FvH4_3g39132

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000333
Physical Location & Seq
Forward (+)
33363558 .. 33366797
3240 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g39132.t1

Sequence Viewer

Length: 729 bp
ATGGCTTATTTTGACCCCGCTATGGGATACCCGGAACTGCAGACGACCCTCAGGCTCGACTTCGCCGTCGACTACTTTCATACCTGGAAGGATAAACTAGACTTCGTCCTCATCAACAAAGACGTCGACTACGTCCTCACCGTCCCAAAGCCCCCGGAAAACGAGGTCGCTGGCTACAAGAAGTGGATCCGCGACGACCGCATCGCCCGGTACCTCATCATCGGAGCCATGCACGAACGCCTGTACTCGAGCTACAAGGAACACGAGACAGCCAAGTCCCTCATGGACGCTCTCACCGCCACTTTCACAAAACCCTCGATGATGAAACGGATGACAAAGCTCAGCAAATACGTAGGGCACAAGATGGCCGAGGGCAAACCGGTCTTTGAGCACATTCTGGAGATGGGTTCGATGGCTGGTGACCTCGAGCGCGAGGGGTTGAAGATTCCGGAGGAAGTTCAGACTGTGATGCTGATGAATAGCATGCCGGAGAGTTGGAACGATGTGGTGACCTCGTTGAAGTTGAGCATGGATTTCGATAAGTCTAAGTGGGGTGAGCCGGATTTGGGTTTGGACATGGTTAGCAGAAGGCTCAGGGATATTGGGGATATGAAGGAGTTGTATAGGAAGCGGGAGGAGGAGGAAGCCAAGAGGAGGAGGCCGCATTTCAAAGGACATTGCTTTACTTGTGGAGAATATGGGCATCACCGTAATCACTGCACCATGTAA
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
Retrotran_gag_2

Protein Analysis

243

Amino Acids

28.37

Weight (kDa)

6.8

Isoelectric Point (pI)

