FvH4_4g05873

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000258
Physical Location & Seq
Reverse (-)
5261948 .. 5263959
2012 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g05873.t1

Sequence Viewer

Length: 1491 bp
ATGGATCAATCAATTGCTGTTGGGGTTAAGAACCACATTGAGAAGCCGTTTGTGTTCAAGGGAGTGGACTTCAAACGATGGCAGCAAAAGATGCTGTTTTACCTTACAACTCTGAATTTGGCACAAATCATTACTGGAGAGGCTCCTGAAGTGCCAAAAGAGGGTGATATCCCTGCTGCAACGCTCAAGGCTGCTGAGACATGGAACCAAAATGAGTTTCTGTGCAAAAACTACATTCTGAATGCCTTGGATGATGCACTGTATGATGTATATTCCTCATTCAAAACTGCAAAGGAGTTGTGGGAATCTCTGGACAAGAAGTACAAGTCTGAGGTTGCAAGTGCTAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTCAAGATGAGCGACATGCTTTCTGTTGTGAAACAAGTAGAGGAAATTCAGATAATAGTTCATGAGTTACTGGATGAAGGTATGGAACTCAACGAGACTTTTCTTGTTGCTTCTATCATTGAAAAACTTCCTCCTTCTTGGAAAGATTTCAAGTTACATCTCAAGCATATTACTGAGAGCATGAACCTTGAGCAACTCATACTGAAACTTCGTGTGGAGGAGGAGAATCGCAAAAATGAGAAAGTTGATGCGACTTCTATGGAAGTAAAAGCCAATGTAATTGAAGGTGGCACCTCCAAGCCTAAATTTGCACAAAAGAAGGCTACTGCAAAGAAGGTTGCTACTGCACCAAAGGCTACTACCTTCAAGAAAAAGATTCAAGGAGGCTGTTGGGTGTGTGGAAAGCCTGGACACCGAGCCAAGGACTGCCGCCACAGGAAAGATGGAAGTTCTGGAAACACCAACCAAGCACATGTAGCAGTGGATGATATGCAGTTCATTGGGGTTGTATCTGAGGCAAACACAATGACAATTTCCAATGATTGGTGGGTTGACACCGGTGCTTCAAGGCATGTCTGCGCCATGAAAAGCATGTTTGCTACATATGAGCAAGGATCTAGTGGAGAGAACATCTACATGGGAAATGCAAGTACTGCTGCTGTTGAAGGAAAGGGAAAAGTGATACTGAAACTCACTTCTGGAAAGGAACTTGTGCTCACTGATGTGCTCCATGTTCCTCATATTAGAAAGAATCTGATTTCTGGACCTCTTCTTAGTAATAGGGGATTCAAGTTAGTGTTTGAAGCTGATAAGTTTGTACTCACCAAGGGTGGGGTGTATGTTGGAAAGGGCTACCTATCTGAGGGGCTCTTCAAACTATCTGTTATTTCTGCAATTGCTAATAATAAGAAAAACGCAGGCACTAGCGCTGCTTCTATCTACTTACTTGACTCCTTTAATTTATGGCATGCAAGGCTTGGACATGTTAATAATCGTTCTATAAACAGAATGGTTAATTTAGGACTGATTCCTAAATGCAAGTTAAAATCAGACCTTGATATTGAAAACAACAAATGTGAAACATGCATTGAATCTAAGGAGATTACCCACATATAA
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

497

Amino Acids

55.25

Weight (kDa)

9.05

Isoelectric Point (pI)

30.7

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 206 1.6e-27 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 307 - 388 5.8e-25 Pol polyprotein, beta-barrel domain
gag_pre-integrs PF13976 429 - 491 1.8e-13 GAG-pre-integrase 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: OG0000258)

