FvH4_3g42780

transposition, RNA-mediated

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000324
Physical Location & Seq
Forward (+)
35746047 .. 35747992
1946 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g42780.t1

Sequence Viewer

Length: 930 bp
ATGTCGAGCGATAAGCTGCCGCAAGGACGGCATTTGAGTGGGGTCAGTGTGGTTTACGATGTGGATGTTAGGCGGCCCGGGGAGTTTCAGCCGCAGCTGGAAGTTAGGTCGACGATTACGAACTATGATCCTCAGCTGGTGTTGGGCCGCCAAATAGCGGTGAATAAGTCGTATATATGCTGTGGATTGAAACAGGGGAATATTCGGGTTTTGAATAACCACACCGGATTGGAATGTTTGCTTCGAGCTCATACACAGAGGGTCACAGACATGGCTTTCTTTGCCGAGGATGTTCACCTTTTGGCTAGTGTGAGTGTAGAAGGACGGCTTTTTGTGTGGAAAATATCTGAAGGTCTGGATGAAGGAGGTACGCCACAAATCAAAGGAAAGATTGTTATTGCCATTCAAATAGTTGATGAGGGGGGAGCTGTTCATCCAAGAGTTTGTTGGCACTGTTCTAAACAAGAGGTTTTGTTTGTTGGGGTTGGGAAGCGTGTTCTACGAATTGATACTACTAAAGTTGCAAAGTATGGAGTCCCTTCTGCTGAGGATCCTATCAAATGTCCTGTTGAAAAACTCATTGATGGGGTTCAATTTGTTGGTGAACATGATGGAGAGGTGACAGATGTATCAATGTGCCAAGGGATGACTACCACCCGGCTGGTTTCTGCTTCCATGGATGGAACTATAAAGATCTGGGAAGATCGCAAGTCACAACCACTTATAGTACTGAGACCCTATGATGGCCTTCCTGTTTATTCGTCTATATTTACGACAGCTCCCAACAAACCAGATCACATCATACTTGAAACAGTGGGTCCACTTAATCGGGAAGTGAAGATCTGGTCCTCAGCAACTGAAGTGCTTACCAGTGATGATGAGTCATGGAAATGTACCCAGACCTTAGAGCTCTGCTCAACCTCGAGTTGA
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

310

Amino Acids

34.12

Weight (kDa)

5.93

Isoelectric Point (pI)

