FvH4_3g19661

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000370
Physical Location & Seq
Reverse (-)
12810173 .. 12811241
1069 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g19661.t1

Sequence Viewer

Length: 996 bp
ATGACCAATAGAAGGAACCCACCTGTTGACGCGGAAGATTTTGTCGAAGCCTTCACCAGAAGGATGGAGGCAAATCAAGTCGGCGGGAGGCTAGGACGACTAGTGACACACATAAGGAATTTAGGGGCAAAGAAGTTTGGTGGAGGGAAACCTCACGAGGCTGAAGAATGGATCTACAATTTGGAAATCCACTTTGAAATGATGGATTGTACCCAAGTGGAGTTACGAAAAGTGGCTACTTGCCTCTTAGAAGGTGATGCTCGTTTCTGGTGGGACACAGTTAAACGTGTCACACTCCCTGCTGCATTGGAACTCATGGATTGGACTGCCTTCAAAGAAAAATTCCTAGAAAAATTCTTTCCACAAGTTGAGAAAGACAAGAAAGAATTAGAGTTCATTCAACTTACCCAAGGAAAAATGCCTGTGATTGAGTATGAAACAAAATTCACTAAACTTTCTCGTTTTGCTCCTCACATGGTAGATACTGACGATAAGAAGGCAAGACGTTTCATTAGAGGACTGAATTCCAACATTCGAAGAATGGTCACTCAACGTGGAATCACTTACGAGGAAGCTGTGGGTAAAGCCTTAACTCAAGAAGAGGAAAACCAAAAGTACCGCATGGAGAAAGAAAGAGAGAATAGTTTTCGAGGAAAAAGGAGTCATCCAATGCTTAACCAGAATGGCGGACAACCATGGAAGCAACAAAAAGGGAGAGACGCATTTCGGAAGCCGACAACATCAACTGAGAAGGGGAAAGAGGTGTTTAGAGGGCCAATTCGGTGTTATAATTGTGGAGGGTCTGGACACATGTCTAATGCTTGTCCAAAGCCACGTCGCCTCCCAGGATCATGTTTCAATTGTGGTAAGATGGGGCACTTCTCTAATAAGTGTGATGCTCCGAAACAAACAAACAATCCAGCACCTCGTCCAGTCCAGCTAAATGCCATAGCTTTTGAGAACACGGTGATGGAAGTGCATTTGTCGCAACCTTAG
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

332

Amino Acids

38.23

Weight (kDa)

9.48

Isoelectric Point (pI)

