FvH4_6g27413

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000370
Physical Location & Seq
Reverse (-)
21069409 .. 21071143
1735 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g27413.t1

Sequence Viewer

Length: 942 bp
ATGGAGGATGAAGTTAGTGAGTCTGTTAATAATCAAGTTCAGATGAAAAGAAGTTTGACGAACAAGAGGATTCCTGAAGATTTACAAGTGACTGTTGCTTGTACCTATCTGGAAGGTCAGGCATACCGTTGGTGGGAGTCCGTACTTTGTATTCCAAATACGGTGATTGCAACATGTGCTGAATTCGAGAGAGTTTTTCTTGAGAAATACTTTCCTTCCACTCAGCGTCGTCTGAAGTCAAGGGAATTCTCCACTCTTCAACAAATGAATATGCTGGTTGGAGATTATCAGGCTAAATTTGAGGAATTAATGCGTTTTGCCCCTGAGCTTATCCCAGATGATAATGCTAAAGCAAGGCGTTTTGAAGAAGGACTGCGACCTCAAATCAAGGAGAAGGTAATGATGCTCAAGCTGGATAGGTATACTGACGTAGTAGAATGTGCGCTTATGGTTGAACAGATGATGCGAGAATCAAAAGCTGTGTTTGAGGCTAGTCGGGTGGGAGCTAGACCAAGTAATAAACGTCAACGGCCTAACATCTCTCAATATCAGTCCAACAATCGATATCCTCGACCTCCCTTAAAATGTTACCGATGTGGACAAGAAGGACATCTTGCAAGAGGTTGTCAATGGTCGCAAACATATCAGGCACCCCAGGCCCCACAACCATCATATCGTGTCCCAATTACCCAATACCCTACTGCCCGACCCCAATCTTATGCACCACCACAGCCTTATCGTGCCCCTATCCCGGCACAACAGAATTGGGTTAGATCACAGATCCGACAACCGGCACCCCGTCCTGCTGATCAATCAACTGCAGCTAGACCCCAAGCTGGAGCAAAGAGGCAGGGTCATCCAGCTCAAGGCCAAGTTTATGCTGTGGGTTATGGTGAGGAGGAATTCGAGGGCAATGAAGCTGAAGCAGTTGAGCAATTCTAA
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 Retrotrans_gag zf-CCHC

Protein Analysis

314

Amino Acids

36.12

Weight (kDa)

8.88

Isoelectric Point (pI)

61.82

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 19 - 152 3.2e-06 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 33 - 127 1.3e-14 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: OG0000370)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g29481 FvH4_2g11454 FvH4_3g19661 FvH4_3g28463 FvH4_3g31691 FvH4_3g34551 FvH4_3g35241 FvH4_4g06575 FvH4_4g09082 FvH4_4g15804 FvH4_4g15805 FvH4_4g16178 FvH4_4g16282 FvH4_5g25163 FvH4_6g27413 FvH4_7g02962 FvH4_7g04361
malus_domestica MD01G1095000.v1.1 MD02G1270200.v1.1 MD02G1270300.v1.1 MD02G1270400.v1.1 MD06G1059100.v1.1 MD08G1226500.v1.1
prunus_persica Prupe.1G169500_v2.0.a1 Prupe.5G195800_v2.0.a1
pyrus_communis pycom01g00010 pycom01g00770 pycom02g23140 pycom03g11760 pycom04g06090 pycom05g06900 pycom05g08070 pycom05g14500 pycom06g03050 pycom07g06250 pycom07g07540 pycom07g10580 pycom08g04990 pycom1146g00060 pycom11g01080 pycom11g15270 pycom11g15460 pycom11g24900 pycom12419g00150 pycom12424g00120 pycom13g08740 pycom13g24950 pycom13g25960 pycom13g26030 pycom13g27820 pycom16g23270 pycom16g25020 pycom16g25960 pycom17g07780 pycom17g08210 pycom17g13100
rosa_chinensis RchiOBHm_Chr1g0329421 RchiOBHm_Chr4g0397711 RchiOBHm_Chr4g0403481 RchiOBHm_Chr5g0019091 RchiOBHm_Chr5g0049101
rosa_laevigata RLG00000029892
rosa_multiflora Rmu_sc0001866.1_g000007
rosa_roxburghii Rroxscaffold_2G00094160 Rroxscaffold_3G00229110 Rroxscaffold_4G00321100 Rroxscaffold_7G00196040 Rroxscaffold_7G00196280
rosa_rugosa Rorug05G0160500 Rorug06G0096500
rosa_samantha Rh1AG098600 Rh1AG098800 Rh1BG078200 Rh1BG078700 Rh1BG178500 Rh1CG094600 Rh1CG094900 Rh1DG101700 Rh1DG109600 Rh2AG175800 Rh2AG175900 Rh2AG511400 Rh2BG114700 Rh2CG042200 Rh2CG116600 Rh2CG317500 Rh2DG327700 Rh2DG337800 Rh4CG142700 Rh4DG113100 Rh5BG335800 Rh5CG360600 Rh5DG352000 Rh6BG071400 Rh6BG417100 Rh6CG463300 Rh6CG463400 Rh7BG186600 Rh7CG196500 Rh7CG196600 Rh7CG448900 Rh7DG228300
rosa_wichuraiana Rw4G006560 Rw4G017340 Rw5G030450