36.3

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ge1_WD40 PF16529 44 - 307 4.4e-14 WD40 region of Ge1, enhancer of mRNA-decapping protein
WD40_WDHD1_1st PF24817 51 - 171 2.3e-07 WDHD1 first WD40 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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Orthologous Genes (Group: OG0000324)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G13290 AT3G13300 AT3G13300 AT3G13300
fragaria_vesca FvH4_3g41972 FvH4_3g41980 FvH4_3g41980 FvH4_3g41980 FvH4_3g41980 FvH4_3g42780 FvH4_3g42790 FvH4_3g42820 FvH4_3g42820 FvH4_3g42820 FvH4_3g42820 FvH4_4g01881 FvH4_7g10420
malus_domestica MD00G1013700.v1.1 MD03G1039800.v1.1 MD11G1041300.v1.1 MD11G1094900.v1.1
prunus_persica Prupe.6G032100_v2.0.a1
pyrus_communis pycom03g03070 pycom11g03500 pycom11g08470 pycom12g06730
rosa_chinensis RchiOBHm_Chr1g0328831 RchiOBHm_Chr4g0386471 RchiOBHm_Chr4g0386481 RchiOBHm_Chr4g0386551 RchiOBHm_Chr4g0386701 RchiOBHm_Chr4g0386801 RchiOBHm_Chr4g0386811 RchiOBHm_Chr4g0386821 RchiOBHm_Chr4g0386921 RchiOBHm_Chr4g0386931 RchiOBHm_Chr4g0386941 RchiOBHm_Chr4g0387211 RchiOBHm_Chr4g0389101 RchiOBHm_Chr4g0389111 RchiOBHm_Chr4g0389201 RchiOBHm_Chr4g0389211 RchiOBHm_Chr4g0389321 RchiOBHm_Chr4g0389331 RchiOBHm_Chr4g0389341 RchiOBHm_Chr4g0389411 RchiOBHm_Chr5g0075171
rosa_laevigata RLG00000009985 RLG00000009990 RLG00000009996 RLG00000009998 RLG00000010136 RLG00000010140 RLG00000036537
rosa_multiflora Rmu_co8461959.1_g000001 Rmu_sc0000013.1_g000017 Rmu_sc0000013.1_g000024 Rmu_sc0001015.1_g000001 Rmu_sc0001395.1_g000004 Rmu_sc0001942.1_g000022 Rmu_sc0002498.1_g000018 Rmu_sc0002498.1_g000020 Rmu_sc0002557.1_g000005 Rmu_sc0002604.1_g000010 Rmu_sc0002604.1_g000011 Rmu_sc0004750.1_g000003 Rmu_sc0006571.1_g000001 Rmu_sc0006571.1_g000014 Rmu_sc0006571.1_g000018 Rmu_sc0008050.1_g000016 Rmu_sc0008066.1_g000009 Rmu_sc0008380.1_g000006 Rmu_sc0008380.1_g000010 Rmu_sc0008380.1_g000012 Rmu_sc0010272.1_g000021 Rmu_sc0010693.1_g000010 Rmu_sc0010693.1_g000012 Rmu_sc0010693.1_g000014 Rmu_sc0010693.1_g000015 Rmu_sc0031790.1_g000003 Rmu_sc0040539.1_g000001 Rmu_ssc0000211.1_g000001 Rmu_ssc0000211.1_g000011 Rmu_ssc0000211.1_g000013
rosa_roxburghii Rroxscaffold_1G00006420 Rroxscaffold_1G00006430 Rroxscaffold_5G00334020 Rroxscaffold_5G00334050 Rroxscaffold_5G00335420
rosa_rugosa Rorug03G0307600 Rorug03G0308600 Rorug03G0322400 Rorug05G0437200 Rorug05G0437200 Rorug05G0437200
rosa_samantha Rh1BG075700 Rh4BG010000 Rh4BG010100 Rh4BG010200 Rh4BG020000 Rh4BG020400 Rh4BG172100 Rh4CG015300 Rh4CG016300 Rh5AG494100 Rh5AG494200 Rh5BG515500 Rh5CG539300 Rh5DG528200
rosa_wichuraiana Rw4G000930 Rw4G001980 Rw4G001990 Rw4G011950 Rw5G045850

