FvH4_5g33111

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000756
Physical Location & Seq
Reverse (-)
23919113 .. 23920570
1458 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g33111.t1

Sequence Viewer

Length: 1458 bp
ATGACTGGAGTGTCATCACCAGTTCATGACTATGTGCTGGAAATTCAGAAGGCATGTGAGAGGGATGCTGAAACTCTTTCAATCTTGCAACAGCTAAGGGAAGGTACAAATCCTCCAAGGTCTTTTACTCAACTTCACTCTCAGTTATTATATAAGGGCAGGATCTTTGTGCCACAGTTGGATAATTGGAGACAAAAGGTTATTGTTGAGTTTCATGAAGGGTATAATGGGGGGCATGCTGGTGTTACAAGAACCCATAAGAGAGTGTTCAGGTCTTTTGCTTGGCCTGGTATGAAAGGAGATATTAAGTCTGTGGTTTCTACTTGTCACATTTGTCAGCAGAATCACTATGAGACAGTCAATCCTCCAGGGTTGTTGCAACCAAATGTGATACCGGACAAAGCTTGGACTCAAATCTCTATGGATTTCATTGAAGGCCTTCCAAAGTCAGCTGGAAAAACAGTACTCTTGGTGGTGGTTGATAGATTGACCAAGTATGGTCACTTTATACCAATGTCACACCCTTATACAGCTTCTACTGTGGCTCAACACTTTGTGAAGGAAGTTTTTCGACTACATGGAATGCCAGAATCTATCATATCTGATAGGGATCCAATCTTTCTCAGTAAATTTTGGGAAGCATTCTTCACCTTACAGGGAACTACTTTAAACAAAAGCTCCTCTTACCACCCACAAAGTGATGGCCAAACTGAGAACCTGAATAGGACAGTGGAGCAGTACCTCAGGTGTGTGGTTGGAGAAAGACCAAGTTCTTGGGTTGAAGCCATACCATGGGCTGAGTACTGGTACAACTCAGCTCATCATTCAGCCATTGGCATGACTCCATTTAAAGCTCTATATGGATATGAAGCTCCAGCTGTGAAAGCTTATGAGGTGGGTGGGACTGCAGTGGCATCAGTGGATGCTCAATTACAATTAAGAGATGAGTTATTGGCTAGTCTGAAGAGAAATTTGCAAGTGGCTCAATGCAGAATGAAAAATTTCTATGACAAGCATCACTCAGAGAGAAGTTTTGAAGTGGGAGATTGGGTTTATCTCAAACTACAACCTTATCGGCAGCAGTCAGTGCAAAAGCGATCCAGCCACAAACTAGCTCCAAGGTATTGTGGCCCTTATCTCATTATACAGAAGATCGGATATGTTGCTTATAAGCTGAAATTGCCTGATTCATCAAAGGTTCATCCAGTGTTCCATGTGTCACTGCTAAAGAAGAAAATGGGAGACTCTGTGGTGGTTGCTACACACTTGCCTCCTGACCTTGATCCACATAACCCTAGATGGTACCCAGCAAAAGTTTTGGAAAGAGGGGTTTTCAGGAAGAACAATGCACCAGTAACTAAATGGTTGATTAAATGGCTTGGTGCTGCTGAGGAGGAGGCCACGTGGGAGGAAGCAGATGACATTCAACGCAGGTTCCCAGATTTTACTGATAAGTGA
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

486

Amino Acids

55.52

Weight (kDa)

9.08

Isoelectric Point (pI)

