FvH4_3g03542

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000106
Physical Location & Seq
Forward (+)
1971043 .. 1972422
1380 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g03542.t1

Sequence Viewer

Length: 1380 bp
ATGACTACAGCAGAAAATGGTTCAGAAGTTAGAGTTCCTATCTTCTCAGGAGAGAACTTTGATTTCTGGATTATAAAGATGGAAACCATGTTCATATCATGTGATCTCTTGAGCTATGTGAATGAAGGCTATGTAGTTCCAGCAGCTGAAGGGATGACAAATGCTCAAAGAACTGAGCTGAGGGCAAATATCAAGAAAGATGCAAAAGCTCTTGGTATTTTGCAAACCGCAGTCACAGATGCTATCTTTCCAAGAATTGCAAATGAGAGAATAGCCAAAGGAGCTTGGGATGTTCTGAAGGTGGAGTTCAAAGGCTCAGATAAGGTGAGAGCTGTTAAAGTTCAATCCTTAAGGAGAGATTTTGAATATACCAAAATGAATGAAACTGAGCTGCTAAGTGATTATTGCACTAGATTGACTGATTTAGTTAACCAGATGGAAACCTATGCTGAACCTATACCTGAAAAGAGAGTAGTACAAAAGATCCTTATGAGTTTGAATAGAAAGTATGATGCTATAGCAAGTATTATAGAGGAGACTAGAGATATAGACACTCTTGGTGTGCAGGATTTAATGGGGACACTTAAGGCTTTTGATCAGAGGTTGATGAGTCATGATGAACCAACAGAAAAAGCCTTTCAAACACTAAGCCTAAACACAAATAGTGAGCCATCTAGTTCAAATTCCAAAAAGAAAAAGAATTGGAAAGGCAAAGGCAAGAAGTGGGAGGGTAGATCAGATCAGTCAGGAAAAAGAAAAAATGAAGGAGGCAGTAGTTCAAATTATTCGAAGTGTTCAATCTGTGATAAGATGCATATAGGTGAATGTTGGTTTAAGGGGAAGCCAAAATGTTCAAATTGTAACAAGTTCAGTCATGTCAAGAAGGATTGTGACTACAAAGGAAATCAACTGGCTAGCTGCAGTGAAGAACAAAGTGATGCTAGCATGTTCTGTGTCACTTATGCTGCAACCACTGCGGTGAATGAGAATGTGTGGTTTGTTGATAGTGCTTACAGTAATCATATGACTGCAAATGCCAACCTTCTCTATGACATTGACTACAACAGCATTACAAAGGTGAAGATGACAAATGGAATGTTGGTGGATACAAAAGGCAAAGGAAGTGTTGCTGTTGAAACCAAAAATGGAAAAATGTTCATCAGAGATGTAATGCTTGTTCCAAATCTTGATTCGAATTTGCTAAGTGTTGGACAACTTGTTGAGCACAAATATCACCTGCATTTTGGTGATGACACTTGCAAAATCTTTGAGAGAGGGAGTAGCAAGAAGCTGATGCTGGAAGTTGAAATGAAGAGGAACAGAAGTTTTCCTCTGACTCTCAAGTATGCAACTGAGAGTGCAAGAAAAATGGAGCTGTAG
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
DUF4219 Retrotran_gag_2 gag_pre-integrs rve zf-CCHC

Protein Analysis

460

Amino Acids

51.87

Weight (kDa)

8.56

Isoelectric Point (pI)

39.32

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 201 1.1e-28 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 332 - 411 1.7e-20 Pol polyprotein, beta-barrel domain
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: OG0000106)