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccI GTMKAC 1 cut(s) 110
AciI CCGC 5 cut(s) 20, 73, 92, 148, 158
AclWI GGATC 3 cut(s) 122, 545, 558
AcuI CTGAAG 2 cut(s) 369, 879
AfaI GTAC 3 cut(s) 370, 729, 895
AfiI CCNNNNNNNGG 2 cut(s) 157, 743
AgsI TTSAA 6 cut(s) 190, 214, 407, 572, 593, 809
AluBI AGCT 7 cut(s) 16, 97, 136, 248, 428, 779, 910
AluI AGCT 7 cut(s) 16, 97, 136, 248, 428, 779, 910
Alw21I GWGCWC 2 cut(s) 250, 912
Alw26I GTCTC 1 cut(s) 727
AlwI GGATC 3 cut(s) 122, 545, 558
AlwNI CAGNNNCTG 1 cut(s) 857
Ama87I CYCGRG 2 cut(s) 77, 922
AoxI GGCC 3 cut(s) 74, 145, 745
ApeKI GCWGC 2 cut(s) 16, 94
AspS9I GGNCC 4 cut(s) 75, 145, 818, 846
AsuC2I CCSGG 3 cut(s) 78, 79, 658
AsuHPI GGTGA 4 cut(s) 172, 287, 614, 631
AvaI CYCGRG 2 cut(s) 77, 922
AvaII GGWCC 2 cut(s) 818, 846
BaeI ACNNNNGTAYC 2 cut(s) 612, 645
BamHI GGATCC 1 cut(s) 550
BanII GRGCYC 2 cut(s) 250, 912
Bbv12I GWGCWC 2 cut(s) 250, 912
BbvCI CCTCAGC 3 cut(s) 132, 546, 850
BbvI GCAGC 2 cut(s) 3, 106
BccI CCATC 4 cut(s) 578, 605, 674, 737
BceAI ACGGC 2 cut(s) 44, 341
BcnI CCSGG 3 cut(s) 78, 79, 658
BcoDI GTCTC 1 cut(s) 727
BfaI CTAG 1 cut(s) 306
BglII AGATCT 2 cut(s) 693, 840
BisI GCNGC 6 cut(s) 17, 20, 74, 92, 95, 148
BlsI GCNGC 6 cut(s) 18, 21, 75, 93, 96, 149
BmcAI AGTACT 1 cut(s) 729
Bme1390I CCNGG 3 cut(s) 78, 79, 658
Bme18I GGWCC 2 cut(s) 818, 846
BmeT110I CYCGRG 2 cut(s) 77, 922
BmgT120I GGNCC 4 cut(s) 75, 145, 818, 846
BmiI GGNNCC 2 cut(s) 552, 819
BmrFI CCNGG 3 cut(s) 78, 79, 658
BplI GAGNNNNNCTC 1 cut(s) 899
Bpu10I CCTNAGC 3 cut(s) 132, 546, 850
BpuMI CCSGG 3 cut(s) 78, 79, 658
BsaI GGTCTC 1 cut(s) 727
BsaJI CCNNGG 5 cut(s) 77, 78, 285, 640, 675
BsaWI WCCGGW 1 cut(s) 224
BsaXI ACNNNNNCTCC 2 cut(s) 763, 793
Bsc4I CCNNNNNNNGG 2 cut(s) 157, 743
Bse1I ACTGG 1 cut(s) 870
BseDI CCNNGG 5 cut(s) 77, 78, 285, 640, 675
BseGI GGATG 6 cut(s) 70, 295, 364, 433, 651, 685
BseLI CCNNNNNNNGG 2 cut(s) 157, 743
BseMII CTCAG 4 cut(s) 146, 537, 722, 864
BseNI ACTGG 1 cut(s) 870
BseXI GCAGC 2 cut(s) 3, 106
BshFI GGCC 3 cut(s) 76, 147, 747
BsiHKAI GWGCWC 2 cut(s) 250, 912
BsiHKCI CYCGRG 2 cut(s) 77, 922
BsiSI CCGG 3 cut(s) 78, 225, 658
BslFI GGGAC 1 cut(s) 521
BslI CCNNNNNNNGG 2 cut(s) 157, 743
BsmAI GTCTC 1 cut(s) 727
BsmFI GGGAC 1 cut(s) 521
BsnI GGCC 3 cut(s) 76, 147, 747
Bso31I GGTCTC 1 cut(s) 727
BsoBI CYCGRG 2 cut(s) 77, 922
Bsp1286I GDGCHC 2 cut(s) 250, 912
Bsp143I GATC 6 cut(s) 127, 550, 693, 703, 793, 840
Bsp19I CCATGG 1 cut(s) 675
BspACI CCGC 5 cut(s) 20, 73, 92, 148, 158
BspANI GGCC 3 cut(s) 76, 147, 747
BspCNI CTCAG 4 cut(s) 145, 538, 723, 863
BspLI GGNNCC 2 cut(s) 552, 819
BspPI GGATC 3 cut(s) 122, 545, 558
BspTNI GGTCTC 1 cut(s) 727
BsrI ACTGG 1 cut(s) 870
