FvH4_3g37282

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0006394
Physical Location & Seq
Forward (+)
31985529 .. 31989731
4203 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g37282.t1

Sequence Viewer

Length: 1125 bp
ATGGCTGGGAAATCGACAAAGACGGCTGGGAAGTCGGCTATTGAGCCTCTAGTTTCGGGTGAATTATCTCACTTGGAATTTGAGATTCAATCTCATAAGGAGGCTACCGCAGCTCGTCTTGAGGAGCTGCAAACGTCTGTTCAAAAATCTCTTGATGCTAATCTAGTAAGCATTCAAAGCATGATTGCTGAACAGTTGCAGAAGCAGCTCTCGTCCATTAGGTTGGAAGGGAACCAGTTTGTCATAACAAAACCTGGAGCTGCTGCTATTCCTCAACCAGATGGTTCAGTTCGCTTTGGATCTGTAACAGTTCTTACTCAGGGTATGACTGTGGCCACGGAGAGCTCTTCGTCATCAGTTTTGGCTAGATTTGAGGGTAATAATACTTCTTCTGGTCCTTTTGATTTAGATCTAAATGTTAATGACGTGTTTATGCCTTTAGCTCCACTATCTGTTAGTCGGAACCCTATTCTAGGCCTTGGTACAAGTGCTATGATGACTATTGGTGTTGATTCTTCAGTAGATATGTCTATGGTTTTTGGATCTAAGAGTGATGGTGGTTATGACTATTCAATCCATTATAAGTCTGGAAAGAACAATAGTGGCCCGGATGCACTCTCCAGAAGGGAAGAGTTGAGTACACCAACTTCTCAAGTTATCTCCGAGTATAGCTCACTGAACATGGCGTCAGGTTTCTCATCACCCTTGCATAAGTACATTTTGGAAATGCAGGAGGCTTGTAAAAAGGATGCTGAGGCTGCGCCCATCCTAAAGAAACTGGAAGATGGTGAAGTTGTTGACTCAAGATATTCAATGCCTAATGCTCAGCTACTTTACAAGGGAAAAATCTTTGTTCCAAACACAGATGATTGGAGACAAAAAATTGTAGCTGAATTCCACAATGGACTCAGTGGTGGACATCCTGGAGTGCATAGGACTGAAAAAAGAGTAAAGCTCTCATTTGCTTGGCCTGGAATGCATGGTGATATAAAGCAATTTGTTGCAACTTGTCATGTGTGTCAAAAGAACCACTATGAAACTGTCCATCCTCCAGGTTTATTGCAACCAAATTCCATTCCATCCAAAGCTTGGTGTAACACCCTGACCCAGGTGTTAGAAGAATAA
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

375

Amino Acids

40.53

Weight (kDa)

6.02

Isoelectric Point (pI)

