FvH4_4g12501

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000756
Physical Location & Seq
Forward (+)
16173664 .. 16177267
3604 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g12501.t1

Sequence Viewer

Length: 1338 bp
ATGGCTGGGAAATCGATGAAGATGGCTGGTAAGTTGTCTTCCACTGATCCTCCGGTTTCAGGTGAATTATCACACCTGAAATTTGAGTTTCAAGCTCATAAAGAGGCTACTACAGCTCGTTTTAAGGAATTGCAAGCTTCTTTCCAGAAATCTCTAGATGCTAACCTATTGAGTTACCAGAGTATGCTTGCAGAACAATTTCAGAGGCATATGTCATCCTTAAGACTTGAGTGCAACCACCTTGTTTTAACAAAATCTAGAGCTACTACTATTGCACAACCTAATGGTTCAATACGTTTTGGATCTGTGCCAGTGCCCACTCATGGCATGATTATGTCAGAGAGTTCTTCTTCTGCAGTTTTGGTTAGATCTAAGGGTAACAACACTTCTTCTAATTCTTTAAACCTAGATCTGGATGCTAATGATGTGTTTATGTCCTTGCCTCTTTTATCTGCTAGGCAAAACCCTATTTTGGGTCTAGGTATTAATATTATTATGGTTAGTGGTGTTAATGCCTCTAAGAACATGTCTTTGGTTTTAGGAGCTAAAAGTGATAGTAGTACTACAGGTTTTCAACAGGAACTGTTGGAAGCTGGAGTGATTAGACCAAGTAAGAGTCCATACTCTTCTCCAGTGTTGTTGGTTAAGAAGAAGGATGGAACCTGGAGGATGTGTATAGATTACAGAGCTCTTAATGCAGCCACCATTAAGGATAAATATCCGATACCAGTAGTAGATGAACTCTTGGATGAGGTGTTTCGAAGATTGCAGCAGCATGAGCTTAAAGTTAAACAAAGCAAGTGCAGTTTTGGGGTGACACAATTAGAGTACCTAGGGCATGTGATCAGTGAACATGGTGTAGCTGTTGATCCTTCTAAGATTGAGTGCATCAAAACTTGGGCTAAACCTGCCACCTTGAAGGGTCTTTGGGGATTCTTAGGACTTGCAGAATATTACAGGAAGTATGTGAGGCATTTTGGAATTATTGTAAAGCCCTTAACAGACATGTTAAAGATAGGAAGGTTCAAGTGGACACCACTGTCTAAGCAGGCCTTTGAAGATTTGAAGCATGCTTTGATGACTACACCTGTTTTGGCCTTTCCTGATTTTTCAAAGCAGGTTGTTGTGGAATGTGATGCATCAGGAATTAGAATAGGGGCTGTATTATCACAGGATGGTCATCCAATTGCTTTCTTGAGCAAAGCTTTGGCACCAAGACATGTTGCCTTATCAGTCTATGATAAAGAGATGCTAGCTGTAGTGTTTGTTGTGCAGCATTGGAGGCCTTACCTTCTTGGGAATCATTTCAAAATGTTTACTAATCATAGAACTATCTAG
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

446

Amino Acids

49.36

Weight (kDa)

9.53

Isoelectric Point (pI)