Species Orthologous Gene IDs
arabidopsis_thaliana AT3G20980 AT3G21000
fragaria_vesca FvH4_1g15931 FvH4_1g15931 FvH4_1g18381 FvH4_1g18382 FvH4_1g22571 FvH4_1g24950 FvH4_1g29372 FvH4_2g03582 FvH4_2g09851 FvH4_2g13112 FvH4_2g20843 FvH4_2g22701 FvH4_2g22702 FvH4_2g23403 FvH4_2g40201 FvH4_3g03542 FvH4_3g03543 FvH4_3g04761 FvH4_3g10464 FvH4_3g12741 FvH4_3g15781 FvH4_3g30981 FvH4_4g00985 FvH4_4g07035 FvH4_4g08192 FvH4_4g08211 FvH4_4g08553 FvH4_4g14242 FvH4_4g14243 FvH4_4g14641 FvH4_4g14843 FvH4_4g14844 FvH4_4g15061 FvH4_4g16281 FvH4_4g19152 FvH4_4g26451 FvH4_5g06442 FvH4_5g22521 FvH4_5g24301 FvH4_5g38641 FvH4_6g02393 FvH4_6g12782 FvH4_6g13871 FvH4_6g19391 FvH4_6g20105 FvH4_6g21292 FvH4_6g23581 FvH4_6g29153 FvH4_6g29691 FvH4_6g30871 FvH4_6g33351 FvH4_6g37042 FvH4_6g38781 FvH4_6g40340 FvH4_7g11221 FvH4_7g23352 FvH4_7g23352 FvH4_7g31212 FvH4_7g32172 FvH4_7g32173 FvH4_7g33701
malus_domestica MD03G1006900.v1.1 MD04G1039100.v1.1 MD04G1239100.v1.1 MD05G1048700.v1.1 MD08G1001800.v1.1 MD09G1165800.v1.1 MD11G1065200.v1.1 MD11G1138200.v1.1 MD14G1033300.v1.1 MD14G1173900.v1.1 MD15G1218200.v1.1 MD16G1034000.v1.1
prunus_persica Prupe.1G219500_v2.0.a1 Prupe.2G169400_v2.0.a1 Prupe.4G109700_v2.0.a1 Prupe.7G022000_v2.0.a1
pyrus_communis pycom01g02000 pycom02g13350 pycom03g01010 pycom04g05000 pycom04g06100 pycom05g05580 pycom05g09950 pycom05g13280 pycom05g26610 pycom06g05940 pycom06g07760 pycom07g06120 pycom07g24780 pycom08g08820 pycom09g03600 pycom09g07200 pycom10g01280 pycom10g06730 pycom10g08410 pycom10g25520 pycom11g00470 pycom11g05250 pycom11g25180 pycom12g08050 pycom13g14760 pycom13g28170 pycom15g14310 pycom15g19880 pycom15g24230 pycom15g33640 pycom16g02150 pycom16g16240 pycom16g20050 pycom16g21090 pycom17g06100
rosa_chinensis RchiOBHm_Chr1g0322161 RchiOBHm_Chr1g0326341 RchiOBHm_Chr1g0357701 RchiOBHm_Chr1g0379861 RchiOBHm_Chr1g0383421 RchiOBHm_Chr2g0093981 RchiOBHm_Chr2g0139051 RchiOBHm_Chr2g0145501 RchiOBHm_Chr3g0450971 RchiOBHm_Chr3g0451441 RchiOBHm_Chr3g0457411 RchiOBHm_Chr4g0436261 RchiOBHm_Chr5g0051431 RchiOBHm_Chr5g0064031 RchiOBHm_Chr5g0073141 RchiOBHm_Chr5g0080061 RchiOBHm_Chr7g0200561 RchiOBHm_Chr7g0235911