40.77

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Integrase_H2C2 PF17921 63 - 116 6.6e-17 Integrase zinc binding domain
rve PF00665 137 - 230 1.1e-06 Integrase core domain
SH3_Tf2-1 PF24626 348 - 411 3.8e-23 Tf2-1-like, SH3 domain
Chromo PF00385 446 - 482 6.8e-06 Chromo (CHRromatin Organisation MOdifier) 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)
AanI TTATAA 1 cut(s) 1170
AasI GACNNNNNNGTC 1 cut(s) 10
Acc36I ACCTGC 1 cut(s) 1422
Acc65I GGTACC 1 cut(s) 1302
AccB1I GGYRCC 1 cut(s) 1302
AccB7I CCANNNNNTGG 1 cut(s) 792
AclWI GGATC 5 cut(s) 170, 605, 618, 1092, 1277
AcoI YGGCCR 1 cut(s) 703
AcsI RAATTY 4 cut(s) 42, 629, 970, 1000
AcuI CTGAAG 1 cut(s) 983
AcvI CACGTG 1 cut(s) 1404
AdeI CACNNNGTG 2 cut(s) 556, 698
AfaI GTAC 6 cut(s) 106, 465, 740, 803, 809, 1304
AfiI CCNNNNNNNGG 1 cut(s) 792
AgsI TTSAA 5 cut(s) 81, 434, 782, 1037, 1427
AjnI CCWGG 2 cut(s) 286, 367
Alw26I GTCTC 3 cut(s) 184, 347, 1236
AlwI GGATC 5 cut(s) 170, 605, 618, 1092, 1277
AoxI GGCC 5 cut(s) 284, 436, 703, 1129, 1398
ApeKI GCWGC 2 cut(s) 1078, 1385
ApoI RAATTY 4 cut(s) 42, 629, 970, 1000
Asp700I GAANNNNTTC 3 cut(s) 438, 567, 1001
Asp718I GGTACC 1 cut(s) 1302
AspS9I GGNCC 1 cut(s) 1130
AsuHPI GGTGA 2 cut(s) 9, 640
AxyI CCTNAGG 1 cut(s) 743
BalI TGGCCA 1 cut(s) 705
BamHI GGATCC 1 cut(s) 610
BanI GGYRCC 1 cut(s) 1302
BbrPI CACGTG 1 cut(s) 1404
BbvCI CCTCAGC 1 cut(s) 1389
BbvI GCAGC 2 cut(s) 1090, 1372
BccI CCATC 2 cut(s) 695, 1293
BciT130I CCWGG 2 cut(s) 288, 369
BcoDI GTCTC 3 cut(s) 184, 347, 1236
BfaI CTAG 3 cut(s) 957, 1112, 1296
BfmI CTRYAG 1 cut(s) 906
BfuAI ACCTGC 1 cut(s) 1422
BisI GCNGC 2 cut(s) 1079, 1386
BlsI GCNGC 2 cut(s) 1080, 1387
BmcAI AGTACT 2 cut(s) 465, 803
Bme1390I CCNGG 2 cut(s) 288, 369
BmgT120I GGNCC 1 cut(s) 1130
BmiI GGNNCC 3 cut(s) 612, 1304, 1436
BmrFI CCNGG 2 cut(s) 288, 369
BmsI GCATC 4 cut(s) 55, 913, 923, 1024
BpmI CTGGAG 3 cut(s) 27, 351, 858
Bpu10I CCTNAGC 2 cut(s) 95, 1389
BsaAI YACGTR 1 cut(s) 1404
BsaBI GATNNNNATC 1 cut(s) 609
BsaJI CCNNGG 4 cut(s) 116, 368, 791, 1118
BsaWI WCCGGW 1 cut(s) 394
Bsc4I CCNNNNNNNGG 1 cut(s) 792
Bse1I ACTGG 5 cut(s) 10, 20, 809, 1205, 1352
Bse21I CCTNAGG 1 cut(s) 743
Bse8I GATNNNNATC 1 cut(s) 609
BseBI CCWGG 2 cut(s) 288, 369
BseDI CCNNGG 4 cut(s) 116, 368, 791, 1118
BseGI GGATG 3 cut(s) 70, 928, 1201
BseJI GATNNNNATC 1 cut(s) 609
BseLI CCNNNNNNNGG 1 cut(s) 792
BseMII CTCAG 8 cut(s) 155, 637, 702, 757, 789, 828, 1035, 1380
BseNI ACTGG 5 cut(s) 10, 20, 809, 1205, 1352
BseRI GAGGAG 3 cut(s) 670, 1406, 1409