37.62

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RT_RNaseH_2 PF17919 344 - 437 1e-29 RNase H-like domain found in reverse transcriptase
RT_RNaseH PF17917 369 - 444 6e-22 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)
AasI GACNNNNNNGTC 1 cut(s) 1039
Acc36I ACCTGC 2 cut(s) 916, 1108
AccB1I GGYRCC 1 cut(s) 1210
AclWI GGATC 3 cut(s) 41, 310, 863
AcsI RAATTY 1 cut(s) 80
AfaI GTAC 2 cut(s) 562, 830
AfiI CCNNNNNNNGG 5 cut(s) 59, 323, 412, 472, 473
AflII CTTAAG 1 cut(s) 220
AflIII ACRYGT 3 cut(s) 525, 1005, 1219
AgsI TTSAA 9 cut(s) 92, 291, 575, 919, 1027, 1058, 1066, 1113, 1309
AjnI CCWGG 1 cut(s) 662
AjuI GAANNNNNNNTTGG 2 cut(s) 515, 547
Alw21I GWGCWC 1 cut(s) 691
AlwI GGATC 3 cut(s) 41, 310, 863
AlwNI CAGNNNCTG 1 cut(s) 583
AoxI GGCC 3 cut(s) 1050, 1095, 1283
ApeKI GCWGC 4 cut(s) 698, 769, 772, 1273
ApoI RAATTY 1 cut(s) 80
AseI ATTAAT 1 cut(s) 486
Asp700I GAANNNNTTC 2 cut(s) 198, 1304
AspA2I CCTAGG 1 cut(s) 832
AsuHPI GGTGA 2 cut(s) 74, 826
AsuII TTCGAA 1 cut(s) 760
AsuNHI GCTAGC 1 cut(s) 1252
AvrII CCTAGG 1 cut(s) 832
BaeGI GKGCMC 1 cut(s) 318
BanI GGYRCC 1 cut(s) 1210
BanII GRGCYC 1 cut(s) 691
BarI GAAGNNNNNNTAC 4 cut(s) 22, 54, 370, 402
BbsI GAAGAC 1 cut(s) 30
Bbv12I GWGCWC 1 cut(s) 691
BbvI GCAGC 4 cut(s) 710, 781, 784, 1285
BccI CCATC 3 cut(s) 16, 650, 1169
BciT130I CCWGG 1 cut(s) 664
BclI TGATCA 1 cut(s) 843
BfaI CTAG 8 cut(s) 155, 258, 407, 456, 479, 833, 1253, 1336
BfmI CTRYAG 4 cut(s) 111, 354, 564, 1257
BfrI CTTAAG 1 cut(s) 220
BfuAI ACCTGC 2 cut(s) 916, 1108
BglII AGATCT 2 cut(s) 368, 409
BisI GCNGC 4 cut(s) 699, 770, 773, 1274
BlnI CCTAGG 1 cut(s) 832
BlsI GCNGC 4 cut(s) 700, 771, 774, 1275
BmcAI AGTACT 1 cut(s) 562
Bme1390I CCNGG 1 cut(s) 664
BmiI GGNNCC 2 cut(s) 661, 1212
BmrFI CCNGG 1 cut(s) 664
BmsI GCATC 6 cut(s) 148, 406, 897, 1126, 1148, 1239
BmtI GCTAGC 1 cut(s) 1256
BpiI GAAGAC 1 cut(s) 30
BpmI CTGGAG 3 cut(s) 615, 615, 685
Bpu14I TTCGAA 1 cut(s) 760
BpuEI CTTGAG 2 cut(s) 248, 1216
Bsa29I ATCGAT 1 cut(s) 14
BsaBI GATNNNNATC 2 cut(s) 717, 1179
BsaJI CCNNGG 1 cut(s) 832
BsaWI WCCGGW 1 cut(s) 52
BsaXI ACNNNNNCTCC 4 cut(s) 34, 64, 658, 688
Bsc4I CCNNNNNNNGG 5 cut(s) 59, 323, 412, 472, 473
Bse1I ACTGG 3 cut(s) 311, 632, 728
Bse8I GATNNNNATC 2 cut(s) 717, 1179
BseBI CCWGG 1 cut(s) 664
BseCI ATCGAT 1 cut(s) 14
BseDI CCNNGG 1 cut(s) 832
BseGI GGATG 7 cut(s) 215, 421, 661, 675, 754, 1180, 1180
BseJI GATNNNNATC 2 cut(s) 717, 1179
BseLI CCNNNNNNNGG 5 cut(s) 59, 323, 412, 472, 473
BseNI ACTGG 3 cut(s) 311, 632, 728
