FvH4_6g53791

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000128
Physical Location & Seq
Reverse (-)
39375997 .. 39376962
966 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g53791.t1

Sequence Viewer

Length: 870 bp
ATGCAAGTCATGGTGATAGGAGTGATCAACGTGGAAGAACAAGCGGCCCAAATAGCCCAGTTGACTGAAGCGGTGAAGAAGCTCCAAAAGACCATTGAAGAGAAGGATGTAGAAATTGCATTGCTCATGGAGAAGCTAAAAGTTCACCATGAAAATGACTCGAAGAATAACCTTCATGGCGATAAGAAAGACACATCTGCTCAATATGGTGGTACGTCTCGAGATACACTAACGTATTCCAAGCCTTACACCAAGCGGCTAGACAATTTGAGAATGCCAATTGGTTACCAACCTCCTAAGTTTCAACAATTTGATGGCAAAAGTAACCCCAAGCAACACATCGCACATTTCATCGAAACATACAACAGCGTTGGCACCGATAGTGATCATCTTGTGAAGCAATTTGTTCGCTCACTCCGAGGTACGGCATTTGAATGGTTTACAGACTTGGAGCTTGAATCCATTGACAACTGGGAGCAAATGGAAAATGAGTTTTTGAACCGATTCTTCAGCACACGTCACATGGTGAGTATGTTAGAGCTCACCAACACCAAACAACAAAACGGCGAGCCTGTTGTAAAGTTCATCAATCGTTGGCGTACACTAAGTCTCGACTGCAAAGATAAACTCTCAGAATTGTCAGCGGTAGAGATGTGTATTCAAGGCATGCATTGGGATTTGTTGTACATTCTTCAAAGGTGCGAGGCTTTATCCTTTGAAGAACTTGCTACTCGAGCTCATGACATGGAACTTAGTTTGGCTAGTCATGGCCAAAGAAAATATGACATCATGGAGCCAGAGAATCAGGAGTCTTTGGCAATCAACACAACTCCTGCAAGGGTCATGAAACGAGTCAAATCAAATGACTAA
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
Retrotrans_gag

Protein Analysis

290

Amino Acids

33.51

Weight (kDa)

5.85

Isoelectric Point (pI)

