FvH4_2g31621

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb2
OG0000128
Physical Location & Seq
Forward (+)
24201801 .. 24202684
884 bp
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UTR
Exon/CDS
Intron
FvH4_2g31621.t1

Sequence Viewer

Length: 657 bp
ATGAAGCAATTTGTTCGCTCACTCCAAGACACGGCGTTTGAATGGTTTATAGACTTGGAGCCTGAATCCATTGACAGCTGGGAGCAAATGGAAAAAGAGTTCTTGAACCGCTTCTTCAGCACACGTCACATGGTGAGTATGTTAGAGCTCACCAACACCAAACAACGAAAGGGCGAGTCTGCTGTAGAATTCATCAATCGAATAAATCCTCGCACCTTCGAAGAACTTGCCACTCGAGCTCATGACATGGAACTCAGCTTGGCTAGTCATGGCCAAAGAGAAGATCAAGCAAGGAGGCGAACTCTAAGAGAGTTGGAAGCTAAAAGTTACCCTTTTCTAAATTCCGATGTTGTTGAGATGTTGGAAAACTTGCTTGAAAAAGAACTAATCAAATTGCCAGACTGCAAGCGTCCAGAAGAGATGCATCACGTCAATGAACCAAAAAACTGCAAGAACCACCGTGGCATTAGTCATCCGGTGGAGAAATGCTTCATCTTGAAAGACCTCATCATGAAGCTCGCACAACAAGGAAAGATCAGCTTAGACATTGAAGATGATGCGGCTCAGTCAAATTATGCTACCATCATCTTTGAACAACTCGAAGCAGTGTCGTCAACGCCTTTGCTGGGGGCATGCAACCTGCTGAGACTCATGTAG
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

219

Amino Acids

25.48

Weight (kDa)

5.47

Isoelectric Point (pI)