BseSI GKGCMC 1 cut(s) 318
BseXI GCAGC 4 cut(s) 710, 781, 784, 1285
BseYI CCCAGC 1 cut(s) 5
BsgI GTGCAG 2 cut(s) 823, 1292
BshFI GGCC 3 cut(s) 1052, 1097, 1285
BshNI GGYRCC 1 cut(s) 1210
BshVI ATCGAT 1 cut(s) 14
BsiHKAI GWGCWC 1 cut(s) 691
BsiSI CCGG 1 cut(s) 53
BslI CCNNNNNNNGG 5 cut(s) 59, 323, 412, 472, 473
BsnI GGCC 3 cut(s) 1052, 1097, 1285
Bsp119I TTCGAA 1 cut(s) 760
Bsp1286I GDGCHC 2 cut(s) 318, 691
Bsp143I GATC 6 cut(s) 46, 302, 368, 409, 843, 868
BspANI GGCC 3 cut(s) 1052, 1097, 1285
BspDI ATCGAT 1 cut(s) 14
BspLI GGNNCC 2 cut(s) 661, 1212
BspMAI CTGCAG 1 cut(s) 358
BspMI ACCTGC 2 cut(s) 916, 1108
BspOI GCTAGC 1 cut(s) 1256
BspPI GGATC 3 cut(s) 41, 310, 863
BspT104I TTCGAA 1 cut(s) 760
BspT107I GGYRCC 1 cut(s) 1210
BspTI CTTAAG 1 cut(s) 220
BsrI ACTGG 3 cut(s) 311, 632, 728
BssECI CCNNGG 1 cut(s) 832
BssMI GATC 6 cut(s) 46, 302, 368, 409, 843, 868
BssT1I CCWWGG 1 cut(s) 832
Bst2UI CCWGG 1 cut(s) 664
Bst4CI ACNGT 2 cut(s) 585, 1041
Bst6I CTCTTC 1 cut(s) 631
BstAFI CTTAAG 1 cut(s) 220
BstBI TTCGAA 1 cut(s) 760
BstC8I GCNNGC 5 cut(s) 135, 189, 1050, 1071, 1254
BstDEI CTNAG 5 cut(s) 372, 519, 876, 937, 1044
BstF5I GGATG 7 cut(s) 215, 421, 661, 675, 754, 1180, 1180
BstKTI GATC 6 cut(s) 49, 305, 371, 412, 846, 871
BstMBI GATC 6 cut(s) 46, 302, 368, 409, 843, 868
BstMWI GCNNNNNNNGC 5 cut(s) 113, 695, 778, 908, 1282
BstNI CCWGG 1 cut(s) 664
BstNSI RCATGY 5 cut(s) 529, 842, 1009, 1073, 1223
BstSCI CCNGG 1 cut(s) 662
BstSFI CTRYAG 4 cut(s) 111, 354, 564, 1257
BstSLI GKGCMC 1 cut(s) 318
BstV1I GCAGC 4 cut(s) 710, 781, 784, 1285
BstV2I GAAGAC 1 cut(s) 30
BstX2I RGATCY 3 cut(s) 302, 368, 409
BstYI RGATCY 3 cut(s) 302, 368, 409
Bsu15I ATCGAT 1 cut(s) 14
BsuRI GGCC 3 cut(s) 1052, 1097, 1285
BsuTUI ATCGAT 1 cut(s) 14
BtsCI GGATG 7 cut(s) 215, 421, 661, 675, 754, 1180, 1180
BtsIMutI CAGTG 5 cut(s) 42, 318, 639, 853, 1037
BveI ACCTGC 2 cut(s) 916, 1108
Cac8I GCNNGC 5 cut(s) 135, 189, 1050, 1071, 1254
CaiI CAGNNNCTG 1 cut(s) 583
ClaI ATCGAT 1 cut(s) 14
Csp6I GTAC 2 cut(s) 561, 829
CviAII CATG 9 cut(s) 323, 328, 526, 776, 839, 854, 1006, 1070, 1220
CviQI GTAC 2 cut(s) 561, 829
DdeI CTNAG 5 cut(s) 372, 519, 876, 937, 1044
DpnI GATC 6 cut(s) 48, 304, 370, 411, 845, 870
DpnII GATC 6 cut(s) 46, 302, 368, 409, 843, 868
DraI TTTAAA 1 cut(s) 402
DrdI GACNNNNNNGTC 1 cut(s) 1039
DseDI GACNNNNNNGTC 1 cut(s) 1039
Eam1104I CTCTTC 1 cut(s) 631
EarI CTCTTC 1 cut(s) 631
Ecl136II GAGCTC 1 cut(s) 689
Eco130I CCWWGG 1 cut(s) 832
Eco147I AGGCCT 2 cut(s) 1052, 1285
Eco24I GRGCYC 1 cut(s) 691