36.89

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 135 - 224 8.5e-13 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: OG0000128)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g28082 FvH4_2g15191 FvH4_2g31621 FvH4_3g07261 FvH4_3g22806 FvH4_3g26703 FvH4_3g26704 FvH4_3g31360 FvH4_4g01161 FvH4_4g22271 FvH4_4g25732 FvH4_5g00242 FvH4_5g28911 FvH4_5g32461 FvH4_6g13112 FvH4_6g53790 FvH4_6g53791 FvH4_7g03661 FvH4_7g04125 FvH4_7g04126
pyrus_communis pycom01g01950 pycom01g01960 pycom01g03260 pycom01g07760 pycom01g11430 pycom01g23980 pycom02g15030 pycom02g18630 pycom03g12320 pycom03g18810 pycom03g19250 pycom04g05010 pycom04g06520 pycom04g06680 pycom04g09630 pycom04g09640 pycom05g06850 pycom05g07540 pycom05g08940 pycom06g04300 pycom06g05750 pycom06g06960 pycom06g19690 pycom07g08750 pycom07g10700 pycom07g10910 pycom07g27480 pycom07g27790 pycom07g27800 pycom08g13620 pycom09g03540 pycom09g03550 pycom09g09870 pycom09g13480 pycom09g14360 pycom09g14890 pycom09g14930 pycom09g15760 pycom10g02190 pycom10g05270 pycom10g06810 pycom10g06830 pycom10g08060 pycom10g08520 pycom11g02350 pycom11g14170 pycom11g15050 pycom11g19270 pycom11g20160 pycom11g22420 pycom12g08620 pycom12g08630 pycom12g10440 pycom12g16590 pycom133g00190 pycom13g20730 pycom13g22230 pycom13g22670 pycom13g23230 pycom13g23250 pycom13g24880 pycom13g25300 pycom13g28040 pycom13g29010 pycom14g07570 pycom14g18650 pycom15g04500 pycom15g09310 pycom15g27210 pycom15g30810 pycom15g34920 pycom16g16040 pycom16g17260 pycom16g17940 pycom16g20990 pycom16g23470 pycom16g24160 pycom16g24720 pycom16g25910 pycom16g25920 pycom16g26370 pycom17g03310 pycom17g12670 pycom17g17530 pycom17g25090 pycom17g27300 pycom17g27310 pycom420g00140 pycom420g00160 pycom420g00320 pycom505g00220 pycom520g00740 pycom520g01010 pycom520g01020 pycom576g00060 pycom675g00040
rosa_laevigata RLG00000022630
rosa_multiflora Rmu_co7993280.1_g000001 Rmu_co8054704.1_g000001 Rmu_co8148394.1_g000001 Rmu_co8243015.1_g000001 Rmu_co8272095.1_g000001 Rmu_co8282359.1_g000001 Rmu_co8334783.1_g000001 Rmu_co8404405.1_g000001 Rmu_sc0000161.1_g000030 Rmu_sc0000418.1_g000026 Rmu_sc0000488.1_g000015 Rmu_sc0000706.1_g000041 Rmu_sc0000720.1_g000013 Rmu_sc0000776.1_g000022 Rmu_sc0000948.1_g000017 Rmu_sc0001167.1_g000045 Rmu_sc0001167.1_g000047 Rmu_sc0001211.1_g000054 Rmu_sc0001241.1_g000019 Rmu_sc0001307.1_g000021 Rmu_sc0001438.1_g000043 Rmu_sc0001468.1_g000032 Rmu_sc0001851.1_g000020 Rmu_sc0002026.1_g000023 Rmu_sc0002811.1_g000016 Rmu_sc0002958.1_g000002 Rmu_sc0002958.1_g000003 Rmu_sc0003745.1_g000010 Rmu_sc0004234.1_g000006 Rmu_sc0004234.1_g000008 Rmu_sc0005035.1_g000001 Rmu_sc0005320.1_g000010 Rmu_sc0005866.1_g000006 Rmu_sc0006139.1_g000009 Rmu_sc0006504.1_g000008 Rmu_sc0006695.1_g000049 Rmu_sc0006695.1_g000050 Rmu_sc0006981.1_g000001 Rmu_sc0007108.1_g000012 Rmu_sc0007355.1_g000001 Rmu_sc0007873.1_g000015 Rmu_sc0007961.1_g000003 Rmu_sc0008991.1_g000005 Rmu_sc0009528.1_g000009 Rmu_sc0013299.1_g000003 Rmu_sc0013532.1_g000015 Rmu_sc0015524.1_g000001 Rmu_sc0015793.1_g000001 Rmu_sc0015817.1_g000006 Rmu_sc0015930.1_g000003 Rmu_sc0015930.1_g000006 Rmu_sc0016952.1_g000002 Rmu_sc0016952.1_g000003 Rmu_sc0018715.1_g000003 Rmu_sc0018715.1_g000005 Rmu_sc0023934.1_g000003 Rmu_sc0023989.1_g000002 Rmu_sc0023989.1_g000003 Rmu_sc0028612.1_g000001 Rmu_sc0029049.1_g000001 Rmu_sc0029639.1_g000001 Rmu_sc0035263.1_g000001 Rmu_sc0037892.1_g000001 Rmu_ssc0000170.1_g000024 Rmu_ssc0000233.1_g000057 Rmu_ssc0000259.1_g000055 Rmu_ssc0000259.1_g000057
rosa_roxburghii Rroxscaffold_4G00287780 Rroxscaffold_4G00325290 Rroxscaffold_5G00333910 Rroxscaffold_7G00211350
rosa_rugosa Rorug01G0056300 Rorug04G0149000 Rorug07G0222000
rosa_samantha Rh1AG072900 Rh1CG072000
rosa_wichuraiana Rw0G003630 Rw0G005250 Rw0G020770 Rw0G023770 Rw1G005460 Rw1G005980 Rw1G007190 Rw1G011350 Rw1G022520 Rw1G028660 Rw2G018620 Rw2G019490 Rw4G006910 Rw4G013020 Rw4G023970 Rw5G044650 Rw6G006590 Rw6G012210 Rw6G023750 Rw7G027370 Rw7G027460 Rw7G035570

