FvH4_4g03471

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000385
Physical Location & Seq
Forward (+)
3125606 .. 3126397
792 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g03471.t1

Sequence Viewer

Length: 792 bp
ATGACCGGTGACACATTGAAAGATCGCATTGCACGAGTCGAGGATTTTCTCGGCTACCCAACAAGTGATAGAGCGATTAGTCTCTCACTACAAGTTGATGAACTGAAGAATGAAACAAGAAGGATGCGAGAAGCATTCACGGTGCATGTTACCGAGGCGGAGACCAAGTTCCATGACATGATACAAGACTTAAATGCTTTATCGGATGCGGTAAAGGTAAGATTGACTGACATAGAAAAGAACATGGCATTGGCTGTAGCGCTTTTCACCAATGTTGGGCTCAACATGGAGGGTGGTATCATTCAAAAAGTTAGAGTCCCGGAGCCTAAGATGTTCAATGGAGAGAGGAATGCCAAAGTCTTAGAGAATTTCATATGGGACATCGAGCAATACTTCAAAATTGCTCGCATAGCGGATGGGGAGAAAGTCTCAATGGCCTTAATGTATCTTGAAGGAGATGCAAAGTTATGGTGGATAACGAGAGTGCAAGACGCGGAGGAGAATGAAGCTGAGCACCTACTTGAAAATTGGGATGCTCTCAAGAGGGAGTTACAGAGTCAGTTTATGCCTTGCAACTCGACATGGATGGCTCGTGAAGCATTAAGGAATCTGAAAATGGATTCCTCCATAAGAGAGTACGTCAAGGAGTTTTGTTCCTTGTTGCTTGACATCCACAACATGGCAGAAGAAGACAAGCTATTTAGCTTCATGGTGGGATTACAACCTTGGGCGAGACAAGAATTACGAAGGCAAAACGTTGGAGATTTGCAATCTGCACTAGCCTTATCCTAA
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

264

Amino Acids

30.42

Weight (kDa)

5.01

Isoelectric Point (pI)

