FvH4_5g31701

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000385
Physical Location & Seq
Forward (+)
22865996 .. 22868293
2298 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g31701.t1

Sequence Viewer

Length: 1623 bp
ATGCAAAGAGGCTGCGCTAAACAAGTCATAAGGGCCAAAGGAGACGAAGGTATTGACTCTTTCAAACCCAAATCCTTTAGTGAGAAGAGGGAAGCTAAAGAGCTTGACACCTTTCTATGGAACATGGAAAGGTACTTCAAGTATCTAAAGCTTGAGGATGACGAGTCCAAAATTTCAACGGCTACCATGTTCTTGGCTGACAATGCCCTTATGTGGTGGGGTCGAAGGAGCATGGAAATCGAGCAAGGTACGTTCTCTCTTGATACTTGGGAAGAATTCAAGAATGATATCAAGTTGCATTTCTATCCCCAAAATGCTCAATATGAAGCAAAGGAGAAGCTTAGGTGGCTAAAGCAAACGGGTAGCGTCAAGGATTATGTCAACACCTTTGTTAACTTGCTATTCGAAGTGCCCAACATGACGGAGGAGGACAAGCTCATATACTTCATGAGTGGATTACAAAGTTGGGCAAAGCTTGAGTTGCAAAGAAGACAAGTGCAAACCTTGTCACAAGCCATTGCCGCCGTCGAGTCCCTTATTGAATTTAAGACTAGCCACCAAGGCGACACCAAGTTCAAGGGGAAGAAGGTTAACTATGAGAAAAGTGGGGGAGACGTGCCAAAGCCGAAGGAAAAGCCCGAGTCAAGCTACAAGCCGAAGGCGAAGAGGTTCGAGAAGCACGACAAGTCCGCAAACAAGACTTGGGAAATGAAGTGCTACTTATGCGGCGGCCCTCACATGATGCGCGATTGCCCTCAAAAGAAGACACTCAAAGCCATGACCTTGCAAGAGCCTAGGACCGAGGAGGAGGAAGATAATGAAGCAAGGATGGGATGCATCCAGTTGCTCAATGCCGTGAAGGCTAGCGTCCCTCAACCAAGGCGACAAGCGGAAGAAGCAAGGAAGCTTGGCCTTCGAGTCACGAAGGAGTCGAGCAGCATGAAGACGGTGAATACACCTGCCACACCTATTGTTGGGGTAGCACGCGATGTGGAGGTTCATATCGACGCTTGGAAGGGGAAAGTCGACTTCACCGTGGTCAAGATGGATGACTATGGCGTAGTAATCGGCCTTGAATTCATGGACAAGGTACGAGCATTTCCCATTCCATTCTATAACATCTTTTGCATTGTAGCTGATGGAGAGTTGCCTTGCGTGGTGCCCGTGGCGAGGCAAGCAAAGGAGAAGACAAAGGCTCTATCCGCCATGCAACTCGCCAAAGCTTGGAAGAAGGGCGAGCCGACATTCCTAGCAACCCTCAAGATGGATGAGGAGGTTGGAGGAAAGTCTGAACCGTTGCCAAAAGCAATAGAGGCAATCCTTGAGGAGTTTGGAGATGTGATGCCCAAGGAGTTGCCGAAGAGGGAGAACGAACTCTATGTGAAGAAGGAGAAATGTTCCTTTGCCAAGGAGGAAGTGGACTTCCTAGGACACAAGATCGAGGATGGAAAGCTCTTGATGGAGGAAAGCAAGGTGAAGGCCATCCAAGATTGGGAGCCGCCAACCAATGTACCCGCACTTCGATCTTTCCTTGGCTTGGTTAATTATTATCGAAGGTTCATCAAAGGATACTCCGCCATTGCGGCACCCTTGACGGACCTCTTGAAGAAAAACAAGACATAG
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
Asp_protease_2 Chromo RVT_1 Retrotrans_gag gag-asp_proteas rve

Protein Analysis

541

Amino Acids

61.95

Weight (kDa)

8.8

Isoelectric Point (pI)