rosa_laevigata RLG00000000145 RLG00000000429 RLG00000020339 RLG00000035212
rosa_multiflora Rmu_co7977988.1_g000001 Rmu_co8037866.1_g000001 Rmu_co8243895.1_g000001 Rmu_co8363787.1_g000001 Rmu_co8381003.1_g000001 Rmu_sc0000263.1_g000006 Rmu_sc0000349.1_g000002 Rmu_sc0000455.1_g000031 Rmu_sc0000936.1_g000022 Rmu_sc0001035.1_g000023 Rmu_sc0001169.1_g000019 Rmu_sc0001250.1_g000026 Rmu_sc0002200.1_g000051 Rmu_sc0002230.1_g000027 Rmu_sc0002591.1_g000039 Rmu_sc0003182.1_g000003 Rmu_sc0003441.1_g000068 Rmu_sc0003722.1_g000018 Rmu_sc0003764.1_g000007 Rmu_sc0006014.1_g000016 Rmu_sc0012582.1_g000002 Rmu_sc0013519.1_g000002 Rmu_sc0014550.1_g000005 Rmu_sc0014857.1_g000007 Rmu_sc0019855.1_g000001 Rmu_sc0030839.1_g000001 Rmu_sc0031308.1_g000001
rosa_roxburghii Rroxscaffold_1G00011290 Rroxscaffold_1G00041340 Rroxscaffold_1G00053780 Rroxscaffold_1G00059130 Rroxscaffold_1G00061580 Rroxscaffold_2G00080940 Rroxscaffold_2G00109540 Rroxscaffold_3G00228400 Rroxscaffold_3G00237710 Rroxscaffold_4G00285210 Rroxscaffold_4G00299600 Rroxscaffold_4G00324940 Rroxscaffold_4G00330580 Rroxscaffold_5G00333000 Rroxscaffold_5G00347920 Rroxscaffold_5G00375310 Rroxscaffold_6G00394760 Rroxscaffold_6G00406260 Rroxscaffold_7G00165690 Rroxscaffold_7G00187680
rosa_rugosa Rorug01G0050200 Rorug02G0273800 Rorug06G0490600 Rorug06G0490600 Rorug06G0490700
rosa_samantha Rh1AG348400 Rh5AG222600 Rh6DG000500 Rh6DG194500 Rh7BG452700
rosa_wichuraiana Rw0G003060 Rw0G010530 Rw0G012970 Rw0G022560 Rw0G023390 Rw1G001270 Rw1G001530 Rw1G006070 Rw1G008210 Rw1G022090 Rw1G023320 Rw2G003790 Rw2G004140 Rw2G005280 Rw2G006460 Rw2G019620 Rw2G019840 Rw2G022530 Rw2G023280 Rw2G024990 Rw2G042380 Rw2G051390 Rw3G001640 Rw3G016720 Rw3G017100 Rw3G020890 Rw3G020900 Rw3G021100 Rw4G004820 Rw4G014950 Rw4G030920 Rw4G031400 Rw5G008500 Rw5G017950 Rw5G020170 Rw5G030160 Rw5G033050 Rw5G034640 Rw5G043920 Rw6G005060 Rw6G005540 Rw6G006720 Rw6G008460 Rw6G008670 Rw6G014780 Rw6G019100 Rw6G019350 Rw6G026310 Rw7G016810 Rw7G019180 Rw7G022890 Rw7G025880 Rw7G026390 Rw7G028340 Rw7G034850 Rw7G035170 Rw7G035420 Rw7G037990 Rw7G041560