39.75

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 109 - 262 8.9e-10 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 145 - 242 2.2e-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)
AccB7I CCANNNNNTGG 1 cut(s) 679
AccII CGCG 1 cut(s) 494
AciI CCGC 4 cut(s) 158, 209, 413, 494
AclI AACGTT 1 cut(s) 756
AcsI RAATTY 1 cut(s) 367
AcuI CTGAAG 1 cut(s) 125
AfaI GTAC 1 cut(s) 638
AfeI AGCGCT 1 cut(s) 261
AfiI CCNNNNNNNGG 2 cut(s) 276, 679
AgeI ACCGGT 1 cut(s) 5
AgsI TTSAA 6 cut(s) 19, 305, 337, 397, 452, 524
AjuI GAANNNNNNNTTGG 2 cut(s) 233, 265
AloI GAACNNNNNNTCC 2 cut(s) 152, 184
AluBI AGCT 3 cut(s) 509, 697, 705
AluI AGCT 3 cut(s) 509, 697, 705
Alw21I GWGCWC 1 cut(s) 516
Alw26I GTCTC 4 cut(s) 86, 155, 433, 727
Aor51HI AGCGCT 1 cut(s) 261
AoxI GGCC 1 cut(s) 435
ApoI RAATTY 1 cut(s) 367
AsiGI ACCGGT 1 cut(s) 5
AspLEI GCGC 1 cut(s) 262
AsuC2I CCSGG 1 cut(s) 320
AsuHPI GGTGA 2 cut(s) 20, 259
BanII GRGCYC 1 cut(s) 282
BauI CACGAG 2 cut(s) 33, 591
BbsI GAAGAC 1 cut(s) 696
Bbv12I GWGCWC 1 cut(s) 516
BccI CCATC 2 cut(s) 410, 580
BcnI CCSGG 1 cut(s) 320
BcoDI GTCTC 4 cut(s) 86, 155, 433, 727
BfaI CTAG 1 cut(s) 779
BfmI CTRYAG 1 cut(s) 255
BfoI RGCGCY 1 cut(s) 263
BlpI GCTNAGC 1 cut(s) 510
Bme1390I CCNGG 1 cut(s) 320
BmiI GGNNCC 1 cut(s) 324
BmrFI CCNGG 1 cut(s) 320
BmsI GCATC 4 cut(s) 114, 196, 448, 523
BpiI GAAGAC 1 cut(s) 696
BplI GAGNNNNNCTC 2 cut(s) 413, 445
Bpu1102I GCTNAGC 1 cut(s) 510
BpuEI CTTGAG 1 cut(s) 524
BpuMI CCSGG 1 cut(s) 320
BsaI GGTCTC 1 cut(s) 155
BsaJI CCNNGG 2 cut(s) 153, 725
BsaWI WCCGGW 1 cut(s) 5
BsaXI ACNNNNNCTCC 2 cut(s) 152, 182
Bsc4I CCNNNNNNNGG 2 cut(s) 276, 679
Bse118I RCCGGY 1 cut(s) 5
Bse3DI GCAATG 1 cut(s) 27
BseDI CCNNGG 2 cut(s) 153, 725
BseGI GGATG 6 cut(s) 129, 211, 421, 538, 591, 669
BseLI CCNNNNNNNGG 2 cut(s) 276, 679
BseMI GCAATG 1 cut(s) 27
BseMII CTCAG 1 cut(s) 501
BseRI GAGGAG 1 cut(s) 512
BsgI GTGCAG 1 cut(s) 759
Bsh1236I CGCG 1 cut(s) 494
BshFI GGCC 1 cut(s) 437
BshTI ACCGGT 1 cut(s) 5
BsiHKAI GWGCWC 1 cut(s) 516
BsiSI CCGG 2 cut(s) 6, 320
BslFI GGGAC 2 cut(s) 302, 392
BslI CCNNNNNNNGG 2 cut(s) 276, 679
BsmAI GTCTC 4 cut(s) 86, 155, 433, 727
BsmFI GGGAC 2 cut(s) 302, 392
BsmI GAATGC 2 cut(s) 134, 355
BsnI GGCC 1 cut(s) 437
Bso31I GGTCTC 1 cut(s) 155
Bsp1286I GDGCHC 2 cut(s) 282, 516
Bsp143I GATC 1 cut(s) 22
Bsp1720I GCTNAGC 1 cut(s) 510
BspACI CCGC 4 cut(s) 158, 209, 413, 494
BspANI GGCC 1 cut(s) 437
BspCNI CTCAG 1 cut(s) 502
BspFNI CGCG 1 cut(s) 494
BspLI GGNNCC 1 cut(s) 324
BspTNI GGTCTC 1 cut(s) 155
BsrDI GCAATG 1 cut(s) 27
BsrFI RCCGGY 1 cut(s) 5
BssAI RCCGGY 1 cut(s) 5
BssECI CCNNGG 2 cut(s) 153, 725
BssMI GATC 1 cut(s) 22
BssSI CACGAG 2 cut(s) 33, 591
BssT1I CCWWGG 1 cut(s) 725
Bst2BI CACGAG 2 cut(s) 33, 591
Bst4CI ACNGT 1 cut(s) 142
BstC8I GCNNGC 1 cut(s) 406
BstDEI CTNAG 3 cut(s) 327, 361, 510
BstF5I GGATG 6 cut(s) 129, 211, 421, 538, 591, 669
BstFNI CGCG 1 cut(s) 494
BstH2I RGCGCY 1 cut(s) 263
BstHHI GCGC 1 cut(s) 262
BstKTI GATC 1 cut(s) 25
BstMAI GTCTC 4 cut(s) 86, 155, 433, 727
BstMBI GATC 1 cut(s) 22
BstMWI GCNNNNNNNGC 2 cut(s) 410, 596
BstNSI RCATGY 1 cut(s) 149
BstSCI CCNGG 1 cut(s) 318
BstSFI CTRYAG 1 cut(s) 255
BstUI CGCG 1 cut(s) 494
BstV2I GAAGAC 1 cut(s) 696
BsuRI GGCC 1 cut(s) 437
BtsCI GGATG 6 cut(s) 129, 211, 421, 538, 591, 669
Cac8I GCNNGC 1 cut(s) 406
CfoI GCGC 1 cut(s) 262
Cfr10I RCCGGY 1 cut(s) 5
CseI GACGC 1 cut(s) 500
Csp6I GTAC 1 cut(s) 637
CspAI ACCGGT 1 cut(s) 5
CviAII CATG 8 cut(s) 146, 173, 178, 244, 286, 582, 679, 709
CviQI GTAC 1 cut(s) 637