45.28

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 23 - 176 1.4e-10 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 61 - 154 9.9e-15 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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Orthologous Genes (Group: OG0000385)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g23713 FvH4_1g25744 FvH4_2g00261 FvH4_2g00262 FvH4_2g15681 FvH4_2g17851 FvH4_2g35550 FvH4_3g05280 FvH4_3g10531 FvH4_3g25910 FvH4_3g28953 FvH4_3g33371 FvH4_3g33536 FvH4_3g36090 FvH4_4g03471 FvH4_4g03480 FvH4_4g06701 FvH4_4g19351 FvH4_4g34281 FvH4_5g00040 FvH4_5g03811 FvH4_5g03812 FvH4_5g11822 FvH4_5g30921 FvH4_5g31701 FvH4_6g12161 FvH4_6g15222 FvH4_6g15223 FvH4_6g17701 FvH4_6g17710 FvH4_6g19301 FvH4_6g33011 FvH4_6g34501 FvH4_6g50161 FvH4_7g04111 FvH4_7g04120 FvH4_7g04121 FvH4_7g04122 FvH4_7g04123 FvH4_7g28231 FvH4_c7g00010
malus_domestica MD12G1084200.v1.1
prunus_persica Prupe.1G206200_v2.0.a1 Prupe.8G085600_v2.0.a1
pyrus_communis pycom01g11080 pycom02g20500 pycom09g18370 pycom12555g00210 pycom13g23120 pycom14g10590 pycom16g17620 pycom16g22750
rosa_chinensis RchiOBHm_Chr2g0137481 RchiOBHm_Chr6g0251961 RchiOBHm_Chr7g0185821
rosa_laevigata RLG00000005585 RLG00000010281 RLG00000010912 RLG00000030342 RLG00000034281
rosa_multiflora Rmu_sc0000096.1_g000010 Rmu_sc0002481.1_g000045 Rmu_sc0003598.1_g000009 Rmu_sc0003863.1_g000019 Rmu_sc0003973.1_g000002 Rmu_sc0004823.1_g000050 Rmu_sc0005621.1_g000007 Rmu_sc0006537.1_g000030 Rmu_sc0006608.1_g000014 Rmu_sc0008506.1_g000007 Rmu_sc0014428.1_g000001 Rmu_sc0035437.1_g000001 Rmu_ssc0000396.1_g000022
rosa_roxburghii Rroxscaffold_175G00432300 Rroxscaffold_17G00435390 Rroxscaffold_27G00446590 Rroxscaffold_29G00441820 Rroxscaffold_31G00438110 Rroxscaffold_32G00442750 Rroxscaffold_33G00439810 Rroxscaffold_37G00445160 Rroxscaffold_4G00306500 Rroxscaffold_4G00327700 Rroxscaffold_4G00332630 Rroxscaffold_52G00439360 Rroxscaffold_63G00444420 Rroxscaffold_76G00448580 Rroxscaffold_7G00156270
rosa_rugosa Rorug03G0295200
rosa_samantha Rh1BG433700 Rh1CG115400 Rh2AG676300 Rh2CG341800 Rh2DG381400 Rh3BG370100 Rh3BG370200 Rh4AG441600 Rh4BG076500 Rh4BG107400 Rh5BG005600 Rh6BG010100 Rh7BG000200
rosa_wichuraiana Rw0G003820