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 74
AarI CACCTGC 1 cut(s) 1245
Acc36I ACCTGC 1 cut(s) 1245
AciI CCGC 2 cut(s) 228, 977
AclWI GGATC 1 cut(s) 478
AcsI RAATTY 2 cut(s) 682, 1195
AcuI CTGAAG 2 cut(s) 168, 317
AfaI GTAC 1 cut(s) 477
AflII CTTAAG 2 cut(s) 349, 584
AjuI GAANNNNNNNTTGG 2 cut(s) 1174, 1206
AleI CACNNNNGTG 1 cut(s) 977
AloI GAACNNNNNNTCC 2 cut(s) 74, 106
Alw21I GWGCWC 1 cut(s) 1227
Alw26I GTCTC 1 cut(s) 530
AlwI GGATC 1 cut(s) 478
AlwNI CAGNNNCTG 1 cut(s) 146
ApeKI GCWGC 4 cut(s) 143, 391, 918, 965
ApoI RAATTY 2 cut(s) 682, 1195
AsuHPI GGTGA 6 cut(s) 337, 833, 991, 1090, 1226, 1259
AsuII TTCGAA 2 cut(s) 788, 1193
AsuNHI GCTAGC 2 cut(s) 914, 941
Bbv12I GWGCWC 1 cut(s) 1227
BbvCI CCTCAGC 1 cut(s) 179
BbvI GCAGC 4 cut(s) 155, 378, 905, 952
BccI CCATC 3 cut(s) 73, 430, 679
BciVI GTATCC 1 cut(s) 1099
BclI TGATCA 1 cut(s) 595
BcoDI GTCTC 1 cut(s) 530
BfaI CTAG 5 cut(s) 411, 540, 675, 915, 942
BfmI CTRYAG 4 cut(s) 6, 516, 919, 1376
BfrI CTTAAG 2 cut(s) 349, 584
BfuAI ACCTGC 1 cut(s) 1245
BfuI GTATCC 1 cut(s) 1099
BisI GCNGC 4 cut(s) 144, 392, 919, 966
BlsI GCNGC 4 cut(s) 145, 393, 920, 967
BmsI GCATC 6 cut(s) 190, 229, 502, 801, 928, 1284
BmtI GCTAGC 2 cut(s) 918, 945
Bpu10I CCTNAGC 1 cut(s) 179
Bpu14I TTCGAA 2 cut(s) 788, 1193
BpuEI CTTGAG 2 cut(s) 130, 1325
Bse1I ACTGG 1 cut(s) 915
BseGI GGATG 2 cut(s) 159, 295
BseMII CTCAG 6 cut(s) 60, 165, 170, 330, 378, 1344
BseNI ACTGG 1 cut(s) 915
BseRI GAGGAG 1 cut(s) 548
BseXI GCAGC 4 cut(s) 155, 378, 905, 952
BsgI GTGCAG 1 cut(s) 584
BsiHKAI GWGCWC 1 cut(s) 1227
BslFI GGGAC 1 cut(s) 592
BsmAI GTCTC 1 cut(s) 530
BsmFI GGGAC 1 cut(s) 592
Bsp119I TTCGAA 2 cut(s) 788, 1193
Bsp1286I GDGCHC 1 cut(s) 1227
Bsp143I GATC 5 cut(s) 103, 483, 595, 734, 739
BspACI CCGC 2 cut(s) 228, 977
BspCNI CTCAG 6 cut(s) 59, 166, 171, 329, 379, 1345
BspHI TCATGA 1 cut(s) 613
BspMAI CTGCAG 1 cut(s) 923
BspMI ACCTGC 1 cut(s) 1245
BspOI GCTAGC 2 cut(s) 918, 945
BspPI GGATC 1 cut(s) 478
BspT104I TTCGAA 2 cut(s) 788, 1193
BspTI CTTAAG 2 cut(s) 349, 584
BsrI ACTGG 1 cut(s) 915
BssMI GATC 5 cut(s) 103, 483, 595, 734, 739
Bst4CI ACNGT 1 cut(s) 1016
Bst6I CTCTTC 1 cut(s) 1307
BstAFI CTTAAG 2 cut(s) 349, 584
BstAPI GCANNNNNTGC 1 cut(s) 974
BstBI TTCGAA 2 cut(s) 788, 1193
BstC8I GCNNGC 2 cut(s) 916, 943
BstDEI CTNAG 9 cut(s) 46, 174, 179, 316, 387, 395, 647, 1202, 1353
BstF5I GGATG 2 cut(s) 159, 295
