC 3 cut(s) 137, 140, 381
BlsI GCNGC 3 cut(s) 138, 141, 382
BmcAI AGTACT 1 cut(s) 203
Bme1390I CCNGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
BmeT110I CYCGRG 1 cut(s) 1161
BmgBI CACGTC 1 cut(s) 964
BmgT120I GGNCC 1 cut(s) 844
BmiI GGNNCC 5 cut(s) 108, 171, 813, 921, 945
BmrFI CCNGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
BmsI GCATC 2 cut(s) 123, 265
BpuEI CTTGAG 3 cut(s) 488, 744, 910
Bsa29I ATCGAT 1 cut(s) 280
BsaI GGTCTC 1 cut(s) 578
BsaJI CCNNGG 7 cut(s) 384, 457, 542, 632, 682, 967, 1162
BsaWI WCCGGW 2 cut(s) 223, 954
Bsc4I CCNNNNNNNGG 3 cut(s) 315, 644, 743
Bse118I RCCGGY 1 cut(s) 404
Bse1I ACTGG 3 cut(s) 173, 847, 989
Bse21I CCTNAGG 1 cut(s) 471
BseAI TCCGGA 1 cut(s) 223
BseBI CCWGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
BseCI ATCGAT 1 cut(s) 280
BseDI CCNNGG 7 cut(s) 384, 457, 542, 632, 682, 967, 1162
BseGI GGATG 5 cut(s) 513, 628, 1017, 1072, 1131
BseLI CCNNNNNNNGG 3 cut(s) 315, 644, 743
BseMII CTCAG 2 cut(s) 288, 462
BseNI ACTGG 3 cut(s) 173, 847, 989
BseRI GAGGAG 4 cut(s) 726, 824, 893, 956
BseXI GCAGC 1 cut(s) 392
BshFI GGCC 4 cut(s) 272, 619, 637, 846
BshVI ATCGAT 1 cut(s) 280
BsiHKAI GWGCWC 1 cut(s) 1041
BsiHKCI CYCGRG 1 cut(s) 1161
BsiSI CCGG 5 cut(s) 224, 295, 405, 838, 955
BslFI GGGAC 2 cut(s) 513, 889
BslI CCNNNNNNNGG 3 cut(s) 315, 644, 743
BsmAI GTCTC 1 cut(s) 578
BsmFI GGGAC 2 cut(s) 513, 889
BsnI GGCC 4 cut(s) 272, 619, 637, 846
Bso31I GGTCTC 1 cut(s) 578
BsoBI CYCGRG 1 cut(s) 1161
Bsp1286I GDGCHC 3 cut(s) 457, 816, 1041
Bsp13I TCCGGA 1 cut(s) 223
Bsp143I GATC 6 cut(s) 106, 169, 277, 775, 910, 951
BspACI CCGC 2 cut(s) 136, 139
BspANI GGCC 4 cut(s) 272, 619, 637, 846
BspCNI CTCAG 2 cut(s) 287, 463
BspDI ATCGAT 1 cut(s) 280
BspEI TCCGGA 1 cut(s) 223
BspHI TCATGA 1 cut(s) 339
BspLI GGNNCC 5 cut(s) 108, 171, 813, 921, 945
BspPI GGATC 5 cut(s) 101, 114, 164, 177, 946
BspTNI GGTCTC 1 cut(s) 578
BsrFI RCCGGY 1 cut(s) 404
BsrI ACTGG 3 cut(s) 173, 847, 989
BssAI RCCGGY 1 cut(s) 404
BssECI CCNNGG 7 cut(s) 384, 457, 542, 632, 682, 967, 1162
BssMI GATC 6 cut(s) 106, 169, 277, 775, 910, 951
BssSI CACGAG 1 cut(s) 299
BssT1I CCWWGG 1 cut(s) 384
Bst2BI CACGAG 1 cut(s) 299
Bst2UI CCWGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
Bst4CI ACNGT 3 cut(s) 201, 240, 1080
BstAPI GCANNNNNTGC 1 cut(s) 1145
BstC8I GCNNGC 2 cut(s) 726, 783
BstDEI CTNAG 2 cut(s) 274, 471
BstF5I GGATG 5 cut(s) 513, 628, 1017, 1072, 1131
BstKTI GATC 6 cut(s) 109, 172, 280, 778, 913, 954
BstMAI GTCTC 1 cut(s) 578
BstMBI GATC 6 cut(s) 106, 169, 277, 775, 910, 951
BstMWI GCNNNNNNNGC 4 cut(s) 136, 386, 843, 1145
BstNI CCWGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
BstNSI RCATGY 2 cut(s) 55, 728
BstSCI CCNGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
BstV1I GCAGC 1 cut(s) 392
BstX2I RGATCY 2 cut(s) 106, 169
BstXI CCANNNNNNTGG 1 cut(s) 180