BssECI CCNNGG 5 cut(s) 77, 78, 285, 640, 675
BssMI GATC 6 cut(s) 127, 550, 693, 703, 793, 840
BssT1I CCWWGG 2 cut(s) 640, 675
Bst4CI ACNGT 2 cut(s) 455, 814
BstDEI CTNAG 5 cut(s) 132, 546, 731, 850, 904
BstDSI CCRYGG 1 cut(s) 675
BstF5I GGATG 6 cut(s) 70, 295, 364, 433, 651, 685
BstKTI GATC 6 cut(s) 130, 553, 696, 706, 796, 843
BstMAI GTCTC 1 cut(s) 727
BstMBI GATC 6 cut(s) 127, 550, 693, 703, 793, 840
BstMWI GCNNNNNNNGC 2 cut(s) 28, 281
BstSCI CCNGG 3 cut(s) 76, 77, 656
BstV1I GCAGC 2 cut(s) 3, 106
BstX2I RGATCY 3 cut(s) 550, 693, 840
BstXI CCANNNNNNTGG 1 cut(s) 661
BstYI RGATCY 3 cut(s) 550, 693, 840
BsuRI GGCC 3 cut(s) 76, 147, 747
BtgI CCRYGG 1 cut(s) 675
BtsCI GGATG 6 cut(s) 70, 295, 364, 433, 651, 685
BtsIMutI CAGTG 4 cut(s) 52, 451, 819, 877
CaiI CAGNNNCTG 1 cut(s) 857
Cfr13I GGNCC 4 cut(s) 75, 145, 818, 846
Cfr9I CCCGGG 1 cut(s) 77
Csp6I GTAC 3 cut(s) 369, 728, 894
CviAII CATG 4 cut(s) 271, 608, 676, 885
CviQI GTAC 3 cut(s) 369, 728, 894
DdeI CTNAG 5 cut(s) 132, 546, 731, 850, 904
DpnI GATC 6 cut(s) 129, 552, 695, 705, 795, 842
DpnII GATC 6 cut(s) 127, 550, 693, 703, 793, 840
Ecl136II GAGCTC 2 cut(s) 248, 910
Eco130I CCWWGG 2 cut(s) 640, 675
Eco24I GRGCYC 2 cut(s) 250, 912
Eco31I GGTCTC 1 cut(s) 727
Eco47I GGWCC 2 cut(s) 818, 846
Eco53kI GAGCTC 2 cut(s) 248, 910
Eco57I CTGAAG 2 cut(s) 369, 879
Eco88I CYCGRG 2 cut(s) 77, 922
EcoICRI GAGCTC 2 cut(s) 248, 910
EcoT14I CCWWGG 2 cut(s) 640, 675
EcoT38I GRGCYC 2 cut(s) 250, 912
ErhI CCWWGG 2 cut(s) 640, 675
FaeI CATG 4 cut(s) 274, 611, 679, 888
FalI AAGNNNNNCTT 2 cut(s) 312, 344
FaqI GGGAC 1 cut(s) 521
FatI CATG 4 cut(s) 270, 607, 675, 884
FblI GTMKAC 1 cut(s) 110
Fnu4HI GCNGC 6 cut(s) 17, 20, 74, 92, 95, 148
FokI GGATG 6 cut(s) 77, 302, 371, 420, 658, 692
FriOI GRGCYC 2 cut(s) 250, 912
Fsp4HI GCNGC 6 cut(s) 17, 20, 74, 92, 95, 148
FspBI CTAG 1 cut(s) 306
GluI GCNGC 6 cut(s) 17, 20, 74, 92, 95, 148
HaeIII GGCC 3 cut(s) 76, 147, 747
HapII CCGG 3 cut(s) 78, 225, 658
Hin1II CATG 4 cut(s) 274, 611, 679, 888
HincII GTYRAC 1 cut(s) 111
HindII GTYRAC 1 cut(s) 111
HinfI GANTC 2 cut(s) 534, 881
HpaII CCGG 3 cut(s) 78, 225, 658
HphI GGTGA 4 cut(s) 172, 287, 614, 631
Hpy166II GTNNAC 5 cut(s) 55, 111, 295, 605, 821
Hpy188I TCNGA 1 cut(s) 349
Hpy188III TCNNGA 2 cut(s) 356, 830
Hpy8I GTNNAC 5 cut(s) 55, 111, 295, 605, 821
Hpy99I CGWCG 1 cut(s) 115
HpyAV CCTTC 5 cut(s) 314, 344, 356, 549, 758
HpyCH4III ACNGT 2 cut(s) 455, 814
HpyCH4V TGCA 1 cut(s) 524
HpyF10VI GCNNNNNNNGC 2 cut(s) 28, 281
HpyF3I CTNAG 5 cut(s) 132, 546, 731, 850, 904
Hsp92II CATG 4 cut(s) 274, 611, 679, 888
Kzo9I GATC 6 cut(s) 127, 550, 693, 703, 793, 840
LmnI GCTCC 2 cut(s) 425, 784
Lsp1109I GCAGC 2 cut(s) 3, 106
MaeI CTAG 1 cut(s) 306