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 374
AciI CCGC 4 cut(s) 44, 71, 256, 644
AcoI YGGCCR 1 cut(s) 769
AcuI CTGAAG 2 cut(s) 87, 493
AdeI CACNNNGTG 1 cut(s) 526
AfaI GTAC 4 cut(s) 214, 424, 601, 686
AfiI CCNNNNNNNGG 1 cut(s) 424
AflIII ACRYGT 1 cut(s) 515
AgsI TTSAA 8 cut(s) 98, 305, 434, 458, 499, 662, 695, 719
AjiI CACGTC 1 cut(s) 518
AluBI AGCT 5 cut(s) 82, 136, 454, 541, 737
AluI AGCT 5 cut(s) 82, 136, 454, 541, 737
Alw21I GWGCWC 2 cut(s) 543, 739
Alw26I GTCTC 2 cut(s) 222, 614
Ama87I CYCGRG 2 cut(s) 219, 732
AoxI GGCC 2 cut(s) 45, 769
Asp700I GAANNNNTTC 1 cut(s) 503
AspS9I GGNCC 1 cut(s) 46
AsuHPI GGTGA 5 cut(s) 25, 85, 137, 535, 538
AvaI CYCGRG 2 cut(s) 219, 732
BalI TGGCCA 1 cut(s) 771
BanI GGYRCC 1 cut(s) 374
BanII GRGCYC 2 cut(s) 543, 739
Bbv12I GWGCWC 2 cut(s) 543, 739
BccI CCATC 1 cut(s) 308
BceAI ACGGC 2 cut(s) 441, 580
BcgI CGANNNNNNTGC 2 cut(s) 389, 423
BclI TGATCA 2 cut(s) 24, 385
BcoDI GTCTC 2 cut(s) 222, 614
BfaI CTAG 2 cut(s) 260, 762
BisI GCNGC 2 cut(s) 45, 257
BlsI GCNGC 2 cut(s) 46, 258
BmeT110I CYCGRG 2 cut(s) 219, 732
BmgBI CACGTC 1 cut(s) 518
BmgT120I GGNCC 1 cut(s) 46
BmiI GGNNCC 2 cut(s) 376, 795
BmrI ACTGGG 2 cut(s) 52, 481
BmuI ACTGGG 2 cut(s) 52, 481
BsaBI GATNNNNATC 1 cut(s) 384
BsaJI CCNNGG 1 cut(s) 418
Bsc4I CCNNNNNNNGG 1 cut(s) 424
Bse1I ACTGG 2 cut(s) 58, 476
Bse3DI GCAATG 1 cut(s) 119
Bse8I GATNNNNATC 1 cut(s) 384
BseDI CCNNGG 1 cut(s) 418
BseGI GGATG 1 cut(s) 112
BseJI GATNNNNATC 1 cut(s) 384
BseLI CCNNNNNNNGG 1 cut(s) 424
BseMI GCAATG 1 cut(s) 119
BseMII CTCAG 1 cut(s) 645
BseNI ACTGG 2 cut(s) 58, 476
BshFI GGCC 2 cut(s) 47, 771
BshNI GGYRCC 1 cut(s) 374
BsiHKAI GWGCWC 2 cut(s) 543, 739
BsiHKCI CYCGRG 2 cut(s) 219, 732
BslI CCNNNNNNNGG 1 cut(s) 424
BsmAI GTCTC 2 cut(s) 222, 614
BsmBI CGTCTC 1 cut(s) 222
BsmI GAATGC 1 cut(s) 279
BsnI GGCC 2 cut(s) 47, 771
BsoBI CYCGRG 2 cut(s) 219, 732
Bsp1286I GDGCHC 2 cut(s) 543, 739
Bsp1407I TGTACA 1 cut(s) 684
Bsp143I GATC 2 cut(s) 24, 385
BspACI CCGC 4 cut(s) 44, 71, 256, 644
BspANI GGCC 2 cut(s) 47, 771
BspCNI CTCAG 1 cut(s) 644
BspHI TCATGA 2 cut(s) 739, 843
BspLI GGNNCC 2 cut(s) 376, 795
BspT107I GGYRCC 1 cut(s) 374
BsrDI GCAATG 1 cut(s) 119
BsrGI TGTACA 1 cut(s) 684
BsrI ACTGG 2 cut(s) 58, 476
BssECI CCNNGG 1 cut(s) 418