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 2 cut(s) 649, 793
AccI GTMKAC 1 cut(s) 422
AclWI GGATC 1 cut(s) 775
AcsI RAATTY 4 cut(s) 182, 245, 296, 902
AcuI CTGAAG 3 cut(s) 96, 254, 942
AfaI GTAC 2 cut(s) 103, 144
AfiI CCNNNNNNNGG 5 cut(s) 133, 751, 790, 836, 866
AflIII ACRYGT 1 cut(s) 173
AgsI TTSAA 3 cut(s) 260, 365, 455
AjnI CCWGG 1 cut(s) 654
AluBI AGCT 8 cut(s) 328, 412, 479, 506, 824, 836, 863, 920
AluI AGCT 8 cut(s) 328, 412, 479, 506, 824, 836, 863, 920
AlwI GGATC 1 cut(s) 775
AoxI GGCC 3 cut(s) 530, 657, 868
ApeKI GCWGC 1 cut(s) 821
ApoI RAATTY 4 cut(s) 182, 245, 296, 902
AseI ATTAAT 1 cut(s) 308
AspLEI GCGC 1 cut(s) 445
AspS9I GGNCC 1 cut(s) 658
AsuC2I CCSGG 1 cut(s) 752
AsuHPI GGTGA 2 cut(s) 175, 905
BaeGI GKGCMC 1 cut(s) 745
BanI GGYRCC 2 cut(s) 649, 793
BbvI GCAGC 1 cut(s) 833
BccI CCATC 1 cut(s) 676
BceAI ACGGC 1 cut(s) 545
BciT130I CCWGG 1 cut(s) 656
BclI TGATCA 1 cut(s) 808
BcnI CCSGG 1 cut(s) 752
BfaI CTAG 3 cut(s) 492, 507, 825
BfmI CTRYAG 1 cut(s) 819
BisI GCNGC 1 cut(s) 822
BlsI GCNGC 1 cut(s) 823
Bme1390I CCNGG 2 cut(s) 656, 752
BmgT120I GGNCC 1 cut(s) 658
BmiI GGNNCC 3 cut(s) 651, 660, 795
BmrFI CCNGG 2 cut(s) 656, 752
BmsI GCATC 2 cut(s) 393, 453
BpmI CTGGAG 1 cut(s) 858
Bpu10I CCTNAGC 1 cut(s) 324
BpuEI CTTGAG 3 cut(s) 221, 392, 849
BpuMI CCSGG 1 cut(s) 752
Bsa29I ATCGAT 1 cut(s) 562
BsaJI CCNNGG 1 cut(s) 654
Bsc4I CCNNNNNNNGG 5 cut(s) 133, 751, 790, 836, 866
Bse118I RCCGGY 1 cut(s) 790
Bse3DI GCAATG 1 cut(s) 919
BseBI CCWGG 1 cut(s) 656
BseCI ATCGAT 1 cut(s) 562
BseDI CCNNGG 1 cut(s) 654
BseGI GGATG 2 cut(s) 13, 856
BseLI CCNNNNNNNGG 5 cut(s) 133, 751, 790, 836, 866
BseMI GCAATG 1 cut(s) 919
BseMII CTCAG 2 cut(s) 236, 315
BseRI GAGGAG 1 cut(s) 911
BseSI GKGCMC 1 cut(s) 745
BseXI GCAGC 1 cut(s) 833
BshFI GGCC 3 cut(s) 532, 659, 870
BshNI GGYRCC 2 cut(s) 649, 793
BshVI ATCGAT 1 cut(s) 562
BsiSI CCGG 2 cut(s) 752, 791
BslFI GGGAC 1 cut(s) 665
BslI CCNNNNNNNGG 5 cut(s) 133, 751, 790, 836, 866
BsmFI GGGAC 1 cut(s) 665
BsnI GGCC 3 cut(s) 532, 659, 870
Bsp1286I GDGCHC 1 cut(s) 745
Bsp143I GATC 3 cut(s) 773, 780, 808
BspANI GGCC 3 cut(s) 532, 659, 870
BspCNI CTCAG 2 cut(s) 235, 316
BspDI ATCGAT 1 cut(s) 562
BspLI GGNNCC 3 cut(s) 651, 660, 795
BspMAI CTGCAG 1 cut(s) 823
BspPI GGATC 1 cut(s) 775
BspT107I GGYRCC 2 cut(s) 649, 793
BsrDI GCAATG 1 cut(s) 919
BsrFI RCCGGY 1 cut(s) 790
BssAI RCCGGY 1 cut(s) 790
BssECI CCNNGG 1 cut(s) 654