46.35

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Integrase_H2C2 PF17921 290 - 344 1.3e-18 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)
AanI TTATAA 1 cut(s) 582
AccB7I CCANNNNNTGG 1 cut(s) 1089
AciI CCGC 1 cut(s) 108
AclWI GGATC 2 cut(s) 307, 550
AcoI YGGCCR 1 cut(s) 333
AcsI RAATTY 3 cut(s) 77, 893, 1069
AcuI CTGAAG 1 cut(s) 501
AcyI GRCGYC 1 cut(s) 686
AfaI GTAC 3 cut(s) 484, 640, 716
AfiI CCNNNNNNNGG 3 cut(s) 473, 1089, 1108
AflIII ACRYGT 1 cut(s) 426
AgsI TTSAA 5 cut(s) 89, 143, 176, 573, 813
AjiI CACGTC 1 cut(s) 427
AjnI CCWGG 5 cut(s) 253, 922, 970, 1051, 1107
Alw21I GWGCWC 1 cut(s) 347
Alw26I GTCTC 1 cut(s) 868
AlwI GGATC 2 cut(s) 307, 550
AoxI GGCC 4 cut(s) 333, 475, 604, 968
ApeKI GCWGC 6 cut(s) 110, 127, 205, 260, 263, 758
ApoI RAATTY 3 cut(s) 77, 893, 1069
AspLEI GCGC 1 cut(s) 763
AspS9I GGNCC 2 cut(s) 395, 605
AsuC2I CCSGG 1 cut(s) 608
AsuHPI GGTGA 4 cut(s) 71, 693, 800, 995
AvaII GGWCC 1 cut(s) 395
BalI TGGCCA 1 cut(s) 335
BanII GRGCYC 1 cut(s) 347
BarI GAAGNNNNNNTAC 4 cut(s) 370, 402, 631, 663
Bbv12I GWGCWC 1 cut(s) 347
BbvCI CCTCAGC 1 cut(s) 753
BbvI GCAGC 6 cut(s) 114, 122, 217, 247, 250, 745
BccI CCATC 6 cut(s) 275, 548, 773, 779, 1053, 1087
BceAI ACGGC 1 cut(s) 39
BciT130I CCWGG 5 cut(s) 255, 924, 972, 1053, 1109
BcnI CCSGG 1 cut(s) 608
BcoDI GTCTC 1 cut(s) 868
BfaI CTAG 4 cut(s) 50, 164, 366, 473
BglII AGATCT 1 cut(s) 409
BisI GCNGC 6 cut(s) 111, 128, 206, 261, 264, 759
BlpI GCTNAGC 1 cut(s) 825
BlsI GCNGC 6 cut(s) 112, 129, 207, 262, 265, 760
Bme1390I CCNGG 6 cut(s) 255, 608, 924, 972, 1053, 1109
Bme18I GGWCC 1 cut(s) 395
BmgBI CACGTC 1 cut(s) 427
BmgT120I GGNCC 2 cut(s) 395, 605
BmiI GGNNCC 2 cut(s) 233, 464
BmrFI CCNGG 6 cut(s) 255, 608, 924, 972, 1053, 1109
BmsI GCATC 3 cut(s) 145, 601, 739
BplI GAGNNNNNCTC 4 cut(s) 656, 688, 939, 971
BpmI CTGGAG 4 cut(s) 276, 604, 945, 1035
Bpu10I CCTNAGC 1 cut(s) 753
Bpu1102I GCTNAGC 1 cut(s) 825
BpuEI CTTGAG 3 cut(s) 140, 636, 787
BpuMI CCSGG 1 cut(s) 608
BsaBI GATNNNNATC 2 cut(s) 159, 408
BsaHI GRCGYC 1 cut(s) 686
BsaJI CCNNGG 3 cut(s) 336, 478, 1107
Bsc4I CCNNNNNNNGG 3 cut(s) 473, 1089, 1108
Bse1I ACTGG 2 cut(s) 235, 783
Bse8I GATNNNNATC 2 cut(s) 159, 408
BseBI CCWGG 5 cut(s) 255, 924, 972, 1053, 1109
BseDI CCNNGG 3 cut(s) 336, 478, 1107
BseGI GGATG 6 cut(s) 616, 754, 765, 919, 1045, 1079
BseJI GATNNNNATC 2 cut(s) 159, 408
BseLI CCNNNNNNNGG 3 cut(s) 473, 1089, 1108