Eco53kI GAGCTC 1 cut(s) 689
EcoICRI GAGCTC 1 cut(s) 689
EcoRII CCWGG 1 cut(s) 662
EcoT14I CCWWGG 1 cut(s) 832
EcoT22I ATGCAT 1 cut(s) 1141
EcoT38I GRGCYC 1 cut(s) 691
ErhI CCWWGG 1 cut(s) 832
FaeI CATG 9 cut(s) 326, 331, 529, 779, 842, 857, 1009, 1073, 1223
FalI AAGNNNNNCTT 2 cut(s) 1037, 1069
FatI CATG 9 cut(s) 322, 327, 525, 775, 838, 853, 1005, 1069, 1219
FauNDI CATATG 1 cut(s) 210
FbaI TGATCA 1 cut(s) 843
Fnu4HI GCNGC 4 cut(s) 699, 770, 773, 1274
FokI GGATG 7 cut(s) 202, 428, 668, 682, 761, 1167, 1187
FriOI GRGCYC 1 cut(s) 691
Fsp4HI GCNGC 4 cut(s) 699, 770, 773, 1274
FspBI CTAG 8 cut(s) 155, 258, 407, 456, 479, 833, 1253, 1336
GluI GCNGC 4 cut(s) 699, 770, 773, 1274
GsaI CCCAGC 1 cut(s) 9
GsuI CTGGAG 3 cut(s) 615, 615, 685
HaeIII GGCC 3 cut(s) 1052, 1097, 1285
HapII CCGG 1 cut(s) 53
Hin1II CATG 9 cut(s) 326, 331, 529, 779, 842, 857, 1009, 1073, 1223
HindIII AAGCTT 2 cut(s) 135, 1203
HinfI GANTC 3 cut(s) 616, 933, 1300
HpaII CCGG 1 cut(s) 53
HphI GGTGA 2 cut(s) 74, 826
Hpy166II GTNNAC 3 cut(s) 851, 1032, 1317
Hpy188I TCNGA 3 cut(s) 204, 340, 723
Hpy188III TCNNGA 7 cut(s) 145, 155, 258, 413, 1103, 1143, 1195
Hpy8I GTNNAC 3 cut(s) 851, 1032, 1317
HpyAV CCTTC 5 cut(s) 646, 882, 913, 1014, 1301
HpyCH4III ACNGT 2 cut(s) 585, 1041
HpyCH4IV ACGT 1 cut(s) 295
HpyF10VI GCNNNNNNNGC 5 cut(s) 113, 695, 778, 908, 1282
HpyF3I CTNAG 5 cut(s) 372, 519, 876, 937, 1044
HpySE526I ACGT 1 cut(s) 295
Hsp92II CATG 9 cut(s) 326, 331, 529, 779, 842, 857, 1009, 1073, 1223
Ksp22I TGATCA 1 cut(s) 843
Kzo9I GATC 6 cut(s) 46, 302, 368, 409, 843, 868
LmnI GCTCC 1 cut(s) 542
Lsp1109I GCAGC 4 cut(s) 710, 781, 784, 1285
LweI GCATC 6 cut(s) 148, 406, 897, 1126, 1148, 1239
MaeI CTAG 8 cut(s) 155, 258, 407, 456, 479, 833, 1253, 1336
MaeII ACGT 1 cut(s) 295
MaeIII GTNAC 3 cut(s) 173, 377, 814
MalI GATC 6 cut(s) 48, 304, 370, 411, 845, 870
MboI GATC 6 cut(s) 46, 302, 368, 409, 843, 868
MboII GAAGA 9 cut(s) 30, 31, 339, 342, 381, 618, 661, 774, 1070
MfeI CAATTG 1 cut(s) 1185
MflI RGATCY 3 cut(s) 302, 368, 409
MhlI GDGCHC 2 cut(s) 318, 691
MluCI AATT 9 cut(s) 65, 80, 128, 197, 394, 821, 981, 1146, 1185
MlyI GAGTC 1 cut(s) 625
MmeI TCCRAC 1 cut(s) 567
MnlI CCTC 9 cut(s) 60, 97, 198, 453, 526, 660, 745, 963, 1275
Mph1103I ATGCAT 1 cut(s) 1141
MroXI GAANNNNTTC 2 cut(s) 198, 1304
MslI CAYNNNNRTG 1 cut(s) 332
MspCI CTTAAG 1 cut(s) 220
MspI CCGG 1 cut(s) 53
MspR9I CCNGG 1 cut(s) 664
MunI CAATTG 1 cut(s) 1185
MvaI CCWGG 1 cut(s) 664
MwoI GCNNNNNNNGC 5 cut(s) 113, 695, 778, 908, 1282