BssMI GATC 3 cut(s) 773, 780, 808
BssNAI GTATAC 1 cut(s) 423
Bst1107I GTATAC 1 cut(s) 423
Bst2UI CCWGG 1 cut(s) 656
Bst4CI ACNGT 3 cut(s) 94, 128, 163
Bst6I CTCTTC 1 cut(s) 261
BstAPI GCANNNNNTGC 1 cut(s) 176
BstDEI CTNAG 2 cut(s) 222, 324
BstF5I GGATG 2 cut(s) 13, 856
BstHHI GCGC 1 cut(s) 445
BstKTI GATC 3 cut(s) 776, 783, 811
BstMBI GATC 3 cut(s) 773, 780, 808
BstMWI GCNNNNNNNGC 2 cut(s) 176, 656
BstNI CCWGG 1 cut(s) 656
BstNSI RCATGY 1 cut(s) 177
BstSCI CCNGG 2 cut(s) 654, 750
BstSFI CTRYAG 1 cut(s) 819
BstSLI GKGCMC 1 cut(s) 745
BstV1I GCAGC 1 cut(s) 833
BstX2I RGATCY 1 cut(s) 780
BstYI RGATCY 1 cut(s) 780
BstZ17I GTATAC 1 cut(s) 423
Bsu15I ATCGAT 1 cut(s) 562
BsuRI GGCC 3 cut(s) 532, 659, 870
BsuTUI ATCGAT 1 cut(s) 562
BtsCI GGATG 2 cut(s) 13, 856
CfoI GCGC 1 cut(s) 445
Cfr10I RCCGGY 1 cut(s) 790
Cfr13I GGNCC 1 cut(s) 658
ClaI ATCGAT 1 cut(s) 562
CseI GACGC 1 cut(s) 215
Csp6I GTAC 2 cut(s) 102, 143
CviAII CATG 1 cut(s) 174
CviQI GTAC 2 cut(s) 102, 143
DdeI CTNAG 2 cut(s) 222, 324
DpnI GATC 3 cut(s) 775, 782, 810
DpnII GATC 3 cut(s) 773, 780, 808
Eam1104I CTCTTC 1 cut(s) 261
EarI CTCTTC 1 cut(s) 261
Eco32I GATATC 1 cut(s) 566
Eco57I CTGAAG 3 cut(s) 96, 254, 942
EcoO109I RGGNCCY 1 cut(s) 658
EcoRI GAATTC 3 cut(s) 182, 245, 902
EcoRII CCWGG 1 cut(s) 654
EcoRV GATATC 1 cut(s) 566
FaeI CATG 1 cut(s) 177
FalI AAGNNNNNCTT 2 cut(s) 597, 629
FaqI GGGAC 1 cut(s) 665
FatI CATG 1 cut(s) 173
FbaI TGATCA 1 cut(s) 808
FblI GTMKAC 1 cut(s) 422
Fnu4HI GCNGC 1 cut(s) 822
FokI GGATG 2 cut(s) 20, 843
Fsp4HI GCNGC 1 cut(s) 822
FspBI CTAG 3 cut(s) 492, 507, 825
GlaI GCGC 1 cut(s) 444
GluI GCNGC 1 cut(s) 822
GsuI CTGGAG 1 cut(s) 858
HaeIII GGCC 3 cut(s) 532, 659, 870
HapII CCGG 2 cut(s) 752, 791
HgaI GACGC 1 cut(s) 215
HhaI GCGC 1 cut(s) 445
Hin1II CATG 1 cut(s) 177
Hin6I GCGC 1 cut(s) 443
HinP1I GCGC 1 cut(s) 443
HincII GTYRAC 1 cut(s) 527
HindII GTYRAC 1 cut(s) 527
HinfI GANTC 4 cut(s) 20, 70, 137, 470
HpaII CCGG 2 cut(s) 752, 791
HphI GGTGA 2 cut(s) 175, 905
Hpy166II GTNNAC 3 cut(s) 423, 527, 599
Hpy188I TCNGA 3 cut(s) 42, 234, 785
Hpy188III TCNNGA 4 cut(s) 74, 110, 187, 200
Hpy8I GTNNAC 3 cut(s) 423, 527, 599
Hpy99I CGWCG 1 cut(s) 231
HpyAV CCTTC 5 cut(s) 107, 225, 362, 388, 599
HpyCH4III ACNGT 3 cut(s) 94, 128, 163
HpyCH4IV ACGT 2 cut(s) 429, 523
HpyCH4V TGCA 4 cut(s) 170, 617, 722, 821
HpyF10VI GCNNNNNNNGC 2 cut(s) 176, 656
HpyF3I CTNAG 2 cut(s) 222, 324