Species Orthologous Gene IDs
arabidopsis_thaliana AT4G00980
fragaria_vesca FvH4_1g25682 FvH4_2g13961 FvH4_2g20162 FvH4_2g24753 FvH4_3g12191 FvH4_3g12632 FvH4_3g16171 FvH4_4g05871 FvH4_4g05873 FvH4_4g10121 FvH4_4g15488 FvH4_4g23911 FvH4_4g27782 FvH4_5g08912 FvH4_5g23001 FvH4_5g24552 FvH4_5g32801 FvH4_5g32802 FvH4_6g05093 FvH4_6g19722 FvH4_6g20391 FvH4_6g33792 FvH4_7g01381 FvH4_7g16761 FvH4_7g16761 FvH4_7g16761
malus_domestica MD01G1082500.v1.1 MD15G1436400.v1.1
prunus_persica Prupe.2G021400_v2.0.a1 Prupe.2G052400_v2.0.a1 Prupe.2G065000_v2.0.a1 Prupe.2G187700_v2.0.a1 Prupe.2G187800_v2.0.a1 Prupe.2G189900_v2.0.a1 Prupe.2G191300_v2.0.a1 Prupe.2G191700_v2.0.a1 Prupe.4G265600_v2.0.a1 Prupe.7G014200_v2.0.a1 Prupe.7G039000_v2.0.a1
pyrus_communis pycom01g05590 pycom01g05910 pycom02g12230 pycom02g25840 pycom03g15580 pycom04g04480 pycom05g09230 pycom05g23350 pycom05g23360 pycom07g08380 pycom09g01980 pycom09g01990 pycom11g18190 pycom11g18200 pycom11g21580 pycom13g04160 pycom15g25800 pycom16g16210 pycom16g17230 pycom16g24560 pycom16g25700 pycom17g11020
rosa_chinensis RchiOBHm_Chr1g0359981 RchiOBHm_Chr2g0151961 RchiOBHm_Chr2g0171331 RchiOBHm_Chr5g0081471 RchiOBHm_Chr6g0283031 RchiOBHm_Chr7g0197111 RchiOBHm_Chr7g0222601
rosa_laevigata RLG00000027843 RLG00000027845 RLG00000030065
rosa_multiflora Rmu_sc0000381.1_g000031 Rmu_sc0001179.1_g000035 Rmu_sc0001616.1_g000046 Rmu_sc0001851.1_g000032 Rmu_sc0002152.1_g000013 Rmu_sc0004031.1_g000015 Rmu_sc0004645.1_g000003 Rmu_sc0007393.1_g000001 Rmu_sc0008949.1_g000003 Rmu_sc0009799.1_g000011 Rmu_sc0011614.1_g000001 Rmu_sc0011699.1_g000009 Rmu_sc0019280.1_g000001 Rmu_sc0023984.1_g000001 Rmu_ssc0000050.1_g000036
rosa_roxburghii Rroxscaffold_1G00022650 Rroxscaffold_1G00033480 Rroxscaffold_3G00270250 Rroxscaffold_4G00296600 Rroxscaffold_4G00296760 Rroxscaffold_6G00409840
rosa_rugosa Rorug01G0273800 Rorug01G0273900 Rorug01G0274000
rosa_samantha Rh1AG287300 Rh1AG288100 Rh1BG253000 Rh1BG253500 Rh1BG399800 Rh1CG270400 Rh1CG271000 Rh1DG282000 Rh1DG282500 Rh4DG126500 Rh5DG194600 Rh5DG461100
rosa_wichuraiana Rw0G009130 Rw1G002590 Rw1G008490 Rw1G012210 Rw1G014290 Rw1G014490 Rw1G025510 Rw2G025840 Rw2G026170 Rw2G036510 Rw3G003050 Rw4G009270 Rw5G002350 Rw5G013930 Rw5G019500 Rw5G025890 Rw5G029960 Rw5G032360 Rw6G009890 Rw6G015670 Rw6G015860 Rw7G010030 Rw7G032600 Rw7G032770

