FvH4_7g04123

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb7
OG0000385
Physical Location & Seq
Reverse (-)
4721322 .. 4721786
465 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_7g04123.t1

Sequence Viewer

Length: 465 bp
ATGCCGGGCTTAACATGGAGGGCGGCATCATATGAAAAATTAGTCTCGGAGCCTAAGATGTTCAATGGAGAGAGGAATGCCAAAGTCTTGGAAAATTTCATATGGGACATCGAGCAATACTTCAAAACTGCTCGCATACCAGAATGGGAGAAAGTCTCTATGGCTTCAATGTACCTTGAGGGTGATGCAAAATTATGGTGGAGAACAAGAGTGCAAGACGCAGAGGAGAATGAGGACGAGCATTTACTTGAAAATTGGAATGCTCTAAAGAGGGAGTTACGAAGTCAGTTCATGCCTTCCAACTCGGCATGGATGGCTCGCGAAGCATTGAGGAATTTGAAAATGGATTCCTCCATAAGGGAGTACATCAAGGAGTTATGTTCCTTGATACTTAACATCCATAACATGGCAGAAGAAGATAAGCTATTTAGCTTCATGGCGGGATTACAACCTTGGGCGATATAA
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

155

Amino Acids

18.32

Weight (kDa)

5.2

Isoelectric Point (pI)