HpySE526I ACGT 2 cut(s) 429, 523
Hsp92II CATG 1 cut(s) 177
HspAI GCGC 1 cut(s) 443
Ksp22I TGATCA 1 cut(s) 808
Kzo9I GATC 3 cut(s) 773, 780, 808
LmnI GCTCC 2 cut(s) 503, 839
Lsp1109I GCAGC 1 cut(s) 833
LweI GCATC 2 cut(s) 393, 453
MaeI CTAG 3 cut(s) 492, 507, 825
MaeII ACGT 2 cut(s) 429, 523
MaeIII GTNAC 2 cut(s) 88, 587
MalI GATC 3 cut(s) 775, 782, 810
MboI GATC 3 cut(s) 773, 780, 808
MboII GAAGA 3 cut(s) 89, 248, 377
MflI RGATCY 1 cut(s) 780
MhlI GDGCHC 1 cut(s) 745
MluCI AATT 8 cut(s) 182, 245, 296, 305, 684, 763, 902, 935
MlyI GAGTC 2 cut(s) 29, 146
MmeI TCCRAC 3 cut(s) 259, 579, 808
MseI TTAA 3 cut(s) 27, 308, 581
MspI CCGG 2 cut(s) 752, 791
MspR9I CCNGG 2 cut(s) 656, 752
MvaI CCWGG 1 cut(s) 656
MwoI GCNNNNNNNGC 2 cut(s) 176, 656
NciI CCSGG 1 cut(s) 752
NdeII GATC 3 cut(s) 773, 780, 808
NlaIII CATG 1 cut(s) 177
NlaIV GGNNCC 3 cut(s) 651, 660, 795
NmuCI GTSAC 1 cut(s) 88
NspI RCATGY 1 cut(s) 177
PciI ACATGT 1 cut(s) 173
PcsI WCGNNNNNNNCGW 1 cut(s) 568
PfeI GAWTC 2 cut(s) 70, 470
PkrI GCNGC 1 cut(s) 823
PleI GAGTC 2 cut(s) 28, 145
PpsI GAGTC 2 cut(s) 28, 145
PscI ACATGT 1 cut(s) 173
PshBI ATTAAT 1 cut(s) 308
Psp6I CCWGG 1 cut(s) 654
PspGI CCWGG 1 cut(s) 654
PspN4I GGNNCC 3 cut(s) 651, 660, 795
PspPI GGNCC 1 cut(s) 658
PstI CTGCAG 1 cut(s) 823
PsuI RGATCY 1 cut(s) 780
RsaI GTAC 2 cut(s) 103, 144
RsaNI GTAC 2 cut(s) 102, 143
SaqAI TTAA 3 cut(s) 27, 308, 581
SatI GCNGC 1 cut(s) 822
Sau3AI GATC 3 cut(s) 773, 780, 808
Sau96I GGNCC 1 cut(s) 658
SchI GAGTC 2 cut(s) 29, 146
ScrFI CCNGG 2 cut(s) 656, 752
SduI GDGCHC 1 cut(s) 745
SfaNI GCATC 2 cut(s) 393, 453
SfcI CTRYAG 1 cut(s) 819
SmlI CTYRAG 3 cut(s) 200, 407, 864
SmoI CTYRAG 3 cut(s) 200, 407, 864
Sse9I AATT 8 cut(s) 182, 245, 296, 305, 684, 763, 902, 935
SspMI CTAG 3 cut(s) 492, 507, 825
StyD4I CCNGG 2 cut(s) 654, 750
TaaI ACNGT 3 cut(s) 94, 128, 163
TaiI ACGT 2 cut(s) 432, 526
TaqI TCGA 4 cut(s) 186, 562, 571, 906
TasI AATT 8 cut(s) 182, 245, 296, 305, 684, 763, 902, 935
TfiI GAWTC 2 cut(s) 70, 470
Tru1I TTAA 3 cut(s) 27, 308, 581
Tru9I TTAA 3 cut(s) 27, 308, 581
TseFI GTSAC 1 cut(s) 88
TseI GCWGC 1 cut(s) 821
Tsp45I GTSAC 1 cut(s) 88
TspDTI ATGAA 4 cut(s) 24, 59, 281, 930
TspGWI ACGGA 1 cut(s) 130
VspI ATTAAT 1 cut(s) 308
XapI RAATTY 4 cut(s) 182, 245, 296, 902
XceI RCATGY 1 cut(s) 177
XmiI GTMKAC 1 cut(s) 422
XspI CTAG 3 cut(s) 492, 507, 825
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.