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccB1I GGYRCC 1 cut(s) 665
AccB7I CCANNNNNTGG 1 cut(s) 918
AciI CCGC 1 cut(s) 805
AclWI GGATC 2 cut(s) 12, 997
AcsI RAATTY 5 cut(s) 115, 365, 373, 420, 680
AcuI CTGAAG 1 cut(s) 168
AfaI GTAC 3 cut(s) 323, 1027, 1194
AfeI AGCGCT 1 cut(s) 1303
AfiI CCNNNNNNNGG 5 cut(s) 161, 796, 918, 1206, 1237
AflIII ACRYGT 2 cut(s) 847, 1357
AgeI ACCGGT 1 cut(s) 932
AjnI CCWGG 1 cut(s) 781
AjuI GAANNNNNNNTTGG 2 cut(s) 201, 233
AleI CACNNNNGTG 1 cut(s) 1097
AluBI AGCT 1 cut(s) 1181
AluI AGCT 1 cut(s) 1181
Alw21I GWGCWC 2 cut(s) 1092, 1104
Alw26I GTCTC 2 cut(s) 191, 464
AlwI GGATC 2 cut(s) 12, 997
Aor51HI AGCGCT 1 cut(s) 1303
ApeKI GCWGC 5 cut(s) 82, 176, 191, 1031, 1304
ApoI RAATTY 5 cut(s) 115, 365, 373, 420, 680
AsiGI ACCGGT 1 cut(s) 932
Asp700I GAANNNNTTC 2 cut(s) 501, 521
AspLEI GCGC 2 cut(s) 956, 1304
AspS9I GGNCC 1 cut(s) 1139
AsuHPI GGTGA 2 cut(s) 176, 1189
AvaII GGWCC 1 cut(s) 1139
BanI GGYRCC 1 cut(s) 665
BanII GRGCYC 1 cut(s) 1245
Bbv12I GWGCWC 2 cut(s) 1092, 1104
BbvI GCAGC 5 cut(s) 94, 163, 178, 1018, 1291
BccI CCATC 2 cut(s) 72, 812
BceAI ACGGC 1 cut(s) 31
BciT130I CCWGG 1 cut(s) 783
BcoDI GTCTC 2 cut(s) 191, 464
BfaI CTAG 2 cut(s) 993, 1299
BfoI RGCGCY 1 cut(s) 1305
BisI GCNGC 6 cut(s) 83, 177, 192, 805, 1032, 1305
BlsI GCNGC 6 cut(s) 84, 178, 193, 806, 1033, 1306
BmcAI AGTACT 1 cut(s) 1027
Bme1390I CCNGG 1 cut(s) 783
Bme18I GGWCC 1 cut(s) 1139
BmgT120I GGNCC 1 cut(s) 1139
BmiI GGNNCC 3 cut(s) 144, 206, 667
BmrFI CCNGG 1 cut(s) 783
BmsI GCATC 3 cut(s) 81, 244, 613
BpmI CTGGAG 1 cut(s) 156
BpuEI CTTGAG 3 cut(s) 170, 521, 584
BsaJI CCNNGG 3 cut(s) 246, 795, 1200
BsaWI WCCGGW 1 cut(s) 932
Bsc4I CCNNNNNNNGG 5 cut(s) 161, 796, 918, 1206, 1237
Bse118I RCCGGY 1 cut(s) 932
Bse1I ACTGG 2 cut(s) 139, 450
BseBI CCWGG 1 cut(s) 783
BseDI CCNNGG 3 cut(s) 246, 795, 1200
BseGI GGATG 3 cut(s) 256, 454, 865
BseLI CCNNNNNNNGG 5 cut(s) 161, 796, 918, 1206, 1237
BseMII CTCAG 5 cut(s) 186, 321, 540, 879, 1227
BseNI ACTGG 2 cut(s) 139, 450
BseRI GAGGAG 2 cut(s) 608, 611
BseXI GCAGC 5 cut(s) 94, 163, 178, 1018, 1291
BsgI GTGCAG 1 cut(s) 705
BshNI GGYRCC 1 cut(s) 665
BshTI ACCGGT 1 cut(s) 932