BseXI GCAGC 2 cut(s) 1090, 1372
BseYI CCCAGC 1 cut(s) 1306
BshFI GGCC 5 cut(s) 286, 438, 705, 1131, 1400
BshNI GGYRCC 1 cut(s) 1302
BsiSI CCGG 1 cut(s) 395
BslFI GGGAC 1 cut(s) 916
BslI CCNNNNNNNGG 1 cut(s) 792
BsmAI GTCTC 3 cut(s) 184, 347, 1236
BsmFI GGGAC 1 cut(s) 916
BsmI GAATGC 2 cut(s) 588, 641
BsnI GGCC 5 cut(s) 286, 438, 705, 1131, 1400
Bsp143I GATC 5 cut(s) 162, 610, 1097, 1152, 1282
Bsp19I CCATGG 1 cut(s) 791
BspANI GGCC 5 cut(s) 286, 438, 705, 1131, 1400
BspCNI CTCAG 8 cut(s) 154, 636, 703, 756, 790, 827, 1034, 1381
BspHI TCATGA 2 cut(s) 25, 214
BspLI GGNNCC 3 cut(s) 612, 1304, 1436
BspMAI CTGCAG 1 cut(s) 910
BspMI ACCTGC 1 cut(s) 1422
BspPI GGATC 5 cut(s) 170, 605, 618, 1092, 1277
BspT107I GGYRCC 1 cut(s) 1302
BsrI ACTGG 5 cut(s) 10, 20, 809, 1205, 1352
BssECI CCNNGG 4 cut(s) 116, 368, 791, 1118
BssMI GATC 5 cut(s) 162, 610, 1097, 1152, 1282
BssT1I CCWWGG 3 cut(s) 116, 791, 1118
Bst2UI CCWGG 2 cut(s) 288, 369
Bst4CI ACNGT 5 cut(s) 177, 358, 463, 541, 730
Bst6I CTCTTC 1 cut(s) 959
BstAPI GCANNNNNTGC 1 cut(s) 1087
BstBAI YACGTR 1 cut(s) 1404
BstC8I GCNNGC 1 cut(s) 237
BstDEI CTNAG 9 cut(s) 95, 141, 623, 711, 743, 798, 814, 1021, 1389
BstDSI CCRYGG 1 cut(s) 791
BstF5I GGATG 3 cut(s) 70, 928, 1201
BstKTI GATC 5 cut(s) 165, 613, 1100, 1155, 1285
BstMAI GTCTC 3 cut(s) 184, 347, 1236
BstMBI GATC 5 cut(s) 162, 610, 1097, 1152, 1282
BstMWI GCNNNNNNNGC 3 cut(s) 884, 1087, 1180
BstNI CCWGG 2 cut(s) 288, 369
BstNSI RCATGY 2 cut(s) 57, 239
BstSCI CCNGG 2 cut(s) 286, 367
BstSFI CTRYAG 1 cut(s) 906
BstV1I GCAGC 2 cut(s) 1090, 1372
BstX2I RGATCY 2 cut(s) 162, 610
BstXI CCANNNNNNTGG 1 cut(s) 774
BstYI RGATCY 2 cut(s) 162, 610
Bsu36I CCTNAGG 1 cut(s) 743
BsuRI GGCC 5 cut(s) 286, 438, 705, 1131, 1400
BtgI CCRYGG 1 cut(s) 791
BtsCI GGATG 3 cut(s) 70, 928, 1201
BtsI GCAGTG 2 cut(s) 915, 1220
BtsIMutI CAGTG 6 cut(s) 735, 915, 924, 1092, 1212, 1220
BveI ACCTGC 1 cut(s) 1422
Cac8I GCNNGC 1 cut(s) 237
CciI TCATGA 2 cut(s) 25, 214
Cfr13I GGNCC 1 cut(s) 1130
Csp6I GTAC 6 cut(s) 105, 464, 739, 802, 808, 1303
CviAII CATG 8 cut(s) 26, 54, 215, 236, 578, 792, 838, 1214
CviQI GTAC 6 cut(s) 105, 464, 739, 802, 808, 1303
DdeI CTNAG 9 cut(s) 95, 141, 623, 711, 743, 798, 814, 1021, 1389
DpnI GATC 5 cut(s) 164, 612, 1099, 1154, 1284
DpnII GATC 5 cut(s) 162, 610, 1097, 1152, 1282
DraI TTTAAA 2 cut(s) 669, 850
DraIII CACNNNGTG 2 cut(s) 556, 698
DrdI GACNNNNNNGTC 1 cut(s) 10
DseDI GACNNNNNNGTC 1 cut(s) 10
EaeI YGGCCR 1 cut(s) 703
Eam1104I CTCTTC 1 cut(s) 959
EarI CTCTTC 1 cut(s) 959