41.92

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 36 - 177 7.5e-24 gag-polypeptide of LTR copia-type
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: OG0000333)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G11910 AT3G11910 AT3G11910 AT3G11910 AT5G06600 AT5G06600 AT5G06600
fragaria_vesca FvH4_3g26930 FvH4_3g39132 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220 FvH4_6g21220
malus_domestica MD02G1261100.v1.1 MD03G1161100.v1.1 MD07G1059900.v1.1 MD11G1177100.v1.1 MD12G1047900.v1.1 MD12G1048000.v1.1 MD12G1048400.v1.1 MD12G1048500.v1.1 MD12G1048700.v1.1 MD12G1048800.v1.1 MD12G1056200.v1.1 MD14G1046300.v1.1 MD14G1046500.v1.1 MD15G1166900.v1.1
prunus_persica Prupe.2G066200_v2.0.a1 Prupe.2G066200_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.6G149500_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1 Prupe.7G087600_v2.0.a1
pyrus_communis pycom02g22320 pycom03g11340 pycom07g04580 pycom11g14290 pycom11g15110 pycom12g04110 pycom12g04140 pycom12g04160 pycom12g04210 pycom12g04220 pycom12g04230 pycom12g04290 pycom12g04320 pycom12g04330 pycom12g04350 pycom12g04360 pycom14g03880 pycom14g03900 pycom16g18750
rosa_chinensis RchiOBHm_Chr1g0324111 RchiOBHm_Chr1g0324241 RchiOBHm_Chr3g0477691 RchiOBHm_Chr5g0049371 RchiOBHm_Chr5g0070531
rosa_laevigata RLG00000008612 RLG00000023698 RLG00000034613 RLG00000036139
rosa_multiflora Rmu_co8271779.1_g000001 Rmu_sc0006187.1_g000014
rosa_roxburghii Rroxscaffold_1G00010670 Rroxscaffold_1G00030450 Rroxscaffold_1G00031950 Rroxscaffold_1G00031970 Rroxscaffold_1G00032320 Rroxscaffold_1G00055490 Rroxscaffold_2G00083610 Rroxscaffold_2G00084480 Rroxscaffold_2G00115610 Rroxscaffold_3G00261320 Rroxscaffold_4G00312220 Rroxscaffold_4G00325820 Rroxscaffold_5G00339170 Rroxscaffold_5G00364030 Rroxscaffold_6G00403750
rosa_rugosa Rorug03G0162700 Rorug03G0162800 Rorug03G0162900 Rorug05G0247700 Rorug05G0406600 Rorug05G0406800
rosa_samantha Rh1AG060300 Rh3AG213000 Rh3BG246600 Rh3CG240400 Rh3DG239700 Rh5AG324400 Rh5AG462100 Rh5BG335500 Rh5BG480200 Rh5BG480300 Rh5CG360200 Rh5CG504500 Rh5CG504600 Rh5DG347800 Rh5DG492200 Rh5DG492300
rosa_wichuraiana Rw3G019270 Rw3G026910 Rw5G030650 Rw5G032610 Rw5G043040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AasI GACNNNNNNGTC 2 cut(s) 65, 274
AatII GACGTC 1 cut(s) 126
Acc65I GGTACC 1 cut(s) 210
AccB1I GGYRCC 1 cut(s) 210
AccI GTMKAC 2 cut(s) 69, 126
AccII CGCG 2 cut(s) 192, 432
AccIII TCCGGA 1 cut(s) 448
AciI CCGC 6 cut(s) 18, 190, 199, 297, 631, 662
AclWI GGATC 2 cut(s) 181, 194
AcoI YGGCCR 1 cut(s) 366
AcyI GRCGYC 1 cut(s) 123
AfaI GTAC 2 cut(s) 212, 245
AfiI CCNNNNNNNGG 4 cut(s) 22, 23, 566, 654
AgeI ACCGGT 1 cut(s) 379
AgsI TTSAA 3 cut(s) 442, 520, 670
AjnI CCWGG 1 cut(s) 83