BsiHKAI GWGCWC 2 cut(s) 1092, 1104
BsiSI CCGG 1 cut(s) 933
BslI CCNNNNNNNGG 5 cut(s) 161, 796, 918, 1206, 1237
BsmAI GTCTC 2 cut(s) 191, 464
BsmI GAATGC 1 cut(s) 247
Bsp1286I GDGCHC 3 cut(s) 1092, 1104, 1245
Bsp143I GATC 2 cut(s) 4, 989
BspACI CCGC 1 cut(s) 805
BspCNI CTCAG 5 cut(s) 187, 322, 541, 880, 1228
BspHI TCATGA 1 cut(s) 436
BspLI GGNNCC 3 cut(s) 144, 206, 667
BspPI GGATC 2 cut(s) 12, 997
BspQI GCTCTTC 1 cut(s) 1250
BspT107I GGYRCC 1 cut(s) 665
BsrFI RCCGGY 1 cut(s) 932
BsrI ACTGG 2 cut(s) 139, 450
BssAI RCCGGY 1 cut(s) 932
BssECI CCNNGG 3 cut(s) 246, 795, 1200
BssMI GATC 2 cut(s) 4, 989
BssT1I CCWWGG 3 cut(s) 246, 795, 1200
Bst2UI CCWGG 1 cut(s) 783
Bst4CI ACNGT 1 cut(s) 261
Bst6I CTCTTC 2 cut(s) 1149, 1250
BstAPI GCANNNNNTGC 2 cut(s) 91, 1028
BstC8I GCNNGC 2 cut(s) 1294, 1344
BstDEI CTNAG 8 cut(s) 195, 330, 345, 549, 888, 1148, 1236, 1470
BstENI CCTNNNNNAGG 1 cut(s) 1235
BstF5I GGATG 3 cut(s) 256, 454, 865
BstH2I RGCGCY 1 cut(s) 1305
BstHHI GCGC 2 cut(s) 956, 1304
BstKTI GATC 2 cut(s) 7, 992
BstMAI GTCTC 2 cut(s) 191, 464
BstMBI GATC 2 cut(s) 4, 989
BstMWI GCNNNNNNNGC 5 cut(s) 91, 728, 851, 1028, 1348
BstNI CCWGG 1 cut(s) 783
BstNSI RCATGY 7 cut(s) 394, 851, 950, 970, 1346, 1361, 1461
BstSCI CCNGG 1 cut(s) 781
BstV1I GCAGC 5 cut(s) 94, 163, 178, 1018, 1291
BstX2I RGATCY 1 cut(s) 989
BstYI RGATCY 1 cut(s) 989
BtsCI GGATG 3 cut(s) 256, 454, 865
BtsI GCAGTG 1 cut(s) 861
BtsIMutI CAGTG 3 cut(s) 257, 861, 1092
Cac8I GCNNGC 2 cut(s) 1294, 1344
CciI TCATGA 1 cut(s) 436
CfoI GCGC 2 cut(s) 956, 1304
Cfr10I RCCGGY 1 cut(s) 932
Cfr13I GGNCC 1 cut(s) 1139
Csp6I GTAC 3 cut(s) 322, 1026, 1193
CspAI ACCGGT 1 cut(s) 932
CviQI GTAC 3 cut(s) 322, 1026, 1193
DdeI CTNAG 8 cut(s) 195, 330, 345, 549, 888, 1148, 1236, 1470
DpnI GATC 2 cut(s) 6, 991
DpnII GATC 2 cut(s) 4, 989
Eam1104I CTCTTC 2 cut(s) 1149, 1250
EarI CTCTTC 2 cut(s) 1149, 1250
Eco130I CCWWGG 3 cut(s) 246, 795, 1200
Eco24I GRGCYC 1 cut(s) 1245
Eco32I GATATC 1 cut(s) 169
Eco47I GGWCC 1 cut(s) 1139
Eco47III AGCGCT 1 cut(s) 1303
Eco57I CTGAAG 1 cut(s) 168
EcoNI CCTNNNNNAGG 1 cut(s) 1235
EcoRII CCWGG 1 cut(s) 781
EcoRV GATATC 1 cut(s) 169