41.66

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Ty3_capsid PF19259 51 - 205 3.3e-08 Ty3 transposon capsid-like protein
Retrotrans_gag PF03732 77 - 175 4.4e-22 Retrotransposon gag protein
zf-CCHC PF00098 261 - 277 5.9e-06 Zinc knuckle
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AanI TTATAA 1 cut(s) 789
AccII CGCG 1 cut(s) 32
AciI CCGC 4 cut(s) 32, 84, 619, 687
AclWI GGATC 2 cut(s) 179, 856
AcsI RAATTY 5 cut(s) 118, 341, 353, 443, 523
AcuI CTGAAG 1 cut(s) 183
AfaI GTAC 2 cut(s) 211, 617
AfiI CCNNNNNNNGG 1 cut(s) 12
AflIII ACRYGT 2 cut(s) 286, 810
AgsI TTSAA 4 cut(s) 197, 334, 401, 859
AhlI ACTAGT 1 cut(s) 100
AjiI CACGTC 1 cut(s) 836
AjnI CCWGG 1 cut(s) 844
AluBI AGCT 3 cut(s) 575, 940, 953
AluI AGCT 3 cut(s) 575, 940, 953
Alw26I GTCTC 1 cut(s) 711
AlwI GGATC 2 cut(s) 179, 856
AoxI GGCC 1 cut(s) 773
ApeKI GCWGC 1 cut(s) 302
ApoI RAATTY 5 cut(s) 118, 341, 353, 443, 523
AspS9I GGNCC 1 cut(s) 773
AsuHPI GGTGA 3 cut(s) 46, 266, 979
AsuII TTCGAA 1 cut(s) 535
BaeGI GKGCMC 1 cut(s) 879
BauI CACGAG 1 cut(s) 155
BbvI GCAGC 1 cut(s) 289
BccI CCATC 4 cut(s) 58, 196, 865, 964
BciT130I CCWGG 1 cut(s) 846
BcoDI GTCTC 1 cut(s) 711
BcuI ACTAGT 1 cut(s) 100
BfaI CTAG 3 cut(s) 92, 101, 347
BisI GCNGC 1 cut(s) 303
BlsI GCNGC 1 cut(s) 304
Bme1390I CCNGG 1 cut(s) 846
BmgBI CACGTC 1 cut(s) 836
BmgT120I GGNCC 1 cut(s) 773
BmiI GGNNCC 1 cut(s) 17
BmrFI CCNGG 1 cut(s) 846
BmsI GCATC 2 cut(s) 247, 886
BoxI GACNNNNGTC 1 cut(s) 811
Bpu14I TTCGAA 1 cut(s) 535
BpuEI CTTGAG 1 cut(s) 579
BsaJI CCNNGG 3 cut(s) 409, 695, 844
BsaXI ACNNNNNCTCC 2 cut(s) 825, 855
Bsc4I CCNNNNNNNGG 1 cut(s) 12
Bse1I ACTGG 1 cut(s) 932
BseBI CCWGG 1 cut(s) 846
BseDI CCNNGG 3 cut(s) 409, 695, 844
BseGI GGATG 2 cut(s) 69, 664
BseLI CCNNNNNNNGG 1 cut(s) 12
BseMII CTCAG 1 cut(s) 738
BseNI ACTGG 1 cut(s) 932
BseRI GAGGAG 1 cut(s) 459
BseSI GKGCMC 1 cut(s) 879
BseXI GCAGC 1 cut(s) 289
Bsh1236I CGCG 1 cut(s) 32
BshFI GGCC 1 cut(s) 775
BslFI GGGAC 1 cut(s) 287
BslI CCNNNNNNNGG 1 cut(s) 12
BsmAI GTCTC 1 cut(s) 711
BsmBI CGTCTC 1 cut(s) 711
BsmFI GGGAC 1 cut(s) 287
BsnI GGCC 1 cut(s) 775
Bsp119I TTCGAA 1 cut(s) 535
Bsp1286I GDGCHC 1 cut(s) 879
Bsp143I GATC 2 cut(s) 171, 848
Bsp19I CCATGG 1 cut(s) 695
BspACI CCGC 4 cut(s) 32, 84, 619, 687
BspANI GGCC 1 cut(s) 775
BspCNI CTCAG 1 cut(s) 739
BspFNI CGCG 1 cut(s) 32
BspLI GGNNCC 1 cut(s) 17