AluBI AGCT 2 cut(s) 252, 340
AluI AGCT 2 cut(s) 252, 340
Alw21I GWGCWC 1 cut(s) 393
Alw26I GTCTC 1 cut(s) 260
AlwI GGATC 2 cut(s) 181, 194
Ama87I CYCGRG 2 cut(s) 247, 425
Aor13HI TCCGGA 1 cut(s) 448
AoxI GGCC 2 cut(s) 366, 659
AsiGI ACCGGT 1 cut(s) 379
Asp718I GGTACC 1 cut(s) 210
AspLEI GCGC 1 cut(s) 432
AsuC2I CCSGG 3 cut(s) 32, 155, 208
AsuHPI GGTGA 6 cut(s) 130, 286, 431, 520, 566, 698
AvaI CYCGRG 2 cut(s) 247, 425
AxyI CCTNAGG 1 cut(s) 50
BaeGI GKGCMC 1 cut(s) 360
BamHI GGATCC 1 cut(s) 186
BanI GGYRCC 1 cut(s) 210
BauI CACGAG 1 cut(s) 263
Bbv12I GWGCWC 1 cut(s) 393
BccI CCATC 3 cut(s) 358, 397, 406
BceAI ACGGC 1 cut(s) 50
BcgI CGANNNNNNTGC 2 cut(s) 517, 551
BciT130I CCWGG 1 cut(s) 85
BciVI GTATCC 1 cut(s) 20
BcnI CCSGG 3 cut(s) 32, 155, 208
BcoDI GTCTC 1 cut(s) 260
BfaI CTAG 1 cut(s) 98
BfmI CTRYAG 1 cut(s) 38
BfuI GTATCC 1 cut(s) 20
BisI GCNGC 1 cut(s) 662
BlpI GCTNAGC 1 cut(s) 341
BlsI GCNGC 1 cut(s) 663
Bme1390I CCNGG 4 cut(s) 32, 85, 155, 208
BmeT110I CYCGRG 2 cut(s) 247, 425
BmiI GGNNCC 3 cut(s) 188, 212, 226
BmrFI CCNGG 4 cut(s) 32, 85, 155, 208
BmsI GCATC 3 cut(s) 210, 459, 712
BpmI CTGGAG 1 cut(s) 419
Bpu10I CCTNAGC 1 cut(s) 593
Bpu1102I GCTNAGC 1 cut(s) 341
BpuMI CCSGG 3 cut(s) 32, 155, 208
BsaAI YACGTR 1 cut(s) 352
BsaHI GRCGYC 1 cut(s) 123
BsaJI CCNNGG 2 cut(s) 153, 369
BsaWI WCCGGW 2 cut(s) 379, 448
Bsc4I CCNNNNNNNGG 4 cut(s) 22, 23, 566, 654
Bse118I RCCGGY 1 cut(s) 379
Bse21I CCTNAGG 1 cut(s) 50
Bse3DI GCAATG 1 cut(s) 676
BseAI TCCGGA 1 cut(s) 448
BseBI CCWGG 1 cut(s) 85
BseDI CCNNGG 2 cut(s) 153, 369
BseGI GGATG 1 cut(s) 336
BseLI CCNNNNNNNGG 4 cut(s) 22, 23, 566, 654
BseMI GCAATG 1 cut(s) 676
BseMII CTCAG 3 cut(s) 64, 355, 607
BseRI GAGGAG 4 cut(s) 650, 653, 667, 670
BseSI GKGCMC 1 cut(s) 360
BsgI GTGCAG 1 cut(s) 703
Bsh1236I CGCG 2 cut(s) 192, 432
Bsh1285I CGRYCG 1 cut(s) 199
BshFI GGCC 2 cut(s) 368, 661
BshNI GGYRCC 1 cut(s) 210
BshTI ACCGGT 1 cut(s) 379
BsiEI CGRYCG 1 cut(s) 199
BsiHKAI GWGCWC 1 cut(s) 393
BsiHKCI CYCGRG 2 cut(s) 247, 425
BsiSI CCGG 7 cut(s) 32, 155, 208, 380, 449, 488, 560
BslFI GGGAC 2 cut(s) 128, 262
BslI CCNNNNNNNGG 4 cut(s) 22, 23, 566, 654
BsmAI GTCTC 1 cut(s) 260
BsmFI GGGAC 2 cut(s) 128, 262
BsnI GGCC 2 cut(s) 368, 661
BsoBI CYCGRG 2 cut(s) 247, 425
Bsp1286I GDGCHC 2 cut(s) 360, 393
Bsp13I TCCGGA 1 cut(s) 448
Bsp143I GATC 1 cut(s) 186
Bsp1720I GCTNAGC 1 cut(s) 341
BspACI CCGC 6 cut(s) 18, 190, 199, 297, 631, 662
BspANI GGCC 2 cut(s) 368, 661
BspCNI CTCAG 3 cut(s) 63, 354, 606
BspEI TCCGGA 1 cut(s) 448
BspFNI CGCG 2 cut(s) 192, 432
BspLI GGNNCC 3 cut(s) 188, 212, 226
BspMAI CTGCAG 1 cut(s) 42
BspPI GGATC 2 cut(s) 181, 194
BspT107I GGYRCC 1 cut(s) 210
BsrDI GCAATG 1 cut(s) 676
BsrFI RCCGGY 1 cut(s) 379
BssAI RCCGGY 1 cut(s) 379