BstKTI GATC 5 cut(s) 106, 486, 598, 737, 742
BstMAI GTCTC 1 cut(s) 530
BstMBI GATC 5 cut(s) 103, 483, 595, 734, 739
BstMWI GCNNNNNNNGC 2 cut(s) 281, 974
BstNSI RCATGY 1 cut(s) 949
BstSFI CTRYAG 4 cut(s) 6, 516, 919, 1376
BstV1I GCAGC 4 cut(s) 155, 378, 905, 952
BstX2I RGATCY 1 cut(s) 483
BstYI RGATCY 1 cut(s) 483
BsuI GTATCC 1 cut(s) 1099
BtsCI GGATG 2 cut(s) 159, 295
BtsI GCAGTG 2 cut(s) 928, 972
BtsIMutI CAGTG 2 cut(s) 928, 972
BveI ACCTGC 1 cut(s) 1245
Cac8I GCNNGC 2 cut(s) 916, 943
CaiI CAGNNNCTG 1 cut(s) 146
CciI TCATGA 1 cut(s) 613
Csp6I GTAC 1 cut(s) 476
CviAII CATG 5 cut(s) 88, 99, 614, 875, 946
CviQI GTAC 1 cut(s) 476
DdeI CTNAG 9 cut(s) 46, 174, 179, 316, 387, 395, 647, 1202, 1353
DpnI GATC 5 cut(s) 105, 485, 597, 736, 741
DpnII GATC 5 cut(s) 103, 483, 595, 734, 739
Eam1104I CTCTTC 1 cut(s) 1307
EarI CTCTTC 1 cut(s) 1307
Eco57I CTGAAG 2 cut(s) 168, 317
EcoT22I ATGCAT 1 cut(s) 816
FaeI CATG 5 cut(s) 91, 102, 617, 878, 949
FaqI GGGAC 1 cut(s) 592
FatI CATG 5 cut(s) 87, 98, 613, 874, 945
FauNDI CATATG 1 cut(s) 1023
FbaI TGATCA 1 cut(s) 595
Fnu4HI GCNGC 4 cut(s) 144, 392, 919, 966
FokI GGATG 2 cut(s) 166, 302
Fsp4HI GCNGC 4 cut(s) 144, 392, 919, 966
FspBI CTAG 5 cut(s) 411, 540, 675, 915, 942
GluI GCNGC 4 cut(s) 144, 392, 919, 966
Hin1II CATG 5 cut(s) 91, 102, 617, 878, 949
HincII GTYRAC 1 cut(s) 430
HindII GTYRAC 1 cut(s) 430
HinfI GANTC 3 cut(s) 610, 1190, 1336
HpaI GTTAAC 1 cut(s) 430
HphI GGTGA 6 cut(s) 337, 833, 991, 1090, 1226, 1259
Hpy166II GTNNAC 1 cut(s) 430
Hpy188I TCNGA 7 cut(s) 25, 297, 319, 600, 739, 1163, 1335
Hpy188III TCNNGA 8 cut(s) 48, 67, 109, 193, 614, 747, 880, 1187
Hpy8I GTNNAC 1 cut(s) 430
HpyAV CCTTC 6 cut(s) 119, 143, 292, 758, 877, 1052
HpyCH4III ACNGT 1 cut(s) 1016
HpyF10VI GCNNNNNNNGC 2 cut(s) 281, 974
HpyF3I CTNAG 9 cut(s) 46, 174, 179, 316, 387, 395, 647, 1202, 1353
Hsp92II CATG 5 cut(s) 91, 102, 617, 878, 949
Ksp22I TGATCA 1 cut(s) 595
KspAI GTTAAC 1 cut(s) 430
Kzo9I GATC 5 cut(s) 103, 483, 595, 734, 739
LmnI GCTCC 2 cut(s) 281, 1372
Lsp1109I GCAGC 4 cut(s) 155, 378, 905, 952
LweI GCATC 6 cut(s) 190, 229, 502, 801, 928, 1284
MaeI CTAG 5 cut(s) 411, 540, 675, 915, 942
MaeIII GTNAC 4 cut(s) 232, 860, 890, 955
MalI GATC 5 cut(s) 105, 485, 597, 736, 741
MboI GATC 5 cut(s) 103, 483, 595, 734, 739
MboII GAAGA 4 cut(s) 34, 938, 1093, 1324
MflI RGATCY 1 cut(s) 483
MhlI GDGCHC 1 cut(s) 1227