BspPI GGATC 2 cut(s) 179, 856
BspT104I TTCGAA 1 cut(s) 535
BsrI ACTGG 1 cut(s) 932
BssECI CCNNGG 3 cut(s) 409, 695, 844
BssMI GATC 2 cut(s) 171, 848
BssSI CACGAG 1 cut(s) 155
BssT1I CCWWGG 2 cut(s) 409, 695
Bst2BI CACGAG 1 cut(s) 155
Bst2UI CCWGG 1 cut(s) 846
Bst4CI ACNGT 2 cut(s) 280, 967
Bst6I CTCTTC 1 cut(s) 594
BstBI TTCGAA 1 cut(s) 535
BstDEI CTNAG 3 cut(s) 247, 747, 993
BstDSI CCRYGG 1 cut(s) 695
BstF5I GGATG 2 cut(s) 69, 664
BstFNI CGCG 1 cut(s) 32
BstKTI GATC 2 cut(s) 174, 851
BstMAI GTCTC 1 cut(s) 711
BstMBI GATC 2 cut(s) 171, 848
BstMWI GCNNNNNNNGC 1 cut(s) 985
BstNI CCWGG 1 cut(s) 846
BstNSI RCATGY 1 cut(s) 814
BstPAI GACNNNNGTC 1 cut(s) 811
BstSCI CCNGG 1 cut(s) 844
BstSLI GKGCMC 1 cut(s) 879
BstUI CGCG 1 cut(s) 32
BstV1I GCAGC 1 cut(s) 289
BstX2I RGATCY 1 cut(s) 171
BstXI CCANNNNNNTGG 1 cut(s) 64
BstYI RGATCY 1 cut(s) 171
BsuRI GGCC 1 cut(s) 775
BtgI CCRYGG 1 cut(s) 695
BtrI CACGTC 1 cut(s) 836
BtsCI GGATG 2 cut(s) 69, 664
Cfr13I GGNCC 1 cut(s) 773
CseI GACGC 2 cut(s) 38, 728
Csp6I GTAC 2 cut(s) 210, 616
CviAII CATG 6 cut(s) 316, 475, 622, 696, 811, 852
CviQI GTAC 2 cut(s) 210, 616
DdeI CTNAG 3 cut(s) 247, 747, 993
DpnI GATC 2 cut(s) 173, 850
DpnII GATC 2 cut(s) 171, 848
Eam1104I CTCTTC 1 cut(s) 594
EarI CTCTTC 1 cut(s) 594
EciI GGCGGA 1 cut(s) 702
Eco130I CCWWGG 2 cut(s) 409, 695
Eco57I CTGAAG 1 cut(s) 183
EcoRI GAATTC 1 cut(s) 523
EcoRII CCWGG 1 cut(s) 844
EcoT14I CCWWGG 2 cut(s) 409, 695
ErhI CCWWGG 2 cut(s) 409, 695
Esp3I CGTCTC 1 cut(s) 711
FaeI CATG 6 cut(s) 319, 478, 625, 699, 814, 855
FaqI GGGAC 1 cut(s) 287
FatI CATG 6 cut(s) 315, 474, 621, 695, 810, 851
FauI CCCGC 1 cut(s) 77
Fnu4HI GCNGC 1 cut(s) 303
FokI GGATG 2 cut(s) 76, 651
Fsp4HI GCNGC 1 cut(s) 303
FspBI CTAG 3 cut(s) 92, 101, 347
GluI GCNGC 1 cut(s) 303
HaeIII GGCC 1 cut(s) 775
HgaI GACGC 2 cut(s) 38, 728
Hin1II CATG 6 cut(s) 319, 478, 625, 699, 814, 855
HincII GTYRAC 1 cut(s) 28
HindII GTYRAC 1 cut(s) 28
HinfI GANTC 2 cut(s) 558, 661
HphI GGTGA 3 cut(s) 46, 266, 979
Hpy166II GTNNAC 1 cut(s) 28
Hpy188I TCNGA 2 cut(s) 729, 903
Hpy188III TCNNGA 3 cut(s) 155, 596, 804
Hpy8I GTNNAC 1 cut(s) 28
Hpy99I CGWCG 1 cut(s) 840
HpyAV CCTTC 7 cut(s) 6, 54, 61, 245, 340, 490, 745
HpyCH4III ACNGT 2 cut(s) 280, 967
HpyCH4IV ACGT 4 cut(s) 286, 505, 553, 835
HpyCH4V TGCA 2 cut(s) 305, 979
HpyF10VI GCNNNNNNNGC 1 cut(s) 985