BssECI CCNNGG 2 cut(s) 153, 369
BssMI GATC 1 cut(s) 186
BssNI GRCGYC 1 cut(s) 123
BssSI CACGAG 1 cut(s) 263
Bst2BI CACGAG 1 cut(s) 263
Bst2UI CCWGG 1 cut(s) 85
Bst4CI ACNGT 3 cut(s) 142, 466, 710
BstACI GRCGYC 1 cut(s) 123
BstBAI YACGTR 1 cut(s) 352
BstC8I GCNNGC 2 cut(s) 172, 485
BstDEI CTNAG 4 cut(s) 50, 341, 546, 593
BstEII GGTNACC 2 cut(s) 419, 508
BstF5I GGATG 1 cut(s) 336
BstFNI CGCG 2 cut(s) 192, 432
BstHHI GCGC 1 cut(s) 432
BstKTI GATC 1 cut(s) 189
BstMAI GTCTC 1 cut(s) 260
BstMBI GATC 1 cut(s) 186
BstMCI CGRYCG 1 cut(s) 199
BstMWI GCNNNNNNNGC 2 cut(s) 198, 296
BstNI CCWGG 1 cut(s) 85
BstNSI RCATGY 1 cut(s) 487
BstPI GGTNACC 2 cut(s) 419, 508
BstSCI CCNGG 4 cut(s) 30, 83, 153, 206
BstSFI CTRYAG 1 cut(s) 38
BstSLI GKGCMC 1 cut(s) 360
BstSNI TACGTA 1 cut(s) 352
BstUI CGCG 2 cut(s) 192, 432
BstX2I RGATCY 1 cut(s) 186
BstYI RGATCY 1 cut(s) 186
Bsu36I CCTNAGG 1 cut(s) 50
BsuI GTATCC 1 cut(s) 20
BsuRI GGCC 2 cut(s) 368, 661
BtgZI GCGATG 1 cut(s) 187
BtsCI GGATG 1 cut(s) 336
BtsI GCAGTG 1 cut(s) 715
BtsIMutI CAGTG 1 cut(s) 715
Cac8I GCNNGC 2 cut(s) 172, 485
CfoI GCGC 1 cut(s) 432
Cfr10I RCCGGY 1 cut(s) 379
CseI GACGC 1 cut(s) 296
Csp6I GTAC 2 cut(s) 211, 244
CspAI ACCGGT 1 cut(s) 379
CviAII CATG 6 cut(s) 229, 283, 484, 529, 577, 724
CviQI GTAC 2 cut(s) 211, 244
DdeI CTNAG 4 cut(s) 50, 341, 546, 593
DpnI GATC 1 cut(s) 188
DpnII GATC 1 cut(s) 186
DrdI GACNNNNNNGTC 2 cut(s) 65, 274
DseDI GACNNNNNNGTC 2 cut(s) 65, 274
EaeI YGGCCR 1 cut(s) 366
Eco105I TACGTA 1 cut(s) 352
Eco81I CCTNAGG 1 cut(s) 50
Eco88I CYCGRG 2 cut(s) 247, 425
Eco91I GGTNACC 2 cut(s) 419, 508
EcoO65I GGTNACC 2 cut(s) 419, 508
EcoRII CCWGG 1 cut(s) 83
FaeI CATG 6 cut(s) 232, 286, 487, 532, 580, 727
FaqI GGGAC 2 cut(s) 128, 262
FatI CATG 6 cut(s) 228, 282, 483, 528, 576, 723
FauI CCCGC 2 cut(s) 25, 624
FblI GTMKAC 2 cut(s) 69, 126
Fnu4HI GCNGC 1 cut(s) 662
FokI GGATG 1 cut(s) 343
Fsp4HI GCNGC 1 cut(s) 662
FspBI CTAG 1 cut(s) 98
GlaI GCGC 1 cut(s) 431
GluI GCNGC 1 cut(s) 662
GsuI CTGGAG 1 cut(s) 419
HaeIII GGCC 2 cut(s) 368, 661
HapII CCGG 7 cut(s) 32, 155, 208, 380, 449, 488, 560
HgaI GACGC 1 cut(s) 296
HhaI GCGC 1 cut(s) 432
Hin1I GRCGYC 1 cut(s) 123
Hin1II CATG 6 cut(s) 232, 286, 487, 532, 580, 727
Hin6I GCGC 1 cut(s) 430
HinP1I GCGC 1 cut(s) 430
HincII GTYRAC 2 cut(s) 70, 127
HindII GTYRAC 2 cut(s) 70, 127
HinfI GANTC 1 cut(s) 445
HpaII CCGG 7 cut(s) 32, 155, 208, 380, 449, 488, 560
HphI GGTGA 6 cut(s) 130, 286, 431, 520, 566, 698
Hpy166II GTNNAC 2 cut(s) 70, 127
Hpy188I TCNGA 2 cut(s) 224, 462
Hpy188III TCNNGA 2 cut(s) 398, 449
Hpy8I GTNNAC 2 cut(s) 70, 127
Hpy99I CGWCG 3 cut(s) 71, 128, 197
HpyAV CCTTC 3 cut(s) 82, 582, 607
HpyCH4III ACNGT 3 cut(s) 142, 466, 710
HpyCH4IV ACGT 3 cut(s) 123, 132, 351