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AarI CACCTGC 1 cut(s) 967
Acc36I ACCTGC 1 cut(s) 967
AccB1I GGYRCC 2 cut(s) 1159, 1585
AccB7I CCANNNNNTGG 1 cut(s) 1224
AccI GTMKAC 1 cut(s) 1026
AccII CGCG 2 cut(s) 747, 987
AcsI RAATTY 4 cut(s) 171, 275, 542, 1076
AfaI GTAC 4 cut(s) 134, 250, 1092, 1512
AfiI CCNNNNNNNGG 8 cut(s) 117, 213, 974, 1170, 1224, 1264, 1492, 1537
AgsI TTSAA 8 cut(s) 64, 139, 177, 280, 542, 577, 1076, 1606
AjiI CACGTC 1 cut(s) 616
Alw26I GTCTC 2 cut(s) 36, 606
Ama87I CYCGRG 1 cut(s) 638
AoxI GGCC 5 cut(s) 33, 730, 910, 1069, 1479
ApeKI GCWGC 2 cut(s) 12, 936
ApoI RAATTY 4 cut(s) 171, 275, 542, 1076
Asp700I GAANNNNTTC 1 cut(s) 668
AspA2I CCTAGG 2 cut(s) 794, 1426
AspLEI GCGC 2 cut(s) 17, 747
AspS9I GGNCC 4 cut(s) 33, 731, 798, 1597
AsuHPI GGTGA 3 cut(s) 961, 1024, 1486
AsuII TTCGAA 1 cut(s) 405
AsuNHI GCTAGC 1 cut(s) 863
AvaI CYCGRG 1 cut(s) 638
AvaII GGWCC 2 cut(s) 798, 1597
AvrII CCTAGG 2 cut(s) 794, 1426
BaeGI GKGCMC 2 cut(s) 414, 1164
BaeI ACNNNNGTAYC 2 cut(s) 1494, 1527
BanI GGYRCC 2 cut(s) 1159, 1585
BarI GAAGNNNNNNTAC 2 cut(s) 1503, 1535
BbsI GAAGAC 4 cut(s) 496, 770, 950, 1193
BbvI GCAGC 1 cut(s) 948
BccI CCATC 7 cut(s) 823, 1039, 1133, 1258, 1439, 1453, 1490
BceAI ACGGC 3 cut(s) 195, 509, 839
BcgI CGANNNNNNTGC 2 cut(s) 220, 254
BciVI GTATCC 1 cut(s) 1562
BcoDI GTCTC 2 cut(s) 36, 606
BfaI CTAG 5 cut(s) 552, 795, 864, 1250, 1427
BfuAI ACCTGC 1 cut(s) 967
BfuI GTATCC 1 cut(s) 1562
BglI GCCNNNNNGGC 3 cut(s) 561, 860, 1583
BisI GCNGC 7 cut(s) 13, 522, 727, 730, 937, 1499, 1584
BlnI CCTAGG 2 cut(s) 794, 1426
BlsI GCNGC 7 cut(s) 14, 523, 728, 731, 938, 1500, 1585
Bme18I GGWCC 2 cut(s) 798, 1597
BmeT110I CYCGRG 1 cut(s) 638
BmgBI CACGTC 1 cut(s) 616
BmgT120I GGNCC 4 cut(s) 33, 731, 798, 1597
BmiI GGNNCC 3 cut(s) 1161, 1497, 1587
BmsI GCATC 4 cut(s) 732, 824, 846, 1332
BmtI GCTAGC 1 cut(s) 867
BpiI GAAGAC 4 cut(s) 496, 770, 950, 1193
Bpu10I CCTNAGC 1 cut(s) 341
Bpu14I TTCGAA 1 cut(s) 405
BpuEI CTTGAG 4 cut(s) 173, 497, 1244, 1343
Bsc4I CCNNNNNNNGG 8 cut(s) 117, 213, 974, 1170, 1224, 1264, 1492, 1537
Bse1I ACTGG 1 cut(s) 841
Bse3DI GCAATG 2 cut(s) 516, 1578
BseGI GGATG 8 cut(s) 163, 834, 837, 839, 1054, 1273, 1450, 1482
BseLI CCNNNNNNNGG 8 cut(s) 117, 213, 974, 1170, 1224, 1264, 1492, 1537