HpyF3I CTNAG 3 cut(s) 247, 747, 993
HpySE526I ACGT 4 cut(s) 286, 505, 553, 835
Hsp92II CATG 6 cut(s) 319, 478, 625, 699, 814, 855
Kzo9I GATC 2 cut(s) 171, 848
LmnI GCTCC 2 cut(s) 472, 904
Lsp1109I GCAGC 1 cut(s) 289
LweI GCATC 2 cut(s) 247, 886
MaeI CTAG 3 cut(s) 92, 101, 347
MaeII ACGT 4 cut(s) 286, 505, 553, 835
MaeIII GTNAC 4 cut(s) 103, 222, 289, 544
MalI GATC 2 cut(s) 173, 850
MboI GATC 2 cut(s) 171, 848
MboII GAAGA 4 cut(s) 47, 176, 549, 611
MfeI CAATTG 1 cut(s) 859
MflI RGATCY 1 cut(s) 171
MhlI GDGCHC 1 cut(s) 879
MlyI GAGTC 1 cut(s) 670
MmeI TCCRAC 1 cut(s) 552
MseI TTAA 3 cut(s) 282, 590, 675
MslI CAYNNNNRTG 1 cut(s) 968
MspR9I CCNGG 1 cut(s) 846
MunI CAATTG 1 cut(s) 859
MvaI CCWGG 1 cut(s) 846
MvnI CGCG 1 cut(s) 32
MwoI GCNNNNNNNGC 1 cut(s) 985
NcoI CCATGG 1 cut(s) 695
NdeII GATC 2 cut(s) 171, 848
NlaIII CATG 6 cut(s) 319, 478, 625, 699, 814, 855
NlaIV GGNNCC 1 cut(s) 17
NmuCI GTSAC 3 cut(s) 103, 289, 544
NspI RCATGY 1 cut(s) 814
NspV TTCGAA 1 cut(s) 535
PciI ACATGT 1 cut(s) 810
PfeI GAWTC 1 cut(s) 558
PkrI GCNGC 1 cut(s) 304
PleI GAGTC 1 cut(s) 669
PpsI GAGTC 1 cut(s) 669
PscI ACATGT 1 cut(s) 810
PshAI GACNNNNGTC 1 cut(s) 811
PsiI TTATAA 1 cut(s) 789
Psp6I CCWGG 1 cut(s) 844
PspGI CCWGG 1 cut(s) 844
PspN4I GGNNCC 1 cut(s) 17
PspPI GGNCC 1 cut(s) 773
PsuI RGATCY 1 cut(s) 171
RsaI GTAC 2 cut(s) 211, 617
RsaNI GTAC 2 cut(s) 210, 616
RseI CAYNNNNRTG 1 cut(s) 968
SaqAI TTAA 3 cut(s) 282, 590, 675
SatI GCNGC 1 cut(s) 303
Sau3AI GATC 2 cut(s) 171, 848
Sau96I GGNCC 1 cut(s) 773
SchI GAGTC 1 cut(s) 670
ScrFI CCNGG 1 cut(s) 846
SduI GDGCHC 1 cut(s) 879
SfaNI GCATC 2 cut(s) 247, 886
SfuI TTCGAA 1 cut(s) 535
SmiMI CAYNNNNRTG 1 cut(s) 968
SmlI CTYRAG 1 cut(s) 594
SmoI CTYRAG 1 cut(s) 594
SpeI ACTAGT 1 cut(s) 100
SsiI CCGC 4 cut(s) 32, 84, 619, 687
SspMI CTAG 3 cut(s) 92, 101, 347
StyD4I CCNGG 1 cut(s) 844
StyI CCWWGG 2 cut(s) 409, 695
TaaI ACNGT 2 cut(s) 280, 967
TaiI ACGT 4 cut(s) 289, 508, 556, 838
TaqI TCGA 3 cut(s) 45, 535, 649
TfiI GAWTC 1 cut(s) 558
Tru1I TTAA 3 cut(s) 282, 590, 675
Tru9I TTAA 3 cut(s) 282, 590, 675
TseFI GTSAC 3 cut(s) 103, 289, 544
TseI GCWGC 1 cut(s) 302
Tsp45I GTSAC 3 cut(s) 103, 289, 544
TspDTI ATGAA 3 cut(s) 385, 450, 499
XapI RAATTY 5 cut(s) 118, 341, 353, 443, 523
XceI RCATGY 1 cut(s) 814
XspI CTAG 3 cut(s) 92, 101, 347
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.