NdeI CATATG 1 cut(s) 210
NdeII GATC 6 cut(s) 46, 302, 368, 409, 843, 868
NheI GCTAGC 1 cut(s) 1252
NlaIII CATG 9 cut(s) 326, 331, 529, 779, 842, 857, 1009, 1073, 1223
NlaIV GGNNCC 2 cut(s) 661, 1212
NmuCI GTSAC 1 cut(s) 814
NsiI ATGCAT 1 cut(s) 1141
NspI RCATGY 5 cut(s) 529, 842, 1009, 1073, 1223
NspV TTCGAA 1 cut(s) 760
PaeI GCATGC 1 cut(s) 1073
PceI AGGCCT 2 cut(s) 1052, 1285
PciI ACATGT 3 cut(s) 525, 1005, 1219
PdmI GAANNNNTTC 2 cut(s) 198, 1304
PfeI GAWTC 2 cut(s) 933, 1300
PkrI GCNGC 4 cut(s) 700, 771, 774, 1275
PleI GAGTC 1 cut(s) 624
PpsI GAGTC 1 cut(s) 624
PscI ACATGT 3 cut(s) 525, 1005, 1219
PshBI ATTAAT 1 cut(s) 486
Psp124BI GAGCTC 1 cut(s) 691
Psp6I CCWGG 1 cut(s) 662
PspFI CCCAGC 1 cut(s) 5
PspGI CCWGG 1 cut(s) 662
PspN4I GGNNCC 2 cut(s) 661, 1212
PstI CTGCAG 1 cut(s) 358
PstNI CAGNNNCTG 1 cut(s) 583
PsuI RGATCY 3 cut(s) 302, 368, 409
RsaI GTAC 2 cut(s) 562, 830
RsaNI GTAC 2 cut(s) 561, 829
RseI CAYNNNNRTG 1 cut(s) 332
SacI GAGCTC 1 cut(s) 691
SatI GCNGC 4 cut(s) 699, 770, 773, 1274
Sau3AI GATC 6 cut(s) 46, 302, 368, 409, 843, 868
ScaI AGTACT 1 cut(s) 562
SchI GAGTC 1 cut(s) 625
ScrFI CCNGG 1 cut(s) 664
SduI GDGCHC 2 cut(s) 318, 691
SfaNI GCATC 6 cut(s) 148, 406, 897, 1126, 1148, 1239
SfcI CTRYAG 4 cut(s) 111, 354, 564, 1257
SfuI TTCGAA 1 cut(s) 760
SmiMI CAYNNNNRTG 1 cut(s) 332
SmlI CTYRAG 3 cut(s) 220, 227, 1195
SmoI CTYRAG 3 cut(s) 220, 227, 1195
SphI GCATGC 1 cut(s) 1073
Sse9I AATT 9 cut(s) 65, 80, 128, 197, 394, 821, 981, 1146, 1185
SseBI AGGCCT 2 cut(s) 1052, 1285
SspI AATATT 2 cut(s) 490, 953
SspMI CTAG 8 cut(s) 155, 258, 407, 456, 479, 833, 1253, 1336
SstI GAGCTC 1 cut(s) 691
StuI AGGCCT 2 cut(s) 1052, 1285
StyD4I CCNGG 1 cut(s) 662
StyI CCWWGG 1 cut(s) 832
TaaI ACNGT 2 cut(s) 585, 1041
TaiI ACGT 1 cut(s) 298
TaqI TCGA 2 cut(s) 14, 760
TasI AATT 9 cut(s) 65, 80, 128, 197, 394, 821, 981, 1146, 1185
TatI WGTACW 1 cut(s) 560
TfiI GAWTC 2 cut(s) 933, 1300
TscAI CASTG 5 cut(s) 49, 318, 639, 853, 1044
TseFI GTSAC 1 cut(s) 814
TseI GCWGC 4 cut(s) 698, 769, 772, 1273
Tsp45I GTSAC 1 cut(s) 814
TspDTI ATGAA 2 cut(s) 32, 753
TspRI CASTG 5 cut(s) 49, 318, 639, 853, 1044
Vha464I CTTAAG 1 cut(s) 220
VspI ATTAAT 1 cut(s) 486
XapI RAATTY 1 cut(s) 80
XbaI TCTAGA 2 cut(s) 154, 257
XceI RCATGY 5 cut(s) 529, 842, 1009, 1073, 1223
XmaJI CCTAGG 1 cut(s) 832
XmnI GAANNNNTTC 2 cut(s) 198, 1304
XspI CTAG 8 cut(s) 155, 258, 407, 456, 479, 833, 1253, 1336
ZrmI AGTACT 1 cut(s) 562
Zsp2I ATGCAT 1 cut(s) 1141
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.