BseMII CTCAG 4 cut(s) 332, 744, 839, 922
BseNI ACTGG 2 cut(s) 235, 783
BseRI GAGGAG 1 cut(s) 137
BseXI GCAGC 6 cut(s) 114, 122, 217, 247, 250, 745
BseYI CCCAGC 2 cut(s) 5, 26
BshFI GGCC 4 cut(s) 335, 477, 606, 970
BsiHKAI GWGCWC 1 cut(s) 347
BsiSI CCGG 1 cut(s) 608
BslI CCNNNNNNNGG 3 cut(s) 473, 1089, 1108
BsmAI GTCTC 1 cut(s) 868
BsmI GAATGC 2 cut(s) 171, 981
BsnI GGCC 4 cut(s) 335, 477, 606, 970
Bsp1286I GDGCHC 1 cut(s) 347
Bsp143I GATC 3 cut(s) 299, 409, 542
Bsp1720I GCTNAGC 1 cut(s) 825
BspACI CCGC 1 cut(s) 108
BspANI GGCC 4 cut(s) 335, 477, 606, 970
BspCNI CTCAG 4 cut(s) 331, 745, 838, 921
BspLI GGNNCC 2 cut(s) 233, 464
BspPI GGATC 2 cut(s) 307, 550
BspQI GCTCTTC 1 cut(s) 352
BsrI ACTGG 2 cut(s) 235, 783
BssECI CCNNGG 3 cut(s) 336, 478, 1107
BssMI GATC 3 cut(s) 299, 409, 542
BssNI GRCGYC 1 cut(s) 686
BssT1I CCWWGG 1 cut(s) 478
Bst2UI CCWGG 5 cut(s) 255, 924, 972, 1053, 1109
Bst4CI ACNGT 4 cut(s) 195, 310, 331, 1042
Bst6I CTCTTC 2 cut(s) 352, 624
BstACI GRCGYC 1 cut(s) 686
BstDEI CTNAG 5 cut(s) 318, 546, 753, 825, 908
BstDSI CCRYGG 1 cut(s) 336
BstENI CCTNNNNNAGG 2 cut(s) 471, 1106
BstF5I GGATG 6 cut(s) 616, 754, 765, 919, 1045, 1079
BstHHI GCGC 1 cut(s) 763
BstKTI GATC 3 cut(s) 302, 412, 545
BstMAI GTCTC 1 cut(s) 868
BstMBI GATC 3 cut(s) 299, 409, 542
BstMWI GCNNNNNNNGC 5 cut(s) 110, 177, 205, 758, 976
BstNI CCWGG 5 cut(s) 255, 924, 972, 1053, 1109
BstSCI CCNGG 6 cut(s) 253, 606, 922, 970, 1051, 1107
BstV1I GCAGC 6 cut(s) 114, 122, 217, 247, 250, 745
BstX2I RGATCY 3 cut(s) 299, 409, 542
BstXI CCANNNNNNTGG 1 cut(s) 223
BstYI RGATCY 3 cut(s) 299, 409, 542
BsuRI GGCC 4 cut(s) 335, 477, 606, 970
BtgI CCRYGG 1 cut(s) 336
BtrI CACGTC 1 cut(s) 427
BtsCI GGATG 6 cut(s) 616, 754, 765, 919, 1045, 1079
BtsIMutI CAGTG 2 cut(s) 674, 916
CfoI GCGC 1 cut(s) 763
Cfr13I GGNCC 2 cut(s) 395, 605
CseI GACGC 1 cut(s) 675
Csp6I GTAC 3 cut(s) 483, 639, 715
CviAII CATG 4 cut(s) 181, 682, 980, 1013
CviQI GTAC 3 cut(s) 483, 639, 715
DdeI CTNAG 5 cut(s) 318, 546, 753, 825, 908
DpnI GATC 3 cut(s) 301, 411, 544
DpnII GATC 3 cut(s) 299, 409, 542
EaeI YGGCCR 1 cut(s) 333
Eam1104I CTCTTC 2 cut(s) 352, 624
EarI CTCTTC 2 cut(s) 352, 624
Ecl136II GAGCTC 1 cut(s) 345
Eco130I CCWWGG 1 cut(s) 478
Eco147I AGGCCT 1 cut(s) 477
Eco24I GRGCYC 1 cut(s) 347
Eco47I GGWCC 1 cut(s) 395
Eco53kI GAGCTC 1 cut(s) 345
Eco57I CTGAAG 1 cut(s) 501
EcoICRI GAGCTC 1 cut(s) 345