MaeIII GTNAC 3 cut(s) 262, 619, 711
MalI GATC 6 cut(s) 129, 552, 695, 705, 795, 842
MboI GATC 6 cut(s) 127, 550, 693, 703, 793, 840
MboII GAAGA 2 cut(s) 713, 850
MflI RGATCY 3 cut(s) 550, 693, 840
MhlI GDGCHC 2 cut(s) 250, 912
MluCI AATT 2 cut(s) 504, 593
MlyI GAGTC 2 cut(s) 543, 890
MnlI CCTC 9 cut(s) 141, 252, 280, 359, 412, 460, 541, 610, 859
MseI TTAA 1 cut(s) 825
MslI CAYNNNNRTG 3 cut(s) 36, 269, 889
MspA1I CMGCKG 2 cut(s) 97, 136
MspI CCGG 3 cut(s) 78, 225, 658
MspR9I CCNGG 3 cut(s) 78, 79, 658
MwoI GCNNNNNNNGC 2 cut(s) 28, 281
NciI CCSGG 3 cut(s) 78, 79, 658
NcoI CCATGG 1 cut(s) 675
NdeII GATC 6 cut(s) 127, 550, 693, 703, 793, 840
NlaIII CATG 4 cut(s) 274, 611, 679, 888
NlaIV GGNNCC 2 cut(s) 552, 819
NmeAIII GCCGAG 1 cut(s) 310
NmuCI GTSAC 3 cut(s) 262, 619, 711
PaeR7I CTCGAG 1 cut(s) 922
PcsI WCGNNNNNNNCGW 1 cut(s) 116
PkrI GCNGC 6 cut(s) 18, 21, 75, 93, 96, 149
PleI GAGTC 2 cut(s) 542, 889
PpsI GAGTC 2 cut(s) 542, 889
Psp124BI GAGCTC 2 cut(s) 250, 912
PspN4I GGNNCC 2 cut(s) 552, 819
PspPI GGNCC 4 cut(s) 75, 145, 818, 846
PspXI VCTCGAGB 1 cut(s) 922
PstNI CAGNNNCTG 1 cut(s) 857
PsuI RGATCY 3 cut(s) 550, 693, 840
PvuII CAGCTG 2 cut(s) 97, 136
RsaI GTAC 3 cut(s) 370, 729, 895
RsaNI GTAC 3 cut(s) 369, 728, 894
RseI CAYNNNNRTG 3 cut(s) 36, 269, 889
SacI GAGCTC 2 cut(s) 250, 912
SalI GTCGAC 1 cut(s) 109
SaqAI TTAA 1 cut(s) 825
SatI GCNGC 6 cut(s) 17, 20, 74, 92, 95, 148
Sau3AI GATC 6 cut(s) 127, 550, 693, 703, 793, 840
Sau96I GGNCC 4 cut(s) 75, 145, 818, 846
ScaI AGTACT 1 cut(s) 729
SchI GAGTC 2 cut(s) 543, 890
ScrFI CCNGG 3 cut(s) 78, 79, 658
SduI GDGCHC 2 cut(s) 250, 912
Sfr274I CTCGAG 1 cut(s) 922
SinI GGWCC 2 cut(s) 818, 846
SlaI CTCGAG 1 cut(s) 922
SmaI CCCGGG 1 cut(s) 79
SmiMI CAYNNNNRTG 3 cut(s) 36, 269, 889
SmlI CTYRAG 1 cut(s) 922
SmoI CTYRAG 1 cut(s) 922
Sse9I AATT 2 cut(s) 504, 593
SsiI CCGC 5 cut(s) 20, 73, 92, 148, 158
SspI AATATT 1 cut(s) 202
SspMI CTAG 1 cut(s) 306
SstI GAGCTC 2 cut(s) 250, 912
StyD4I CCNGG 3 cut(s) 76, 77, 656
StyI CCWWGG 2 cut(s) 640, 675
TaaI ACNGT 2 cut(s) 455, 814
TaqI TCGA 4 cut(s) 5, 110, 244, 923
TasI AATT 2 cut(s) 504, 593
TatI WGTACW 1 cut(s) 727
TauI GCSGC 4 cut(s) 22, 76, 94, 150
Tru1I TTAA 1 cut(s) 825
Tru9I TTAA 1 cut(s) 825
TscAI CASTG 4 cut(s) 52, 458, 819, 877
TseFI GTSAC 3 cut(s) 262, 619, 711
TseI GCWGC 2 cut(s) 16, 94
Tsp45I GTSAC 3 cut(s) 262, 619, 711
TspDTI ATGAA 2 cut(s) 375, 422
TspMI CCCGGG 1 cut(s) 77
TspRI CASTG 4 cut(s) 52, 458, 819, 877
VpaK11BI GGWCC 2 cut(s) 818, 846
XcmI CCANNNNNNNNNTGG 1 cut(s) 444
XhoI CTCGAG 1 cut(s) 922
XmaI CCCGGG 1 cut(s) 77
XmiI GTMKAC 1 cut(s) 110
XspI CTAG 1 cut(s) 306
ZrmI AGTACT 1 cut(s) 729
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.