BseMI GCAATG 2 cut(s) 516, 1578
BseNI ACTGG 1 cut(s) 841
BseRI GAGGAG 5 cut(s) 440, 818, 821, 1286, 1340
BseSI GKGCMC 2 cut(s) 414, 1164
BseXI GCAGC 1 cut(s) 948
Bsh1236I CGCG 2 cut(s) 747, 987
BshFI GGCC 5 cut(s) 35, 732, 912, 1071, 1481
BshNI GGYRCC 2 cut(s) 1159, 1585
BsiHKCI CYCGRG 1 cut(s) 638
BslFI GGGAC 2 cut(s) 517, 854
BslI CCNNNNNNNGG 8 cut(s) 117, 213, 974, 1170, 1224, 1264, 1492, 1537
BsmAI GTCTC 2 cut(s) 36, 606
BsmBI CGTCTC 2 cut(s) 36, 606
BsmFI GGGAC 2 cut(s) 517, 854
BsnI GGCC 5 cut(s) 35, 732, 912, 1071, 1481
BsoBI CYCGRG 1 cut(s) 638
Bsp119I TTCGAA 1 cut(s) 405
Bsp1286I GDGCHC 2 cut(s) 414, 1164
Bsp143I GATC 2 cut(s) 1437, 1523
BspANI GGCC 5 cut(s) 35, 732, 912, 1071, 1481
BspFNI CGCG 2 cut(s) 747, 987
BspHI TCATGA 1 cut(s) 447
BspLI GGNNCC 3 cut(s) 1161, 1497, 1587
BspMI ACCTGC 1 cut(s) 967
BspOI GCTAGC 1 cut(s) 867
BspT104I TTCGAA 1 cut(s) 405
BspT107I GGYRCC 2 cut(s) 1159, 1585
BsrDI GCAATG 2 cut(s) 516, 1578
BsrI ACTGG 1 cut(s) 841
BssMI GATC 2 cut(s) 1437, 1523
BssT1I CCWWGG 7 cut(s) 559, 794, 878, 1347, 1407, 1426, 1531
Bst4CI ACNGT 3 cut(s) 949, 1036, 1296
Bst6I CTCTTC 3 cut(s) 80, 659, 1355
BstBI TTCGAA 1 cut(s) 405
BstC8I GCNNGC 4 cut(s) 865, 985, 1176, 1238
BstDEI CTNAG 1 cut(s) 341
BstDSI CCRYGG 2 cut(s) 1035, 1164
BstF5I GGATG 8 cut(s) 163, 834, 837, 839, 1054, 1273, 1450, 1482
BstFNI CGCG 2 cut(s) 747, 987
BstHHI GCGC 2 cut(s) 17, 747
BstKTI GATC 2 cut(s) 1440, 1526
BstMAI GTCTC 2 cut(s) 36, 606
BstMBI GATC 2 cut(s) 1437, 1523
BstSLI GKGCMC 2 cut(s) 414, 1164
BstUI CGCG 2 cut(s) 747, 987
BstV1I GCAGC 1 cut(s) 948
BstV2I GAAGAC 4 cut(s) 496, 770, 950, 1193
BstXI CCANNNNNNTGG 1 cut(s) 193
BsuI GTATCC 1 cut(s) 1562
BsuRI GGCC 5 cut(s) 35, 732, 912, 1071, 1481
BtgI CCRYGG 2 cut(s) 1035, 1164
BtgZI GCGATG 1 cut(s) 1002
BtrI CACGTC 1 cut(s) 616
BtsCI GGATG 8 cut(s) 163, 834, 837, 839, 1054, 1273, 1450, 1482
BveI ACCTGC 1 cut(s) 967
Cac8I GCNNGC 4 cut(s) 865, 985, 1176, 1238
CciI TCATGA 1 cut(s) 447
CfoI GCGC 2 cut(s) 17, 747
Cfr13I GGNCC 4 cut(s) 33, 731, 798, 1597
CseI GACGC 3 cut(s) 355, 856, 1016
Csp6I GTAC 4 cut(s) 133, 249, 1091, 1511
CspCI CAANNNNNGTGG 2 cut(s) 952, 987
CviQI GTAC 4 cut(s) 133, 249, 1091, 1511
DdeI CTNAG 1 cut(s) 341
DpnI GATC 2 cut(s) 1439, 1525