46.53

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 4 - 82 6.9e-09 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)
Acc36I ACCTGC 1 cut(s) 648
AciI CCGC 2 cut(s) 109, 560
AcoI YGGCCR 1 cut(s) 271
AcsI RAATTY 2 cut(s) 188, 340
AcuI CTGAAG 1 cut(s) 100
AdeI CACNNNGTG 1 cut(s) 133
AfiI CCNNNNNNNGG 2 cut(s) 31, 626
AflIII ACRYGT 1 cut(s) 122
AgsI TTSAA 6 cut(s) 41, 106, 377, 499, 551, 593
AjiI CACGTC 2 cut(s) 125, 430
AloI GAACNNNNNNTCC 2 cut(s) 83, 115
AluBI AGCT 7 cut(s) 78, 148, 239, 258, 320, 517, 540
AluI AGCT 7 cut(s) 78, 148, 239, 258, 320, 517, 540
Alw21I GWGCWC 2 cut(s) 150, 241
Alw26I GTCTC 1 cut(s) 640
Ama87I CYCGRG 1 cut(s) 234
AoxI GGCC 1 cut(s) 271
ApoI RAATTY 2 cut(s) 188, 340
ArsI GACNNNNNNTTYG 2 cut(s) 20, 52
Asp700I GAANNNNTTC 2 cut(s) 110, 488
AsuHPI GGTGA 2 cut(s) 142, 145
AsuII TTCGAA 1 cut(s) 219
AvaI CYCGRG 1 cut(s) 234
BalI TGGCCA 1 cut(s) 273
BanII GRGCYC 2 cut(s) 150, 241
Bbv12I GWGCWC 2 cut(s) 150, 241
BccI CCATC 1 cut(s) 590
BceAI ACGGC 1 cut(s) 48
BcgI CGANNNNNNTGC 3 cut(s) 30, 209, 243
BcoDI GTCTC 1 cut(s) 640
BfaI CTAG 1 cut(s) 264
BfmI CTRYAG 1 cut(s) 183
BfuAI ACCTGC 1 cut(s) 648
BisI GCNGC 1 cut(s) 561
BlsI GCNGC 1 cut(s) 562
BmeT110I CYCGRG 1 cut(s) 234
BmgBI CACGTC 2 cut(s) 125, 430
BmiI GGNNCC 1 cut(s) 60
BmsI GCATC 3 cut(s) 411, 433, 547
BplI GAGNNNNNCTC 2 cut(s) 286, 318
Bpu14I TTCGAA 1 cut(s) 219
BsaJI CCNNGG 1 cut(s) 460
BsaWI WCCGGW 1 cut(s) 475
Bsc4I CCNNNNNNNGG 2 cut(s) 31, 626
BseDI CCNNGG 1 cut(s) 460
BseGI GGATG 1 cut(s) 472
BseLI CCNNNNNNNGG 2 cut(s) 31, 626
BseMII CTCAG 3 cut(s) 268, 578, 635
BseYI CCCAGC 2 cut(s) 78, 625
BshFI GGCC 1 cut(s) 273
BsiHKAI GWGCWC 2 cut(s) 150, 241
BsiHKCI CYCGRG 1 cut(s) 234
BsiSI CCGG 1 cut(s) 476
BslI CCNNNNNNNGG 2 cut(s) 31, 626
BsmAI GTCTC 1 cut(s) 640
BsnI GGCC 1 cut(s) 273
BsoBI CYCGRG 1 cut(s) 234
Bsp119I TTCGAA 1 cut(s) 219
Bsp1286I GDGCHC 2 cut(s) 150, 241
Bsp143I GATC 2 cut(s) 283, 534
BspACI CCGC 2 cut(s) 109, 560
BspANI GGCC 1 cut(s) 273
BspCNI CTCAG 3 cut(s) 267, 577, 636
BspHI TCATGA 2 cut(s) 241, 510
BspLI GGNNCC 1 cut(s) 60
BspMI ACCTGC 1 cut(s) 648
BspT104I TTCGAA 1 cut(s) 219
BssECI CCNNGG 1 cut(s) 460
BssMI GATC 2 cut(s) 283, 534
Bst4CI ACNGT 1 cut(s) 461
Bst6I CTCTTC 1 cut(s) 411
BstBI TTCGAA 1 cut(s) 219
BstC8I GCNNGC 3 cut(s) 407, 519, 634
BstDEI CTNAG 5 cut(s) 254, 305, 541, 564, 644
BstDSI CCRYGG 1 cut(s) 460
BstF5I GGATG 1 cut(s) 472
BstKTI GATC 2 cut(s) 286, 537
BstMAI GTCTC 1 cut(s) 640
BstMBI GATC 2 cut(s) 283, 534
BstMWI GCNNNNNNNGC 2 cut(s) 117, 236
BstNSI RCATGY 1 cut(s) 636
BstSFI CTRYAG 1 cut(s) 183
BsuRI GGCC 1 cut(s) 273
BtgI CCRYGG 1 cut(s) 460
BtrI CACGTC 2 cut(s) 125, 430
BtsCI GGATG 1 cut(s) 472
BtsI GCAGTG 1 cut(s) 612
BtsIMutI CAGTG 1 cut(s) 612
BveI ACCTGC 1 cut(s) 648
Cac8I GCNNGC 3 cut(s) 407, 519, 634
CciI TCATGA 2 cut(s) 241, 510
CseI GACGC 1 cut(s) 398
CviAII CATG 7 cut(s) 130, 242, 247, 269, 511, 633, 652
DdeI CTNAG 5 cut(s) 254, 305, 541, 564, 644
DpnI GATC 2 cut(s) 285, 536
DpnII GATC 2 cut(s) 283, 534
DraIII CACNNNGTG 1 cut(s) 133
EaeI YGGCCR 1 cut(s) 271
Eam1104I CTCTTC 1 cut(s) 411
EarI CTCTTC 1 cut(s) 411
Ecl136II GAGCTC 2 cut(s) 148, 239
Eco24I GRGCYC 2 cut(s) 150, 241
Eco53kI GAGCTC 2 cut(s) 148, 239
Eco57I CTGAAG 1 cut(s) 100
Eco88I CYCGRG 1 cut(s) 234
EcoICRI GAGCTC 2 cut(s) 148, 239
EcoRI GAATTC 1 cut(s) 188
EcoT22I ATGCAT 1 cut(s) 426
EcoT38I GRGCYC 2 cut(s) 150, 241
FaeI CATG 7 cut(s) 133, 245, 250, 272, 514, 636, 655