MluCI AATT 6 cut(s) 255, 682, 700, 781, 856, 1195
MlyI GAGTC 2 cut(s) 619, 1330
MmeI TCCRAC 1 cut(s) 1189
MnlI CCTC 8 cut(s) 174, 526, 594, 721, 761, 1268, 1308, 1341
Mph1103I ATGCAT 1 cut(s) 816
MseI TTAA 6 cut(s) 336, 350, 429, 572, 585, 834
MslI CAYNNNNRTG 3 cut(s) 819, 977, 1245
MspA1I CMGCKG 1 cut(s) 146
MspCI CTTAAG 2 cut(s) 349, 584
MwoI GCNNNNNNNGC 2 cut(s) 281, 974
NdeI CATATG 1 cut(s) 1023
NdeII GATC 5 cut(s) 103, 483, 595, 734, 739
NheI GCTAGC 2 cut(s) 914, 941
NlaIII CATG 5 cut(s) 91, 102, 617, 878, 949
NmuCI GTSAC 3 cut(s) 232, 890, 955
NsiI ATGCAT 1 cut(s) 816
NspI RCATGY 1 cut(s) 949
NspV TTCGAA 2 cut(s) 788, 1193
OliI CACNNNNGTG 1 cut(s) 977
PagI TCATGA 1 cut(s) 613
PaqCI CACCTGC 1 cut(s) 1245
PfeI GAWTC 1 cut(s) 1190
PkrI GCNGC 4 cut(s) 145, 393, 920, 967
PleI GAGTC 2 cut(s) 618, 1330
PpsI GAGTC 2 cut(s) 618, 1330
PsiI TTATAA 1 cut(s) 74
PsrI GAACNNNNNNTAC 2 cut(s) 1161, 1193
PstI CTGCAG 1 cut(s) 923
PstNI CAGNNNCTG 1 cut(s) 146
PsuI RGATCY 1 cut(s) 483
PvuII CAGCTG 1 cut(s) 146
RsaI GTAC 1 cut(s) 477
RsaNI GTAC 1 cut(s) 476
RseI CAYNNNNRTG 3 cut(s) 819, 977, 1245
SaqAI TTAA 6 cut(s) 336, 350, 429, 572, 585, 834
SatI GCNGC 4 cut(s) 144, 392, 919, 966
Sau3AI GATC 5 cut(s) 103, 483, 595, 734, 739
SchI GAGTC 2 cut(s) 619, 1330
SduI GDGCHC 1 cut(s) 1227
SfaNI GCATC 6 cut(s) 190, 229, 502, 801, 928, 1284
SfcI CTRYAG 4 cut(s) 6, 516, 919, 1376
SfuI TTCGAA 2 cut(s) 788, 1193
SmiMI CAYNNNNRTG 3 cut(s) 819, 977, 1245
SmlI CTYRAG 4 cut(s) 109, 349, 584, 1340
SmoI CTYRAG 4 cut(s) 109, 349, 584, 1340
Sse9I AATT 6 cut(s) 255, 682, 700, 781, 856, 1195
SsiI CCGC 2 cut(s) 228, 977
SspMI CTAG 5 cut(s) 411, 540, 675, 915, 942
TaaI ACNGT 1 cut(s) 1016
TaqI TCGA 2 cut(s) 788, 1193
TasI AATT 6 cut(s) 255, 682, 700, 781, 856, 1195
TatI WGTACW 1 cut(s) 475
TfiI GAWTC 1 cut(s) 1190
Tru1I TTAA 6 cut(s) 336, 350, 429, 572, 585, 834
Tru9I TTAA 6 cut(s) 336, 350, 429, 572, 585, 834
TscAI CASTG 2 cut(s) 928, 979
TseFI GTSAC 3 cut(s) 232, 890, 955
TseI GCWGC 4 cut(s) 143, 391, 918, 965
Tsp45I GTSAC 3 cut(s) 232, 890, 955
TspDTI ATGAA 8 cut(s) 82, 138, 392, 396, 633, 777, 1147, 1325
TspRI CASTG 2 cut(s) 928, 979
Vha464I CTTAAG 2 cut(s) 349, 584
XapI RAATTY 2 cut(s) 682, 1195
XceI RCATGY 1 cut(s) 949
XspI CTAG 5 cut(s) 411, 540, 675, 915, 942
Zsp2I ATGCAT 1 cut(s) 816
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.