DpnII GATC 2 cut(s) 1437, 1523
Eam1104I CTCTTC 3 cut(s) 80, 659, 1355
EarI CTCTTC 3 cut(s) 80, 659, 1355
EciI GGCGGA 2 cut(s) 1192, 1564
Eco130I CCWWGG 7 cut(s) 559, 794, 878, 1347, 1407, 1426, 1531
Eco32I GATATC 1 cut(s) 289
Eco47I GGWCC 2 cut(s) 798, 1597
Eco88I CYCGRG 1 cut(s) 638
EcoRI GAATTC 2 cut(s) 275, 1076
EcoRV GATATC 1 cut(s) 289
EcoT14I CCWWGG 7 cut(s) 559, 794, 878, 1347, 1407, 1426, 1531
EcoT22I ATGCAT 1 cut(s) 839
ErhI CCWWGG 7 cut(s) 559, 794, 878, 1347, 1407, 1426, 1531
Esp3I CGTCTC 2 cut(s) 36, 606
FalI AAGNNNNNCTT 2 cut(s) 704, 736
FaqI GGGAC 2 cut(s) 517, 854
FauI CCCGC 1 cut(s) 1522
FblI GTMKAC 1 cut(s) 1026
Fnu4HI GCNGC 7 cut(s) 13, 522, 727, 730, 937, 1499, 1584
FokI GGATG 8 cut(s) 170, 824, 841, 846, 1061, 1280, 1457, 1469
Fsp4HI GCNGC 7 cut(s) 13, 522, 727, 730, 937, 1499, 1584
FspBI CTAG 5 cut(s) 552, 795, 864, 1250, 1427
GlaI GCGC 2 cut(s) 16, 746
GluI GCNGC 7 cut(s) 13, 522, 727, 730, 937, 1499, 1584
HaeIII GGCC 5 cut(s) 35, 732, 912, 1071, 1481
HgaI GACGC 3 cut(s) 355, 856, 1016
HhaI GCGC 2 cut(s) 17, 747
Hin6I GCGC 2 cut(s) 15, 745
HinP1I GCGC 2 cut(s) 15, 745
HincII GTYRAC 4 cut(s) 382, 394, 592, 1027
HindII GTYRAC 4 cut(s) 382, 394, 592, 1027
HindIII AAGCTT 5 cut(s) 149, 338, 473, 905, 1221
HinfI GANTC 6 cut(s) 56, 164, 530, 641, 918, 929
HpaI GTTAAC 2 cut(s) 394, 592
HphI GGTGA 3 cut(s) 961, 1024, 1486
Hpy166II GTNNAC 5 cut(s) 382, 394, 592, 1027, 1420
Hpy188I TCNGA 1 cut(s) 1291
Hpy188III TCNNGA 9 cut(s) 260, 280, 448, 673, 922, 1042, 1261, 1456, 1603
Hpy8I GTNNAC 5 cut(s) 382, 394, 592, 1027, 1420
Hpy99I CGWCG 2 cut(s) 530, 1010
HpyCH4III ACNGT 3 cut(s) 949, 1036, 1296
HpyCH4IV ACGT 2 cut(s) 251, 615
HpyCH4V TGCA 8 cut(s) 4, 298, 484, 499, 787, 837, 1128, 1210
HpyF3I CTNAG 1 cut(s) 341
HpySE526I ACGT 2 cut(s) 251, 615
HspAI GCGC 2 cut(s) 15, 745
KspAI GTTAAC 2 cut(s) 394, 592
Kzo9I GATC 2 cut(s) 1437, 1523
LmnI GCTCC 2 cut(s) 228, 1495
LpnPI CCDG 2 cut(s) 854, 972
Lsp1109I GCAGC 1 cut(s) 948
LweI GCATC 4 cut(s) 732, 824, 846, 1332
MaeI CTAG 5 cut(s) 552, 795, 864, 1250, 1427
MaeII ACGT 2 cut(s) 251, 615
MaeIII GTNAC 2 cut(s) 507, 919
MalI GATC 2 cut(s) 1439, 1525
MboI GATC 2 cut(s) 1437, 1523
MhlI GDGCHC 2 cut(s) 414, 1164
MluCI AATT 5 cut(s) 171, 275, 542, 1076, 1543