Eco130I CCWWGG 3 cut(s) 116, 791, 1118
Eco147I AGGCCT 1 cut(s) 438
Eco57I CTGAAG 1 cut(s) 983
Eco72I CACGTG 1 cut(s) 1404
Eco81I CCTNAGG 1 cut(s) 743
EcoRII CCWGG 2 cut(s) 286, 367
EcoT14I CCWWGG 3 cut(s) 116, 791, 1118
ErhI CCWWGG 3 cut(s) 116, 791, 1118
FaeI CATG 8 cut(s) 29, 57, 218, 239, 581, 795, 841, 1217
FalI AAGNNNNNCTT 2 cut(s) 667, 699
FaqI GGGAC 1 cut(s) 916
FatI CATG 8 cut(s) 25, 53, 214, 235, 577, 791, 837, 1213
Fnu4HI GCNGC 2 cut(s) 1079, 1386
FokI GGATG 3 cut(s) 77, 935, 1188
Fsp4HI GCNGC 2 cut(s) 1079, 1386
FspBI CTAG 3 cut(s) 957, 1112, 1296
GluI GCNGC 2 cut(s) 1079, 1386
GsaI CCCAGC 1 cut(s) 1310
GsuI CTGGAG 3 cut(s) 27, 351, 858
HaeIII GGCC 5 cut(s) 286, 438, 705, 1131, 1400
HapII CCGG 1 cut(s) 395
Hin1II CATG 8 cut(s) 29, 57, 218, 239, 581, 795, 841, 1217
HindIII AAGCTT 2 cut(s) 402, 885
HinfI GANTC 6 cut(s) 343, 409, 590, 841, 1187, 1244
HpaII CCGG 1 cut(s) 395
HphI GGTGA 2 cut(s) 9, 640
Hpy188I TCNGA 5 cut(s) 48, 604, 963, 1024, 1157
Hpy188III TCNNGA 4 cut(s) 26, 215, 1274, 1336
HpyAV CCTTC 6 cut(s) 43, 95, 212, 428, 449, 553
HpyCH4III ACNGT 5 cut(s) 177, 358, 463, 541, 730
HpyCH4IV ACGT 1 cut(s) 1403
HpyCH4V TGCA 7 cut(s) 88, 379, 908, 976, 990, 1090, 1349
HpyF10VI GCNNNNNNNGC 3 cut(s) 884, 1087, 1180
HpyF3I CTNAG 9 cut(s) 95, 141, 623, 711, 743, 798, 814, 1021, 1389
HpySE526I ACGT 1 cut(s) 1403
Hsp92II CATG 8 cut(s) 29, 57, 218, 239, 581, 795, 841, 1217
KpnI GGTACC 1 cut(s) 1306
Kzo9I GATC 5 cut(s) 162, 610, 1097, 1152, 1282
LmnI GCTCC 4 cut(s) 683, 733, 877, 1120
Lsp1109I GCAGC 2 cut(s) 1090, 1372
LweI GCATC 4 cut(s) 55, 913, 923, 1024
MaeI CTAG 3 cut(s) 957, 1112, 1296
MaeII ACGT 1 cut(s) 1403
MaeIII GTNAC 6 cut(s) 244, 326, 500, 516, 1218, 1354
MalI GATC 5 cut(s) 164, 612, 1099, 1154, 1284
MboI GATC 5 cut(s) 162, 610, 1097, 1152, 1282
MboII GAAGA 5 cut(s) 637, 976, 1162, 1243, 1351
MflI RGATCY 2 cut(s) 162, 610
MlsI TGGCCA 1 cut(s) 705
MluCI AATT 8 cut(s) 42, 184, 629, 929, 935, 970, 1000, 1178
MluNI TGGCCA 1 cut(s) 705
MlyI GAGTC 3 cut(s) 403, 835, 1238
MmeI TCCRAC 2 cut(s) 159, 736
Mox20I TGGCCA 1 cut(s) 705
MroXI GAANNNNTTC 3 cut(s) 438, 567, 1001
MscI TGGCCA 1 cut(s) 705
MseI TTAA 5 cut(s) 306, 668, 849, 938, 1371
MslI CAYNNNNRTG 3 cut(s) 30, 240, 836
Msp20I TGGCCA 1 cut(s) 705
MspA1I CMGCKG 2 cut(s) 452, 878
MspI CCGG 1 cut(s) 395
MspR9I CCNGG 2 cut(s) 288, 369
Mva1269I GAATGC 2 cut(s) 588, 641
MvaI CCWGG 2 cut(s) 288, 369
MwoI GCNNNNNNNGC 3 cut(s) 884, 1087, 1180
NcoI CCATGG 1 cut(s) 791