BstYI RGATCY 2 cut(s) 106, 169
Bsu15I ATCGAT 1 cut(s) 280
Bsu36I CCTNAGG 1 cut(s) 471
BsuI GTATCC 1 cut(s) 350
BsuRI GGCC 4 cut(s) 272, 619, 637, 846
BsuTUI ATCGAT 1 cut(s) 280
BtrI CACGTC 1 cut(s) 964
BtsCI GGATG 5 cut(s) 513, 628, 1017, 1072, 1131
BtsI GCAGTG 1 cut(s) 415
BtsIMutI CAGTG 7 cut(s) 157, 166, 415, 800, 930, 947, 996
Cac8I GCNNGC 2 cut(s) 726, 783
CciI TCATGA 1 cut(s) 339
Cfr10I RCCGGY 1 cut(s) 404
Cfr13I GGNCC 1 cut(s) 844
ClaI ATCGAT 1 cut(s) 280
Csp6I GTAC 3 cut(s) 202, 769, 1100
CspCI CAANNNNNGTGG 2 cut(s) 1065, 1100
CviAII CATG 9 cut(s) 52, 64, 101, 253, 340, 725, 740, 997, 1034
CviQI GTAC 3 cut(s) 202, 769, 1100
DdeI CTNAG 2 cut(s) 274, 471
DpnI GATC 6 cut(s) 108, 171, 279, 777, 912, 953
DpnII GATC 6 cut(s) 106, 169, 277, 775, 910, 951
Eco130I CCWWGG 1 cut(s) 384
Eco147I AGGCCT 3 cut(s) 272, 619, 637
Eco24I GRGCYC 2 cut(s) 457, 816
Eco31I GGTCTC 1 cut(s) 578
Eco81I CCTNAGG 1 cut(s) 471
Eco88I CYCGRG 1 cut(s) 1161
EcoRI GAATTC 1 cut(s) 146
EcoRII CCWGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
EcoT14I CCWWGG 1 cut(s) 384
EcoT22I ATGCAT 1 cut(s) 258
EcoT38I GRGCYC 2 cut(s) 457, 816
ErhI CCWWGG 1 cut(s) 384
FaeI CATG 9 cut(s) 55, 67, 104, 256, 343, 728, 743, 1000, 1037
FalI AAGNNNNNCTT 2 cut(s) 891, 923
FaqI GGGAC 2 cut(s) 513, 889
FatI CATG 9 cut(s) 51, 63, 100, 252, 339, 724, 739, 996, 1033
FbaI TGATCA 1 cut(s) 910
Fnu4HI GCNGC 3 cut(s) 137, 140, 381
FokI GGATG 5 cut(s) 500, 615, 1024, 1059, 1118
FriOI GRGCYC 2 cut(s) 457, 816
Fsp4HI GCNGC 3 cut(s) 137, 140, 381
FspBI CTAG 3 cut(s) 615, 642, 984
GluI GCNGC 3 cut(s) 137, 140, 381
HaeIII GGCC 4 cut(s) 272, 619, 637, 846
HapII CCGG 5 cut(s) 224, 295, 405, 838, 955
Hin1II CATG 9 cut(s) 55, 67, 104, 256, 343, 728, 743, 1000, 1037
HincII GTYRAC 1 cut(s) 689
HindII GTYRAC 1 cut(s) 689
HinfI GANTC 4 cut(s) 501, 790, 902, 1046
HpaII CCGG 5 cut(s) 224, 295, 405, 838, 955
HphI GGTGA 3 cut(s) 6, 427, 1110
Hpy166II GTNNAC 2 cut(s) 689, 1108
Hpy188I TCNGA 5 cut(s) 265, 277, 370, 546, 699
Hpy188III TCNNGA 6 cut(s) 224, 340, 470, 889, 914, 1050
Hpy8I GTNNAC 2 cut(s) 689, 1108
HpyAV CCTTC 3 cut(s) 125, 630, 835
HpyCH4III ACNGT 3 cut(s) 201, 240, 1080
HpyCH4IV ACGT 1 cut(s) 963
HpyCH4V TGCA 5 cut(s) 256, 713, 724, 1000, 1148
HpyF10VI GCNNNNNNNGC 4 cut(s) 136, 386, 843, 1145
HpyF3I CTNAG 2 cut(s) 274, 471
HpySE526I ACGT 1 cut(s) 963
Hsp92II CATG 9 cut(s) 55, 67, 104, 256, 343, 728, 743, 1000, 1037
Kpn2I TCCGGA 1 cut(s) 223
Ksp22I TGATCA 1 cut(s) 910
Kzo9I GATC 6 cut(s) 106, 169, 277, 775, 910, 951
LmnI GCTCC 4 cut(s) 733, 811, 943, 1052
Lsp1109I GCAGC 1 cut(s) 392
LweI GCATC 2 cut(s) 123, 265
MaeI CTAG 3 cut(s) 615, 642, 984
MaeII ACGT 1 cut(s) 963
MaeIII GTNAC 4 cut(s) 396, 865, 957, 991
MalI GATC 6 cut(s) 108, 171, 279, 777, 912, 953
MboI GATC 6 cut(s) 106, 169, 277, 775, 910, 951
MboII GAAGA 1 cut(s) 1099
MflI RGATCY 2 cut(s) 106, 169