HpyCH4V TGCA 3 cut(s) 40, 232, 720
HpyF10VI GCNNNNNNNGC 2 cut(s) 198, 296
HpyF3I CTNAG 4 cut(s) 50, 341, 546, 593
HpySE526I ACGT 3 cut(s) 123, 132, 351
Hsp92I GRCGYC 1 cut(s) 123
Hsp92II CATG 6 cut(s) 232, 286, 487, 532, 580, 727
HspAI GCGC 1 cut(s) 430
Kpn2I TCCGGA 1 cut(s) 448
KpnI GGTACC 1 cut(s) 214
Kzo9I GATC 1 cut(s) 186
LmnI GCTCC 1 cut(s) 224
LweI GCATC 3 cut(s) 210, 459, 712
MaeI CTAG 1 cut(s) 98
MaeII ACGT 3 cut(s) 123, 132, 351
MaeIII GTNAC 2 cut(s) 419, 508
MalI GATC 1 cut(s) 188
MboI GATC 1 cut(s) 186
MboII GAAGA 1 cut(s) 454
MflI RGATCY 1 cut(s) 186
MhlI GDGCHC 2 cut(s) 360, 393
MmeI TCCRAC 1 cut(s) 476
MroI TCCGGA 1 cut(s) 448
MspI CCGG 7 cut(s) 32, 155, 208, 380, 449, 488, 560
MspR9I CCNGG 4 cut(s) 32, 85, 155, 208
MvaI CCWGG 1 cut(s) 85
MvnI CGCG 2 cut(s) 192, 432
MwoI GCNNNNNNNGC 2 cut(s) 198, 296
NciI CCSGG 3 cut(s) 32, 155, 208
NdeII GATC 1 cut(s) 186
NlaIII CATG 6 cut(s) 232, 286, 487, 532, 580, 727
NlaIV GGNNCC 3 cut(s) 188, 212, 226
NmeAIII GCCGAG 1 cut(s) 394
NmuCI GTSAC 2 cut(s) 419, 508
NspI RCATGY 1 cut(s) 487
PaeI GCATGC 1 cut(s) 487
PaeR7I CTCGAG 2 cut(s) 247, 425
PcsI WCGNNNNNNNCGW 3 cut(s) 63, 129, 138
PfeI GAWTC 1 cut(s) 445
PflFI GACNNNGTC 2 cut(s) 104, 131
PinAI ACCGGT 1 cut(s) 379
PkrI GCNGC 1 cut(s) 663
Ppu21I YACGTR 1 cut(s) 352
Psp6I CCWGG 1 cut(s) 83
PspEI GGTNACC 2 cut(s) 419, 508
PspGI CCWGG 1 cut(s) 83
PspN4I GGNNCC 3 cut(s) 188, 212, 226
PspXI VCTCGAGB 2 cut(s) 247, 425
PstI CTGCAG 1 cut(s) 42
PsuI RGATCY 1 cut(s) 186
PsyI GACNNNGTC 2 cut(s) 104, 131
RsaI GTAC 2 cut(s) 212, 245
RsaNI GTAC 2 cut(s) 211, 244
SalI GTCGAC 2 cut(s) 68, 125
SatI GCNGC 1 cut(s) 662
Sau3AI GATC 1 cut(s) 186
ScrFI CCNGG 4 cut(s) 32, 85, 155, 208
SduI GDGCHC 2 cut(s) 360, 393
SfaNI GCATC 3 cut(s) 210, 459, 712
SfcI CTRYAG 1 cut(s) 38
Sfr274I CTCGAG 2 cut(s) 247, 425
SlaI CTCGAG 2 cut(s) 247, 425
SmlI CTYRAG 2 cut(s) 247, 425
SmoI CTYRAG 2 cut(s) 247, 425
SnaBI TACGTA 1 cut(s) 352
SphI GCATGC 1 cut(s) 487
SsiI CCGC 6 cut(s) 18, 190, 199, 297, 631, 662
SspMI CTAG 1 cut(s) 98
StyD4I CCNGG 4 cut(s) 30, 83, 153, 206
TaaI ACNGT 3 cut(s) 142, 466, 710
TaiI ACGT 3 cut(s) 126, 135, 354
TaqI TCGA 8 cut(s) 57, 69, 126, 248, 317, 410, 426, 537
TatI WGTACW 1 cut(s) 243
TauI GCSGC 1 cut(s) 664
TfiI GAWTC 1 cut(s) 445
TscAI CASTG 1 cut(s) 722
TseFI GTSAC 2 cut(s) 419, 508
Tsp45I GTSAC 2 cut(s) 419, 508
TspDTI ATGAA 4 cut(s) 68, 338, 491, 626
TspGWI ACGGA 1 cut(s) 343
TspRI CASTG 1 cut(s) 722
Tth111I GACNNNGTC 2 cut(s) 104, 131
XceI RCATGY 1 cut(s) 487
XcmI CCANNNNNNNNNTGG 1 cut(s) 280
XhoI CTCGAG 2 cut(s) 247, 425
XmiI GTMKAC 2 cut(s) 69, 126
XspI CTAG 1 cut(s) 98
ZraI GACGTC 1 cut(s) 124
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.