DdeI CTNAG 3 cut(s) 327, 361, 510
DpnI GATC 1 cut(s) 24
DpnII GATC 1 cut(s) 22
EciI GGCGGA 1 cut(s) 173
Eco130I CCWWGG 1 cut(s) 725
Eco24I GRGCYC 1 cut(s) 282
Eco31I GGTCTC 1 cut(s) 155
Eco47III AGCGCT 1 cut(s) 261
Eco57I CTGAAG 1 cut(s) 125
EcoT14I CCWWGG 1 cut(s) 725
EcoT38I GRGCYC 1 cut(s) 282
ErhI CCWWGG 1 cut(s) 725
FaeI CATG 8 cut(s) 149, 176, 181, 247, 289, 585, 682, 712
FaqI GGGAC 2 cut(s) 302, 392
FatI CATG 8 cut(s) 145, 172, 177, 243, 285, 581, 678, 708
FauNDI CATATG 1 cut(s) 374
FokI GGATG 6 cut(s) 136, 218, 428, 545, 598, 656
FriOI GRGCYC 1 cut(s) 282
FspBI CTAG 1 cut(s) 779
GlaI GCGC 1 cut(s) 261
HaeII RGCGCY 1 cut(s) 263
HaeIII GGCC 1 cut(s) 437
HapII CCGG 2 cut(s) 6, 320
HgaI GACGC 1 cut(s) 500
HhaI GCGC 1 cut(s) 262
Hin1II CATG 8 cut(s) 149, 176, 181, 247, 289, 585, 682, 712
Hin6I GCGC 1 cut(s) 260
HinP1I GCGC 1 cut(s) 260
HinfI GANTC 5 cut(s) 36, 315, 556, 607, 620
HpaII CCGG 2 cut(s) 6, 320
HphI GGTGA 2 cut(s) 20, 259
Hpy188I TCNGA 2 cut(s) 205, 612
Hpy188III TCNNGA 3 cut(s) 449, 541, 593
HpyAV CCTTC 3 cut(s) 114, 446, 741
HpyCH4III ACNGT 1 cut(s) 142
HpyCH4IV ACGT 2 cut(s) 639, 756
HpyCH4V TGCA 7 cut(s) 32, 145, 461, 487, 573, 769, 776
HpyF10VI GCNNNNNNNGC 2 cut(s) 410, 596
HpyF3I CTNAG 3 cut(s) 327, 361, 510
HpySE526I ACGT 2 cut(s) 639, 756
Hsp92II CATG 8 cut(s) 149, 176, 181, 247, 289, 585, 682, 712
HspAI GCGC 1 cut(s) 260
Kzo9I GATC 1 cut(s) 22
LmnI GCTCC 1 cut(s) 322
LpnPI CCDG 2 cut(s) 19, 333
LweI GCATC 4 cut(s) 114, 196, 448, 523
MaeI CTAG 1 cut(s) 779
MaeII ACGT 2 cut(s) 639, 756
MaeIII GTNAC 3 cut(s) 8, 148, 549
MalI GATC 1 cut(s) 24
MboI GATC 1 cut(s) 22
MboII GAAGA 3 cut(s) 118, 698, 701
MhlI GDGCHC 2 cut(s) 282, 516
MluCI AATT 4 cut(s) 367, 399, 526, 740
MlyI GAGTC 3 cut(s) 45, 324, 565
MmeI TCCRAC 1 cut(s) 739
MnlI CCTC 7 cut(s) 34, 148, 283, 339, 490, 537, 634
MseI TTAA 3 cut(s) 191, 440, 602
MspI CCGG 2 cut(s) 6, 320
MspR9I CCNGG 1 cut(s) 320
Mva1269I GAATGC 2 cut(s) 134, 355
MvnI CGCG 1 cut(s) 494
MwoI GCNNNNNNNGC 2 cut(s) 410, 596
NciI CCSGG 1 cut(s) 320
NdeI CATATG 1 cut(s) 374
NdeII GATC 1 cut(s) 22
NlaIII CATG 8 cut(s) 149, 176, 181, 247, 289, 585, 682, 712
NlaIV GGNNCC 1 cut(s) 324
NmeAIII GCCGAG 1 cut(s) 30
NmuCI GTSAC 1 cut(s) 8
NspI RCATGY 1 cut(s) 149
PcsI WCGNNNNNNNCGW 1 cut(s) 31
PctI GAATGC 2 cut(s) 134, 355
PfeI GAWTC 2 cut(s) 607, 620
PflMI CCANNNNNTGG 1 cut(s) 679
PfoI TCCNGGA 1 cut(s) 318
PinAI ACCGGT 1 cut(s) 5
PleI GAGTC 3 cut(s) 44, 323, 564
PpsI GAGTC 3 cut(s) 44, 323, 564
Psp1406I AACGTT 1 cut(s) 756
PspN4I GGNNCC 1 cut(s) 324
RsaI GTAC 1 cut(s) 638
RsaNI GTAC 1 cut(s) 637
SaqAI TTAA 3 cut(s) 191, 440, 602
Sau3AI GATC 1 cut(s) 22
SchI GAGTC 3 cut(s) 45, 324, 565
ScrFI CCNGG 1 cut(s) 320
SduI GDGCHC 2 cut(s) 282, 516
SetI ASST 8 cut(s) 219, 511, 519, 642, 699, 707, 727, 759
SfaNI GCATC 4 cut(s) 114, 196, 448, 523
SfcI CTRYAG 1 cut(s) 255
SmlI CTYRAG 1 cut(s) 539
SmoI CTYRAG 1 cut(s) 539
Sse9I AATT 4 cut(s) 367, 399, 526, 740
SsiI CCGC 4 cut(s) 158, 209, 413, 494
SspMI CTAG 1 cut(s) 779
StyD4I CCNGG 1 cut(s) 318
StyI CCWWGG 1 cut(s) 725
TaaI ACNGT 1 cut(s) 142
TaiI ACGT 2 cut(s) 642, 759
TaqI TCGA 3 cut(s) 39, 384, 578
TasI AATT 4 cut(s) 367, 399, 526, 740
TfiI GAWTC 2 cut(s) 607, 620
Tru1I TTAA 3 cut(s) 191, 440, 602
Tru9I TTAA 3 cut(s) 191, 440, 602
TseFI GTSAC 1 cut(s) 8
Tsp45I GTSAC 1 cut(s) 8
TspDTI ATGAA 5 cut(s) 114, 126, 361, 519, 697
Van91I CCANNNNNTGG 1 cut(s) 679
XapI RAATTY 1 cut(s) 367
XceI RCATGY 1 cut(s) 149
XspI CTAG 1 cut(s) 779
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.