EcoT14I CCWWGG 3 cut(s) 246, 795, 1200
EcoT22I ATGCAT 1 cut(s) 1463
EcoT38I GRGCYC 1 cut(s) 1245
ErhI CCWWGG 3 cut(s) 246, 795, 1200
FauNDI CATATG 1 cut(s) 979
Fnu4HI GCNGC 6 cut(s) 83, 177, 192, 805, 1032, 1305
FokI GGATG 3 cut(s) 263, 461, 872
FriOI GRGCYC 1 cut(s) 1245
Fsp4HI GCNGC 6 cut(s) 83, 177, 192, 805, 1032, 1305
FspBI CTAG 2 cut(s) 993, 1299
GlaI GCGC 2 cut(s) 955, 1303
GluI GCNGC 6 cut(s) 83, 177, 192, 805, 1032, 1305
GsuI CTGGAG 1 cut(s) 156
HaeII RGCGCY 1 cut(s) 1305
HapII CCGG 1 cut(s) 933
HhaI GCGC 2 cut(s) 956, 1304
Hin6I GCGC 2 cut(s) 954, 1302
HinP1I GCGC 2 cut(s) 954, 1302
HincII GTYRAC 1 cut(s) 928
HindII GTYRAC 1 cut(s) 928
HinfI GANTC 8 cut(s) 305, 601, 751, 1126, 1161, 1325, 1402, 1466
HpaII CCGG 1 cut(s) 933
HphI GGTGA 2 cut(s) 176, 1189
Hpy166II GTNNAC 2 cut(s) 67, 928
Hpy188I TCNGA 9 cut(s) 114, 240, 331, 372, 426, 889, 1131, 1237, 1426
Hpy188III TCNNGA 8 cut(s) 146, 311, 379, 437, 742, 828, 1074, 1137
Hpy8I GTNNAC 2 cut(s) 67, 928
HpyAV CCTTC 7 cut(s) 446, 519, 653, 688, 703, 748, 1034
HpyCH4III ACNGT 1 cut(s) 261
HpyF10VI GCNNNNNNNGC 5 cut(s) 91, 728, 851, 1028, 1348
HpyF3I CTNAG 8 cut(s) 195, 330, 345, 549, 888, 1148, 1236, 1470
HspAI GCGC 2 cut(s) 954, 1302
Kzo9I GATC 2 cut(s) 4, 989
LguI GCTCTTC 1 cut(s) 1250
LmnI GCTCC 2 cut(s) 148, 1107
Lsp1109I GCAGC 5 cut(s) 94, 163, 178, 1018, 1291
LweI GCATC 3 cut(s) 81, 244, 613
MaeI CTAG 2 cut(s) 993, 1299
MaeIII GTNAC 2 cut(s) 441, 528
MalI GATC 2 cut(s) 6, 991
MboI GATC 2 cut(s) 4, 989
MboII GAAGA 2 cut(s) 1136, 1237
MfeI CAATTG 2 cut(s) 12, 1269
MflI RGATCY 1 cut(s) 989
MhlI GDGCHC 3 cut(s) 1092, 1104, 1245
MlyI GAGTC 1 cut(s) 1319
MmeI TCCRAC 2 cut(s) 340, 1198
Mph1103I ATGCAT 1 cut(s) 1463
MroXI GAANNNNTTC 2 cut(s) 501, 521
MseI TTAA 5 cut(s) 27, 1332, 1362, 1389, 1418
MslI CAYNNNNRTG 2 cut(s) 1010, 1097
MspI CCGG 1 cut(s) 933
MspR9I CCNGG 1 cut(s) 783
MunI CAATTG 2 cut(s) 12, 1269
Mva1269I GAATGC 1 cut(s) 247
MvaI CCWGG 1 cut(s) 783
MwoI GCNNNNNNNGC 5 cut(s) 91, 728, 851, 1028, 1348
NdeI CATATG 1 cut(s) 979
NdeII GATC 2 cut(s) 4, 989
NlaIV GGNNCC 3 cut(s) 144, 206, 667
NsiI ATGCAT 1 cut(s) 1463
NspI RCATGY 7 cut(s) 394, 851, 950, 970, 1346, 1361, 1461