EcoNI CCTNNNNNAGG 2 cut(s) 471, 1106
EcoRI GAATTC 1 cut(s) 893
EcoRII CCWGG 5 cut(s) 253, 922, 970, 1051, 1107
EcoT14I CCWWGG 1 cut(s) 478
EcoT22I ATGCAT 1 cut(s) 981
EcoT38I GRGCYC 1 cut(s) 347
ErhI CCWWGG 1 cut(s) 478
FaeI CATG 4 cut(s) 184, 685, 983, 1016
FatI CATG 4 cut(s) 180, 681, 979, 1012
Fnu4HI GCNGC 6 cut(s) 111, 128, 206, 261, 264, 759
FokI GGATG 6 cut(s) 623, 752, 761, 906, 1032, 1066
FriOI GRGCYC 1 cut(s) 347
Fsp4HI GCNGC 6 cut(s) 111, 128, 206, 261, 264, 759
FspBI CTAG 4 cut(s) 50, 164, 366, 473
GlaI GCGC 1 cut(s) 762
GluI GCNGC 6 cut(s) 111, 128, 206, 261, 264, 759
GsaI CCCAGC 2 cut(s) 9, 30
GsuI CTGGAG 4 cut(s) 276, 604, 945, 1035
HaeIII GGCC 4 cut(s) 335, 477, 606, 970
HapII CCGG 1 cut(s) 608
HgaI GACGC 1 cut(s) 675
HhaI GCGC 1 cut(s) 763
Hin1I GRCGYC 1 cut(s) 686
Hin1II CATG 4 cut(s) 184, 685, 983, 1016
Hin6I GCGC 1 cut(s) 761
HinP1I GCGC 1 cut(s) 761
HincII GTYRAC 1 cut(s) 799
HindII GTYRAC 1 cut(s) 799
HindIII AAGCTT 1 cut(s) 1086
HinfI GANTC 4 cut(s) 85, 512, 800, 906
HpaII CCGG 1 cut(s) 608
HphI GGTGA 4 cut(s) 71, 693, 800, 995
Hpy166II GTNNAC 3 cut(s) 641, 799, 917
Hpy188I TCNGA 2 cut(s) 462, 664
Hpy188III TCNNGA 5 cut(s) 119, 152, 588, 621, 804
Hpy8I GTNNAC 3 cut(s) 641, 799, 917
HpyAV CCTTC 2 cut(s) 221, 618
HpyCH4III ACNGT 4 cut(s) 195, 310, 331, 1042
HpyCH4IV ACGT 2 cut(s) 134, 426
HpyCH4V TGCA 9 cut(s) 130, 199, 614, 709, 730, 931, 979, 1004, 1063
HpyF10VI GCNNNNNNNGC 5 cut(s) 110, 177, 205, 758, 976
HpyF3I CTNAG 5 cut(s) 318, 546, 753, 825, 908
HpySE526I ACGT 2 cut(s) 134, 426
Hsp92I GRCGYC 1 cut(s) 686
Hsp92II CATG 4 cut(s) 184, 685, 983, 1016
HspAI GCGC 1 cut(s) 761
Kzo9I GATC 3 cut(s) 299, 409, 542
LguI GCTCTTC 1 cut(s) 352
LmnI GCTCC 3 cut(s) 124, 257, 448
Lsp1109I GCAGC 6 cut(s) 114, 122, 217, 247, 250, 745
LweI GCATC 3 cut(s) 145, 601, 739
MaeI CTAG 4 cut(s) 50, 164, 366, 473
MaeII ACGT 2 cut(s) 134, 426
MaeIII GTNAC 2 cut(s) 304, 1094
MalI GATC 3 cut(s) 301, 411, 544
MboI GATC 3 cut(s) 299, 409, 542
MboII GAAGA 5 cut(s) 339, 381, 507, 641, 794
MflI RGATCY 3 cut(s) 299, 409, 542
MhlI GDGCHC 1 cut(s) 347
MlsI TGGCCA 1 cut(s) 335
MluCI AATT 6 cut(s) 62, 77, 882, 893, 995, 1069
MluNI TGGCCA 1 cut(s) 335
MlyI GAGTC 2 cut(s) 794, 900
MmeI TCCRAC 2 cut(s) 204, 440
MnlI CCTC 8 cut(s) 57, 94, 115, 282, 367, 727, 748, 1059
Mox20I TGGCCA 1 cut(s) 335
Mph1103I ATGCAT 1 cut(s) 981
MscI TGGCCA 1 cut(s) 335
MseI TTAA 1 cut(s) 420