BssMI GATC 2 cut(s) 24, 385
Bst6I CTCTTC 1 cut(s) 93
BstAUI TGTACA 1 cut(s) 684
BstC8I GCNNGC 2 cut(s) 569, 668
BstDEI CTNAG 4 cut(s) 297, 605, 631, 752
BstEII GGTNACC 1 cut(s) 284
BstF5I GGATG 1 cut(s) 112
BstKTI GATC 2 cut(s) 27, 388
BstMAI GTCTC 2 cut(s) 222, 614
BstMBI GATC 2 cut(s) 24, 385
BstMWI GCNNNNNNNGC 2 cut(s) 53, 734
BstNSI RCATGY 1 cut(s) 670
BstPI GGTNACC 1 cut(s) 284
BsuRI GGCC 2 cut(s) 47, 771
BtgZI GCGATG 1 cut(s) 325
BtrI CACGTC 1 cut(s) 518
BtsCI GGATG 1 cut(s) 112
Cac8I GCNNGC 2 cut(s) 569, 668
CciI TCATGA 2 cut(s) 739, 843
Cfr13I GGNCC 1 cut(s) 46
Csp6I GTAC 4 cut(s) 213, 423, 600, 685
CviQI GTAC 4 cut(s) 213, 423, 600, 685
DdeI CTNAG 4 cut(s) 297, 605, 631, 752
DpnI GATC 2 cut(s) 26, 387
DpnII GATC 2 cut(s) 24, 385
DraIII CACNNNGTG 1 cut(s) 526
EaeI YGGCCR 1 cut(s) 769
Eam1104I CTCTTC 1 cut(s) 93
EarI CTCTTC 1 cut(s) 93
Ecl136II GAGCTC 2 cut(s) 541, 737
Eco24I GRGCYC 2 cut(s) 543, 739
Eco53kI GAGCTC 2 cut(s) 541, 737
Eco57I CTGAAG 2 cut(s) 87, 493
Eco88I CYCGRG 2 cut(s) 219, 732
Eco91I GGTNACC 1 cut(s) 284
EcoICRI GAGCTC 2 cut(s) 541, 737
EcoO65I GGTNACC 1 cut(s) 284
EcoT22I ATGCAT 1 cut(s) 672
EcoT38I GRGCYC 2 cut(s) 543, 739
Esp3I CGTCTC 1 cut(s) 222
FbaI TGATCA 2 cut(s) 24, 385
Fnu4HI GCNGC 2 cut(s) 45, 257
FokI GGATG 1 cut(s) 119
FriOI GRGCYC 2 cut(s) 543, 739
Fsp4HI GCNGC 2 cut(s) 45, 257
FspBI CTAG 2 cut(s) 260, 762
GluI GCNGC 2 cut(s) 45, 257
HaeIII GGCC 2 cut(s) 47, 771
HincII GTYRAC 1 cut(s) 63
HindII GTYRAC 1 cut(s) 63
HinfI GANTC 6 cut(s) 158, 458, 504, 802, 809, 852
HphI GGTGA 5 cut(s) 25, 85, 137, 535, 538
Hpy166II GTNNAC 4 cut(s) 63, 145, 441, 602
Hpy188I TCNGA 2 cut(s) 419, 634
Hpy188III TCNNGA 6 cut(s) 219, 221, 611, 740, 806, 844
Hpy8I GTNNAC 4 cut(s) 63, 145, 441, 602
HpyAV CCTTC 2 cut(s) 97, 182
HpyCH4IV ACGT 4 cut(s) 30, 215, 233, 517
HpyCH4V TGCA 5 cut(s) 4, 119, 618, 670, 836
HpyF10VI GCNNNNNNNGC 2 cut(s) 53, 734
HpyF3I CTNAG 4 cut(s) 297, 605, 631, 752
HpySE526I ACGT 4 cut(s) 30, 215, 233, 517
Ksp22I TGATCA 2 cut(s) 24, 385
Kzo9I GATC 2 cut(s) 24, 385
LmnI GCTCC 4 cut(s) 87, 451, 475, 793
LpnPI CCDG 6 cut(s) 71, 457, 585, 791, 810, 846
MaeI CTAG 2 cut(s) 260, 762
MaeII ACGT 4 cut(s) 30, 215, 233, 517
MaeIII GTNAC 3 cut(s) 284, 323, 518
MalI GATC 2 cut(s) 26, 387
MboI GATC 2 cut(s) 24, 385