NdeII GATC 5 cut(s) 162, 610, 1097, 1152, 1282
NlaIII CATG 8 cut(s) 29, 57, 218, 239, 581, 795, 841, 1217
NlaIV GGNNCC 3 cut(s) 612, 1304, 1436
NmuCI GTSAC 4 cut(s) 326, 500, 516, 1218
NspI RCATGY 2 cut(s) 57, 239
PaeI GCATGC 1 cut(s) 239
PagI TCATGA 2 cut(s) 25, 214
PceI AGGCCT 1 cut(s) 438
PctI GAATGC 2 cut(s) 588, 641
PdmI GAANNNNTTC 3 cut(s) 438, 567, 1001
PfeI GAWTC 3 cut(s) 343, 590, 1187
PflMI CCANNNNNTGG 1 cut(s) 792
PkrI GCNGC 2 cut(s) 1080, 1387
PleI GAGTC 3 cut(s) 403, 835, 1238
PmaCI CACGTG 1 cut(s) 1404
PmlI CACGTG 1 cut(s) 1404
PpsI GAGTC 3 cut(s) 403, 835, 1238
Ppu21I YACGTR 1 cut(s) 1404
PsiI TTATAA 1 cut(s) 1170
Psp6I CCWGG 2 cut(s) 286, 367
PspCI CACGTG 1 cut(s) 1404
PspFI CCCAGC 1 cut(s) 1306
PspGI CCWGG 2 cut(s) 286, 367
PspN4I GGNNCC 3 cut(s) 612, 1304, 1436
PspPI GGNCC 1 cut(s) 1130
PstI CTGCAG 1 cut(s) 910
PsuI RGATCY 2 cut(s) 162, 610
PvuII CAGCTG 2 cut(s) 452, 878
RsaI GTAC 6 cut(s) 106, 465, 740, 803, 809, 1304
RsaNI GTAC 6 cut(s) 105, 464, 739, 802, 808, 1303
RseI CAYNNNNRTG 3 cut(s) 30, 240, 836
SaqAI TTAA 5 cut(s) 306, 668, 849, 938, 1371
SatI GCNGC 2 cut(s) 1079, 1386
Sau3AI GATC 5 cut(s) 162, 610, 1097, 1152, 1282
Sau96I GGNCC 1 cut(s) 1130
ScaI AGTACT 2 cut(s) 465, 803
SchI GAGTC 3 cut(s) 403, 835, 1238
ScrFI CCNGG 2 cut(s) 288, 369
SfaNI GCATC 4 cut(s) 55, 913, 923, 1024
SfcI CTRYAG 1 cut(s) 906
SmiMI CAYNNNNRTG 3 cut(s) 30, 240, 836
SphI GCATGC 1 cut(s) 239
Sse9I AATT 8 cut(s) 42, 184, 629, 929, 935, 970, 1000, 1178
SseBI AGGCCT 1 cut(s) 438
SspMI CTAG 3 cut(s) 957, 1112, 1296
StuI AGGCCT 1 cut(s) 438
StyD4I CCNGG 2 cut(s) 286, 367
StyI CCWWGG 3 cut(s) 116, 791, 1118
TaaI ACNGT 5 cut(s) 177, 358, 463, 541, 730
TaiI ACGT 1 cut(s) 1406
TaqI TCGA 1 cut(s) 571
TasI AATT 8 cut(s) 42, 184, 629, 929, 935, 970, 1000, 1178
TatI WGTACW 2 cut(s) 463, 801
TfiI GAWTC 3 cut(s) 343, 590, 1187
Tru1I TTAA 5 cut(s) 306, 668, 849, 938, 1371
Tru9I TTAA 5 cut(s) 306, 668, 849, 938, 1371
TscAI CASTG 6 cut(s) 735, 915, 924, 1092, 1212, 1227
TseFI GTSAC 4 cut(s) 326, 500, 516, 1218
TseI GCWGC 2 cut(s) 1078, 1385
Tsp45I GTSAC 4 cut(s) 326, 500, 516, 1218
TspDTI ATGAA 9 cut(s) 14, 203, 231, 308, 418, 882, 1010, 1179, 1190
TspRI CASTG 6 cut(s) 735, 915, 924, 1092, 1212, 1227
Van91I CCANNNNNTGG 1 cut(s) 792
XapI RAATTY 4 cut(s) 42, 629, 970, 1000
XceI RCATGY 2 cut(s) 57, 239
XcmI CCANNNNNNNNNTGG 1 cut(s) 1359
XmnI GAANNNNTTC 3 cut(s) 438, 567, 1001
XspI CTAG 3 cut(s) 957, 1112, 1296
ZrmI AGTACT 2 cut(s) 465, 803
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.