OliI CACNNNNGTG 1 cut(s) 1097
PaeI GCATGC 1 cut(s) 1346
PagI TCATGA 1 cut(s) 436
PciI ACATGT 2 cut(s) 847, 1357
PciSI GCTCTTC 1 cut(s) 1250
PctI GAATGC 1 cut(s) 247
PdmI GAANNNNTTC 2 cut(s) 501, 521
PfeI GAWTC 7 cut(s) 305, 601, 751, 1126, 1161, 1402, 1466
PflMI CCANNNNNTGG 1 cut(s) 918
PinAI ACCGGT 1 cut(s) 932
PkrI GCNGC 6 cut(s) 84, 178, 193, 806, 1033, 1306
PleI GAGTC 1 cut(s) 1319
PpsI GAGTC 1 cut(s) 1319
PscI ACATGT 2 cut(s) 847, 1357
Psp6I CCWGG 1 cut(s) 781
PspGI CCWGG 1 cut(s) 781
PspN4I GGNNCC 3 cut(s) 144, 206, 667
PspPI GGNCC 1 cut(s) 1139
PsuI RGATCY 1 cut(s) 989
RsaI GTAC 3 cut(s) 323, 1027, 1194
RsaNI GTAC 3 cut(s) 322, 1026, 1193
RseI CAYNNNNRTG 2 cut(s) 1010, 1097
SapI GCTCTTC 1 cut(s) 1250
SaqAI TTAA 5 cut(s) 27, 1332, 1362, 1389, 1418
SatI GCNGC 6 cut(s) 83, 177, 192, 805, 1032, 1305
Sau3AI GATC 2 cut(s) 4, 989
Sau96I GGNCC 1 cut(s) 1139
ScaI AGTACT 1 cut(s) 1027
SchI GAGTC 1 cut(s) 1319
ScrFI CCNGG 1 cut(s) 783
SduI GDGCHC 3 cut(s) 1092, 1104, 1245
SfaNI GCATC 3 cut(s) 81, 244, 613
SgrAI CRCCGGYG 1 cut(s) 932
SinI GGWCC 1 cut(s) 1139
SmiMI CAYNNNNRTG 2 cut(s) 1010, 1097
SmlI CTYRAG 3 cut(s) 185, 536, 563
SmoI CTYRAG 3 cut(s) 185, 536, 563
SphI GCATGC 1 cut(s) 1346
SsiI CCGC 1 cut(s) 805
SspMI CTAG 2 cut(s) 993, 1299
StyD4I CCNGG 1 cut(s) 781
StyI CCWWGG 3 cut(s) 246, 795, 1200
TaaI ACNGT 1 cut(s) 261
TatI WGTACW 3 cut(s) 321, 1025, 1192
TauI GCSGC 1 cut(s) 807
TfiI GAWTC 7 cut(s) 305, 601, 751, 1126, 1161, 1402, 1466
Tru1I TTAA 5 cut(s) 27, 1332, 1362, 1389, 1418
Tru9I TTAA 5 cut(s) 27, 1332, 1362, 1389, 1418
TscAI CASTG 3 cut(s) 264, 861, 1099
TseI GCWGC 5 cut(s) 82, 176, 191, 1031, 1304
TspDTI ATGAA 5 cut(s) 425, 465, 572, 862, 974
TspRI CASTG 3 cut(s) 264, 861, 1099
Van91I CCANNNNNTGG 1 cut(s) 918
VpaK11BI GGWCC 1 cut(s) 1139
XagI CCTNNNNNAGG 1 cut(s) 1235
XapI RAATTY 5 cut(s) 115, 365, 373, 420, 680
XceI RCATGY 7 cut(s) 394, 851, 950, 970, 1346, 1361, 1461
XcmI CCANNNNNNNNNTGG 1 cut(s) 815
XmnI GAANNNNTTC 2 cut(s) 501, 521
XspI CTAG 2 cut(s) 993, 1299
ZrmI AGTACT 1 cut(s) 1027
Zsp2I ATGCAT 1 cut(s) 1463
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.