MboII GAAGA 7 cut(s) 47, 88, 110, 175, 499, 683, 731
MfeI CAATTG 1 cut(s) 279
MhlI GDGCHC 2 cut(s) 543, 739
MlsI TGGCCA 1 cut(s) 771
MluCI AATT 6 cut(s) 114, 265, 279, 308, 401, 635
MluNI TGGCCA 1 cut(s) 771
MlyI GAGTC 3 cut(s) 152, 818, 861
MnlI CCTC 3 cut(s) 303, 413, 697
Mox20I TGGCCA 1 cut(s) 771
Mph1103I ATGCAT 1 cut(s) 672
MroXI GAANNNNTTC 1 cut(s) 503
MscI TGGCCA 1 cut(s) 771
MslI CAYNNNNRTG 2 cut(s) 153, 433
Msp20I TGGCCA 1 cut(s) 771
MspA1I CMGCKG 1 cut(s) 644
MunI CAATTG 1 cut(s) 279
Mva1269I GAATGC 1 cut(s) 279
MwoI GCNNNNNNNGC 2 cut(s) 53, 734
NdeII GATC 2 cut(s) 24, 385
NlaIV GGNNCC 2 cut(s) 376, 795
NmuCI GTSAC 1 cut(s) 518
NsiI ATGCAT 1 cut(s) 672
NspI RCATGY 1 cut(s) 670
PaeI GCATGC 1 cut(s) 670
PaeR7I CTCGAG 2 cut(s) 219, 732
PagI TCATGA 2 cut(s) 739, 843
PcsI WCGNNNNNNNCGW 1 cut(s) 415
PctI GAATGC 1 cut(s) 279
PdmI GAANNNNTTC 1 cut(s) 503
PfeI GAWTC 3 cut(s) 458, 504, 802
PkrI GCNGC 2 cut(s) 46, 258
PleI GAGTC 3 cut(s) 152, 817, 860
PpsI GAGTC 3 cut(s) 152, 817, 860
Psp124BI GAGCTC 2 cut(s) 543, 739
PspEI GGTNACC 1 cut(s) 284
PspN4I GGNNCC 2 cut(s) 376, 795
PspPI GGNCC 1 cut(s) 46
PspXI VCTCGAGB 1 cut(s) 732
RsaI GTAC 4 cut(s) 214, 424, 601, 686
RsaNI GTAC 4 cut(s) 213, 423, 600, 685
RseI CAYNNNNRTG 2 cut(s) 153, 433
SacI GAGCTC 2 cut(s) 543, 739
SatI GCNGC 2 cut(s) 45, 257
Sau3AI GATC 2 cut(s) 24, 385
Sau96I GGNCC 1 cut(s) 46
SchI GAGTC 3 cut(s) 152, 818, 861
SduI GDGCHC 2 cut(s) 543, 739
Sfr274I CTCGAG 2 cut(s) 219, 732
SlaI CTCGAG 2 cut(s) 219, 732
SmiMI CAYNNNNRTG 2 cut(s) 153, 433
SmlI CTYRAG 2 cut(s) 219, 732
SmoI CTYRAG 2 cut(s) 219, 732
SphI GCATGC 1 cut(s) 670
Sse9I AATT 6 cut(s) 114, 265, 279, 308, 401, 635
SsiI CCGC 4 cut(s) 44, 71, 256, 644
SspMI CTAG 2 cut(s) 260, 762
SstI GAGCTC 2 cut(s) 543, 739
TaiI ACGT 4 cut(s) 33, 218, 236, 520
TaqI TCGA 5 cut(s) 161, 220, 354, 612, 733
TasI AATT 6 cut(s) 114, 265, 279, 308, 401, 635
TatI WGTACW 1 cut(s) 684
TauI GCSGC 2 cut(s) 47, 259
TfiI GAWTC 3 cut(s) 458, 504, 802
TseFI GTSAC 1 cut(s) 518
Tsp45I GTSAC 1 cut(s) 518
TspDTI ATGAA 5 cut(s) 164, 165, 340, 574, 860
XceI RCATGY 1 cut(s) 670
XhoI CTCGAG 2 cut(s) 219, 732
XmnI GAANNNNTTC 1 cut(s) 503
XspI CTAG 2 cut(s) 260, 762
Zsp2I ATGCAT 1 cut(s) 672
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.