53.79

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 17 - 151 5.9e-07 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 54 - 151 2.3e-17 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)
AccB7I CCANNNNNTGG 1 cut(s) 406
AccII CGCG 1 cut(s) 321
AciI CCGC 2 cut(s) 23, 440
AcsI RAATTY 2 cut(s) 94, 334
AfaI GTAC 2 cut(s) 173, 365
AfiI CCNNNNNNNGG 2 cut(s) 357, 406
AgsI TTSAA 5 cut(s) 64, 124, 168, 251, 340
AluBI AGCT 2 cut(s) 424, 432
AluI AGCT 2 cut(s) 424, 432
Alw26I GTCTC 2 cut(s) 49, 160
ApoI RAATTY 2 cut(s) 94, 334
AsuC2I CCSGG 1 cut(s) 6
AsuHPI GGTGA 1 cut(s) 194
BccI CCATC 1 cut(s) 307
BcnI CCSGG 1 cut(s) 6
BcoDI GTCTC 2 cut(s) 49, 160
BisI GCNGC 1 cut(s) 24
BlsI GCNGC 1 cut(s) 25
Bme1390I CCNGG 1 cut(s) 6
BmiI GGNNCC 1 cut(s) 51
BmrFI CCNGG 1 cut(s) 6
BmsI GCATC 2 cut(s) 35, 175
BplI GAGNNNNNCTC 2 cut(s) 140, 172
BpuEI CTTGAG 1 cut(s) 197
BpuMI CCSGG 1 cut(s) 6
BsaJI CCNNGG 1 cut(s) 452
Bsc4I CCNNNNNNNGG 2 cut(s) 357, 406
BseDI CCNNGG 1 cut(s) 452
BseGI GGATG 2 cut(s) 318, 396
BseLI CCNNNNNNNGG 2 cut(s) 357, 406
BseRI GAGGAG 1 cut(s) 239
Bsh1236I CGCG 1 cut(s) 321
BsiSI CCGG 1 cut(s) 5
BslFI GGGAC 1 cut(s) 119
BslI CCNNNNNNNGG 2 cut(s) 357, 406
BsmAI GTCTC 2 cut(s) 49, 160
BsmFI GGGAC 1 cut(s) 119
BsmI GAATGC 2 cut(s) 82, 265
Bsp68I TCGCGA 1 cut(s) 321
BspACI CCGC 2 cut(s) 23, 440
BspFNI CGCG 1 cut(s) 321
BspLI GGNNCC 1 cut(s) 51
BssECI CCNNGG 1 cut(s) 452
BssT1I CCWWGG 1 cut(s) 452
BstC8I GCNNGC 2 cut(s) 133, 319
BstDEI CTNAG 1 cut(s) 54
BstENI CCTNNNNNAGG 1 cut(s) 355
BstF5I GGATG 2 cut(s) 318, 396
BstFNI CGCG 1 cut(s) 321
BstMAI GTCTC 2 cut(s) 49, 160
BstMWI GCNNNNNNNGC 2 cut(s) 314, 323
BstSCI CCNGG 1 cut(s) 4
BstUI CGCG 1 cut(s) 321
BstXI CCANNNNNNTGG 1 cut(s) 88
BtsCI GGATG 2 cut(s) 318, 396
BtuMI TCGCGA 1 cut(s) 321
Cac8I GCNNGC 2 cut(s) 133, 319
CseI GACGC 1 cut(s) 227
Csp6I GTAC 2 cut(s) 172, 364
CviAII CATG 5 cut(s) 15, 292, 309, 406, 436
CviJI RGCY 6 cut(s) 9, 52, 164, 317, 424, 432
CviKI_1 RGCY 6 cut(s) 9, 52, 164, 317, 424, 432
CviQI GTAC 2 cut(s) 172, 364
DdeI CTNAG 1 cut(s) 54
Eco130I CCWWGG 1 cut(s) 452
EcoNI CCTNNNNNAGG 1 cut(s) 355
EcoT14I CCWWGG 1 cut(s) 452
ErhI CCWWGG 1 cut(s) 452
FaeI CATG 5 cut(s) 18, 295, 312, 409, 439
FaqI GGGAC 1 cut(s) 119
FatI CATG 5 cut(s) 14, 291, 308, 405, 435
FauI CCCGC 1 cut(s) 433
FauNDI CATATG 2 cut(s) 31, 101
Fnu4HI GCNGC 1 cut(s) 24
FokI GGATG 2 cut(s) 325, 383
Fsp4HI GCNGC 1 cut(s) 24
GluI GCNGC 1 cut(s) 24
HapII CCGG 1 cut(s) 5
HgaI GACGC 1 cut(s) 227
Hin1II CATG 5 cut(s) 18, 295, 312, 409, 439
HinfI GANTC 1 cut(s) 347
HpaII CCGG 1 cut(s) 5
HphI GGTGA 1 cut(s) 194
Hpy188I TCNGA 1 cut(s) 49
Hpy188III TCNNGA 1 cut(s) 320
HpyAV CCTTC 1 cut(s) 306
HpyCH4V TGCA 2 cut(s) 188, 214
HpyF10VI GCNNNNNNNGC 2 cut(s) 314, 323
HpyF3I CTNAG 1 cut(s) 54
Hsp92II CATG 5 cut(s) 18, 295, 312, 409, 439
LmnI GCTCC 1 cut(s) 49
LpnPI CCDG 2 cut(s) 18, 153
LweI GCATC 2 cut(s) 35, 175
MaeIII GTNAC 1 cut(s) 276
MboII GAAGA 2 cut(s) 425, 428
MluCI AATT 5 cut(s) 38, 94, 191, 253, 334
MmeI TCCRAC 1 cut(s) 324
MnlI CCTC 8 cut(s) 12, 66, 172, 217, 226, 264, 324, 361
MseI TTAA 2 cut(s) 11, 393
MspI CCGG 1 cut(s) 5
MspR9I CCNGG 1 cut(s) 6
Mva1269I GAATGC 2 cut(s) 82, 265
MvnI CGCG 1 cut(s) 321
MwoI GCNNNNNNNGC 2 cut(s) 314, 323
NciI CCSGG 1 cut(s) 6
NdeI CATATG 2 cut(s) 31, 101
NlaIII CATG 5 cut(s) 18, 295, 312, 409, 439
NlaIV GGNNCC 1 cut(s) 51
NmeAIII GCCGAG 1 cut(s) 284
NruI TCGCGA 1 cut(s) 321
PctI GAATGC 2 cut(s) 82, 265
PfeI GAWTC 1 cut(s) 347
PflMI CCANNNNNTGG 1 cut(s) 406
PkrI GCNGC 1 cut(s) 25
PspN4I GGNNCC 1 cut(s) 51
RruI TCGCGA 1 cut(s) 321
RsaI GTAC 2 cut(s) 173, 365
RsaNI GTAC 2 cut(s) 172, 364
SaqAI TTAA 2 cut(s) 11, 393
SatI GCNGC 1 cut(s) 24
ScrFI CCNGG 1 cut(s) 6
SetI ASST 4 cut(s) 177, 426, 434, 454
SfaNI GCATC 2 cut(s) 35, 175
SmlI CTYRAG 1 cut(s) 176
SmoI CTYRAG 1 cut(s) 176
Sse9I AATT 5 cut(s) 38, 94, 191, 253, 334
SsiI CCGC 2 cut(s) 23, 440
StyD4I CCNGG 1 cut(s) 4
StyI CCWWGG 1 cut(s) 452
TaqI TCGA 1 cut(s) 111
TasI AATT 5 cut(s) 38, 94, 191, 253, 334
TatI WGTACW 1 cut(s) 363
TauI GCSGC 1 cut(s) 26
TfiI GAWTC 1 cut(s) 347
Tru1I TTAA 2 cut(s) 11, 393
Tru9I TTAA 2 cut(s) 11, 393
TspDTI ATGAA 4 cut(s) 48, 88, 280, 424
Van91I CCANNNNNTGG 1 cut(s) 406
XagI CCTNNNNNAGG 1 cut(s) 355
XapI RAATTY 2 cut(s) 94, 334
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.