FalI AAGNNNNNCTT 4 cut(s) 316, 348, 524, 556
FatI CATG 7 cut(s) 129, 241, 246, 268, 510, 632, 651
Fnu4HI GCNGC 1 cut(s) 561
FokI GGATG 1 cut(s) 459
FriOI GRGCYC 2 cut(s) 150, 241
Fsp4HI GCNGC 1 cut(s) 561
FspBI CTAG 1 cut(s) 264
GluI GCNGC 1 cut(s) 561
GsaI CCCAGC 2 cut(s) 82, 629
HaeIII GGCC 1 cut(s) 273
HapII CCGG 1 cut(s) 476
HgaI GACGC 1 cut(s) 398
Hin1II CATG 7 cut(s) 133, 245, 250, 272, 514, 636, 655
HincII GTYRAC 1 cut(s) 615
HindII GTYRAC 1 cut(s) 615
HinfI GANTC 3 cut(s) 65, 176, 648
HpaII CCGG 1 cut(s) 476
HphI GGTGA 2 cut(s) 142, 145
Hpy166II GTNNAC 1 cut(s) 615
Hpy188I TCNGA 1 cut(s) 346
Hpy188III TCNNGA 5 cut(s) 103, 242, 413, 496, 511
Hpy8I GTNNAC 1 cut(s) 615
HpyAV CCTTC 1 cut(s) 226
HpyCH4III ACNGT 1 cut(s) 461
HpyCH4IV ACGT 2 cut(s) 124, 429
HpyCH4V TGCA 4 cut(s) 405, 424, 450, 636
HpyF10VI GCNNNNNNNGC 2 cut(s) 117, 236
HpyF3I CTNAG 5 cut(s) 254, 305, 541, 564, 644
HpySE526I ACGT 2 cut(s) 124, 429
Hsp92II CATG 7 cut(s) 133, 245, 250, 272, 514, 636, 655
Kzo9I GATC 2 cut(s) 283, 534
LmnI GCTCC 2 cut(s) 58, 82
LpnPI CCDG 7 cut(s) 64, 75, 411, 426, 489, 611, 653
LweI GCATC 3 cut(s) 411, 433, 547
MaeI CTAG 1 cut(s) 264
MaeII ACGT 2 cut(s) 124, 429
MaeIII GTNAC 2 cut(s) 125, 326
MalI GATC 2 cut(s) 285, 536
MboI GATC 2 cut(s) 283, 534
MboII GAAGA 5 cut(s) 106, 233, 293, 428, 563
MhlI GDGCHC 2 cut(s) 150, 241
MlsI TGGCCA 1 cut(s) 273
MluCI AATT 5 cut(s) 8, 188, 340, 392, 571
MluNI TGGCCA 1 cut(s) 273
MlyI GAGTC 2 cut(s) 185, 642
MmeI TCCRAC 2 cut(s) 294, 342
MnlI CCTC 3 cut(s) 219, 288, 515
Mox20I TGGCCA 1 cut(s) 273
Mph1103I ATGCAT 1 cut(s) 426
MroXI GAANNNNTTC 2 cut(s) 110, 488
MscI TGGCCA 1 cut(s) 273
MslI CAYNNNNRTG 1 cut(s) 432
Msp20I TGGCCA 1 cut(s) 273
MspA1I CMGCKG 1 cut(s) 78
MspI CCGG 1 cut(s) 476
MwoI GCNNNNNNNGC 2 cut(s) 117, 236
NdeII GATC 2 cut(s) 283, 534
NlaIII CATG 7 cut(s) 133, 245, 250, 272, 514, 636, 655
NlaIV GGNNCC 1 cut(s) 60
NmuCI GTSAC 1 cut(s) 125
NsiI ATGCAT 1 cut(s) 426
NspI RCATGY 1 cut(s) 636
NspV TTCGAA 1 cut(s) 219
PaeI GCATGC 1 cut(s) 636
PaeR7I CTCGAG 1 cut(s) 234
PagI TCATGA 2 cut(s) 241, 510
PdmI GAANNNNTTC 2 cut(s) 110, 488
PfeI GAWTC 1 cut(s) 65
PkrI GCNGC 1 cut(s) 562
PleI GAGTC 2 cut(s) 184, 642
PpsI GAGTC 2 cut(s) 184, 642
Psp124BI GAGCTC 2 cut(s) 150, 241
PspFI CCCAGC 2 cut(s) 78, 625
PspN4I GGNNCC 1 cut(s) 60
PspXI VCTCGAGB 1 cut(s) 234
PvuII CAGCTG 1 cut(s) 78
RseI CAYNNNNRTG 1 cut(s) 432
SacI GAGCTC 2 cut(s) 150, 241
SatI GCNGC 1 cut(s) 561
Sau3AI GATC 2 cut(s) 283, 534
SchI GAGTC 2 cut(s) 185, 642
SduI GDGCHC 2 cut(s) 150, 241
SfaNI GCATC 3 cut(s) 411, 433, 547
SfcI CTRYAG 1 cut(s) 183
Sfr274I CTCGAG 1 cut(s) 234
SfuI TTCGAA 1 cut(s) 219
SlaI CTCGAG 1 cut(s) 234
SmiMI CAYNNNNRTG 1 cut(s) 432
SmlI CTYRAG 1 cut(s) 234
SmoI CTYRAG 1 cut(s) 234
SphI GCATGC 1 cut(s) 636
Sse9I AATT 5 cut(s) 8, 188, 340, 392, 571
SsiI CCGC 2 cut(s) 109, 560
SspMI CTAG 1 cut(s) 264
SstI GAGCTC 2 cut(s) 150, 241
TaaI ACNGT 1 cut(s) 461
TaiI ACGT 2 cut(s) 127, 432
TaqI TCGA 4 cut(s) 199, 219, 235, 600
TasI AATT 5 cut(s) 8, 188, 340, 392, 571
TauI GCSGC 1 cut(s) 563
TfiI GAWTC 1 cut(s) 65
TscAI CASTG 1 cut(s) 612
TseFI GTSAC 1 cut(s) 125
Tsp45I GTSAC 1 cut(s) 125
TspDTI ATGAA 5 cut(s) 17, 181, 450, 481, 527
TspRI CASTG 1 cut(s) 612
XapI RAATTY 2 cut(s) 188, 340
XceI RCATGY 1 cut(s) 636
XhoI CTCGAG 1 cut(s) 234
XmnI GAANNNNTTC 2 cut(s) 110, 488
XspI CTAG 1 cut(s) 264
Zsp2I ATGCAT 1 cut(s) 426
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.