MlyI GAGTC 6 cut(s) 50, 173, 539, 650, 927, 938
MmeI TCCRAC 1 cut(s) 1258
Mph1103I ATGCAT 1 cut(s) 839
MroXI GAANNNNTTC 1 cut(s) 668
MseI TTAA 4 cut(s) 393, 546, 591, 1542
MvnI CGCG 2 cut(s) 747, 987
NdeII GATC 2 cut(s) 1437, 1523
NheI GCTAGC 1 cut(s) 863
NlaIV GGNNCC 3 cut(s) 1161, 1497, 1587
NmuCI GTSAC 2 cut(s) 507, 919
NsiI ATGCAT 1 cut(s) 839
NspV TTCGAA 1 cut(s) 405
PagI TCATGA 1 cut(s) 447
PaqCI CACCTGC 1 cut(s) 967
PcsI WCGNNNNNNNCGW 3 cut(s) 678, 929, 1032
PdmI GAANNNNTTC 1 cut(s) 668
PflMI CCANNNNNTGG 1 cut(s) 1224
PkrI GCNGC 7 cut(s) 14, 523, 728, 731, 938, 1500, 1585
PleI GAGTC 6 cut(s) 50, 172, 538, 649, 926, 937
PpsI GAGTC 6 cut(s) 50, 172, 538, 649, 926, 937
PspN4I GGNNCC 3 cut(s) 1161, 1497, 1587
PspPI GGNCC 4 cut(s) 33, 731, 798, 1597
RsaI GTAC 4 cut(s) 134, 250, 1092, 1512
RsaNI GTAC 4 cut(s) 133, 249, 1091, 1511
SalI GTCGAC 1 cut(s) 1025
SaqAI TTAA 4 cut(s) 393, 546, 591, 1542
SatI GCNGC 7 cut(s) 13, 522, 727, 730, 937, 1499, 1584
Sau3AI GATC 2 cut(s) 1437, 1523
Sau96I GGNCC 4 cut(s) 33, 731, 798, 1597
SchI GAGTC 6 cut(s) 50, 173, 539, 650, 927, 938
SduI GDGCHC 2 cut(s) 414, 1164
SfaNI GCATC 4 cut(s) 732, 824, 846, 1332
SfuI TTCGAA 1 cut(s) 405
SinI GGWCC 2 cut(s) 798, 1597
SmlI CTYRAG 4 cut(s) 152, 476, 1259, 1322
SmoI CTYRAG 4 cut(s) 152, 476, 1259, 1322
Sse9I AATT 5 cut(s) 171, 275, 542, 1076, 1543
SspMI CTAG 5 cut(s) 552, 795, 864, 1250, 1427
StyI CCWWGG 7 cut(s) 559, 794, 878, 1347, 1407, 1426, 1531
TaaI ACNGT 3 cut(s) 949, 1036, 1296
TaiI ACGT 2 cut(s) 254, 618
TaqII GACCGA 1 cut(s) 815
TasI AATT 5 cut(s) 171, 275, 542, 1076, 1543
TauI GCSGC 5 cut(s) 524, 729, 732, 1501, 1586
Tru1I TTAA 4 cut(s) 393, 546, 591, 1542
Tru9I TTAA 4 cut(s) 393, 546, 591, 1542
TseFI GTSAC 2 cut(s) 507, 919
TseI GCWGC 2 cut(s) 12, 936
Tsp45I GTSAC 2 cut(s) 507, 919
TspDTI ATGAA 8 cut(s) 339, 436, 725, 834, 956, 989, 1069, 1549
TspGWI ACGGA 2 cut(s) 437, 1610
Van91I CCANNNNNTGG 1 cut(s) 1224
VpaK11BI GGWCC 2 cut(s) 798, 1597
XapI RAATTY 4 cut(s) 171, 275, 542, 1076
XcmI CCANNNNNNNNNTGG 1 cut(s) 1414
XmaJI CCTAGG 2 cut(s) 794, 1426
XmiI GTMKAC 1 cut(s) 1026
XmnI GAANNNNTTC 1 cut(s) 668
XspI CTAG 5 cut(s) 552, 795, 864, 1250, 1427
Zsp2I ATGCAT 1 cut(s) 839
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.