Msp20I TGGCCA 1 cut(s) 335
MspI CCGG 1 cut(s) 608
MspR9I CCNGG 6 cut(s) 255, 608, 924, 972, 1053, 1109
Mva1269I GAATGC 2 cut(s) 171, 981
MvaI CCWGG 5 cut(s) 255, 924, 972, 1053, 1109
MwoI GCNNNNNNNGC 5 cut(s) 110, 177, 205, 758, 976
NciI CCSGG 1 cut(s) 608
NdeII GATC 3 cut(s) 299, 409, 542
NlaIII CATG 4 cut(s) 184, 685, 983, 1016
NlaIV GGNNCC 2 cut(s) 233, 464
NsiI ATGCAT 1 cut(s) 981
PceI AGGCCT 1 cut(s) 477
PciSI GCTCTTC 1 cut(s) 352
PctI GAATGC 2 cut(s) 171, 981
PfeI GAWTC 2 cut(s) 85, 512
PflMI CCANNNNNTGG 1 cut(s) 1089
PfoI TCCNGGA 1 cut(s) 922
PkrI GCNGC 6 cut(s) 112, 129, 207, 262, 265, 760
PleI GAGTC 2 cut(s) 794, 900
PpsI GAGTC 2 cut(s) 794, 900
PsiI TTATAA 1 cut(s) 582
Psp124BI GAGCTC 1 cut(s) 347
Psp6I CCWGG 5 cut(s) 253, 922, 970, 1051, 1107
PspFI CCCAGC 2 cut(s) 5, 26
PspGI CCWGG 5 cut(s) 253, 922, 970, 1051, 1107
PspN4I GGNNCC 2 cut(s) 233, 464
PspPI GGNCC 2 cut(s) 395, 605
PsuI RGATCY 3 cut(s) 299, 409, 542
RsaI GTAC 3 cut(s) 484, 640, 716
RsaNI GTAC 3 cut(s) 483, 639, 715
SacI GAGCTC 1 cut(s) 347
SapI GCTCTTC 1 cut(s) 352
SaqAI TTAA 1 cut(s) 420
SatI GCNGC 6 cut(s) 111, 128, 206, 261, 264, 759
Sau3AI GATC 3 cut(s) 299, 409, 542
Sau96I GGNCC 2 cut(s) 395, 605
SchI GAGTC 2 cut(s) 794, 900
ScrFI CCNGG 6 cut(s) 255, 608, 924, 972, 1053, 1109
SduI GDGCHC 1 cut(s) 347
SfaNI GCATC 3 cut(s) 145, 601, 739
SinI GGWCC 1 cut(s) 395
SmlI CTYRAG 3 cut(s) 119, 651, 802
SmoI CTYRAG 3 cut(s) 119, 651, 802
Sse9I AATT 6 cut(s) 62, 77, 882, 893, 995, 1069
SseBI AGGCCT 1 cut(s) 477
SsiI CCGC 1 cut(s) 108
SspMI CTAG 4 cut(s) 50, 164, 366, 473
SstI GAGCTC 1 cut(s) 347
StuI AGGCCT 1 cut(s) 477
StyD4I CCNGG 6 cut(s) 253, 606, 922, 970, 1051, 1107
StyI CCWWGG 1 cut(s) 478
TaaI ACNGT 4 cut(s) 195, 310, 331, 1042
TaiI ACGT 2 cut(s) 137, 429
TaqI TCGA 1 cut(s) 14
TasI AATT 6 cut(s) 62, 77, 882, 893, 995, 1069
TatI WGTACW 2 cut(s) 638, 714
TfiI GAWTC 2 cut(s) 85, 512
Tru1I TTAA 1 cut(s) 420
Tru9I TTAA 1 cut(s) 420
TscAI CASTG 2 cut(s) 681, 916
TseI GCWGC 6 cut(s) 110, 127, 205, 260, 263, 758
TspDTI ATGAA 1 cut(s) 1050
TspGWI ACGGA 1 cut(s) 353
TspRI CASTG 2 cut(s) 681, 916
Van91I CCANNNNNTGG 1 cut(s) 1089
VpaK11BI GGWCC 1 cut(s) 395
XagI CCTNNNNNAGG 2 cut(s) 471, 1106
XapI RAATTY 3 cut(s) 77, 893, 1069
XcmI CCANNNNNNNNNTGG 2 cut(s) 584, 1086
XspI CTAG 4 cut(s) 50, 164, 366, 473
Zsp2I ATGCAT 1 cut(s) 981
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.