MhlI GDGCHC 3 cut(s) 457, 816, 1041
MluCI AATT 8 cut(s) 4, 146, 219, 347, 431, 566, 832, 1001
MlyI GAGTC 2 cut(s) 495, 911
MmeI TCCRAC 3 cut(s) 143, 288, 755
Mph1103I ATGCAT 1 cut(s) 258
MroI TCCGGA 1 cut(s) 223
MseI TTAA 3 cut(s) 185, 351, 1004
MspI CCGG 5 cut(s) 224, 295, 405, 838, 955
MspR9I CCNGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
MvaI CCWGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
MwoI GCNNNNNNNGC 4 cut(s) 136, 386, 843, 1145
NdeII GATC 6 cut(s) 106, 169, 277, 775, 910, 951
NlaIII CATG 9 cut(s) 55, 67, 104, 256, 343, 728, 743, 1000, 1037
NlaIV GGNNCC 5 cut(s) 108, 171, 813, 921, 945
NmuCI GTSAC 3 cut(s) 396, 865, 991
NsiI ATGCAT 1 cut(s) 258
NspI RCATGY 2 cut(s) 55, 728
PaeI GCATGC 1 cut(s) 728
PagI TCATGA 1 cut(s) 339
PceI AGGCCT 3 cut(s) 272, 619, 637
PciI ACATGT 1 cut(s) 51
PfeI GAWTC 2 cut(s) 790, 1046
PkrI GCNGC 3 cut(s) 138, 141, 382
PleI GAGTC 2 cut(s) 495, 910
PpsI GAGTC 2 cut(s) 495, 910
PscI ACATGT 1 cut(s) 51
Psp6I CCWGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
PspGI CCWGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
PspN4I GGNNCC 5 cut(s) 108, 171, 813, 921, 945
PspPI GGNCC 1 cut(s) 844
PsrI GAACNNNNNNTAC 2 cut(s) 194, 226
PsuI RGATCY 2 cut(s) 106, 169
RsaI GTAC 3 cut(s) 203, 770, 1101
RsaNI GTAC 3 cut(s) 202, 769, 1100
SaqAI TTAA 3 cut(s) 185, 351, 1004
SatI GCNGC 3 cut(s) 137, 140, 381
Sau3AI GATC 6 cut(s) 106, 169, 277, 775, 910, 951
Sau96I GGNCC 1 cut(s) 844
ScaI AGTACT 1 cut(s) 203
SchI GAGTC 2 cut(s) 495, 911
ScrFI CCNGG 8 cut(s) 459, 518, 589, 634, 683, 825, 968, 1136
SduI GDGCHC 3 cut(s) 457, 816, 1041
SfaNI GCATC 2 cut(s) 123, 265
SmlI CTYRAG 3 cut(s) 503, 759, 889
SmoI CTYRAG 3 cut(s) 503, 759, 889
SpeI ACTAGT 1 cut(s) 641
SphI GCATGC 1 cut(s) 728
Sse9I AATT 8 cut(s) 4, 146, 219, 347, 431, 566, 832, 1001
SseBI AGGCCT 3 cut(s) 272, 619, 637
SsiI CCGC 2 cut(s) 136, 139
SspMI CTAG 3 cut(s) 615, 642, 984
StuI AGGCCT 3 cut(s) 272, 619, 637
StyD4I CCNGG 8 cut(s) 457, 516, 587, 632, 681, 823, 966, 1134
StyI CCWWGG 1 cut(s) 384
TaaI ACNGT 3 cut(s) 201, 240, 1080
TaiI ACGT 1 cut(s) 966
TaqI TCGA 1 cut(s) 280
TaqII GACCGA 1 cut(s) 354
TasI AATT 8 cut(s) 4, 146, 219, 347, 431, 566, 832, 1001
TatI WGTACW 2 cut(s) 201, 1099
TauI GCSGC 2 cut(s) 139, 142
TfiI GAWTC 2 cut(s) 790, 1046
Tru1I TTAA 3 cut(s) 185, 351, 1004
Tru9I TTAA 3 cut(s) 185, 351, 1004
TscAI CASTG 7 cut(s) 157, 166, 415, 800, 937, 954, 996
TseFI GTSAC 3 cut(s) 396, 865, 991
TseI GCWGC 1 cut(s) 380
Tsp45I GTSAC 3 cut(s) 396, 865, 991
TspDTI ATGAA 8 cut(s) 17, 140, 481, 609, 1022, 1057, 1061, 1169
TspRI CASTG 7 cut(s) 157, 166, 415, 800, 937, 954, 996
XapI RAATTY 3 cut(s) 146, 219, 347
XceI RCATGY 2 cut(s) 55, 728
XspI CTAG 3 cut(s) 615, 642, 984
ZrmI AGTACT 1 cut(s) 203
Zsp2I ATGCAT 1 cut(s) 258
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.