FvH4_5g08912

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000258
Physical Location & Seq
Forward (+)
5158673 .. 5160219
1547 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g08912.t1

Sequence Viewer

Length: 1395 bp
ATGGATCAATCTGTGTCTGTTCTGAAAAATCATGTTGAGAGACCCGAGAAATTCAAGGGGTCGGATTTCAAACGCTGGCAACAGAAGATGTTGTTCTATTTGACAACACTTCATGTGGCAAATGTTCTCACTGCCGAGGCTCCAAAGGCTCTGCCGGAAGGAGAAGGGGAGAATGCTCCAACGGATGCTCAAATGGCCGAAAATCTGAAGGCTATTGAGACTTGGAACAACAATGAGTATAGTTGCAGAAACTACATCCTCAATGCCTTGGACGATTCCTTGTATGATATCTATTCTACCTTTAAGACGGCAAGGGAATTGTGGGAATCATTGGAGAACAAGTACAAGACTGAAGTTGCTTGTTCCAAGAAGTTTGTCATTGGCAAGTTTTTGAATTTCAAGATGAGCGATGCCAAGTCTGTTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTAGATGTGGAAGGTATGGGTCTTAACCCGAATTTCCTTGTTGGTTCTATTATTGAGAAGTTACCTCCTTCATGGAAAGATTTCAAAATATATCTGAAACATCTAACCGAGGATATGAATTTTGAGCAATTGGTTCTTAAACTTCGAGTTGAAGAGGATAACCGGAAGAATGAAAGGGCTGATGCTATTTCCTTGGAGCCAACTGCAAATATGGTTGGAGGAAGTCCATCAAAGGCCAAGTTTCAGAAAAATAAAGGCAAAGGTGTTGCTGCCAAGCCTCTTTTTATTGCTGGAAAGAACCCTCTCGCCCCACAAAAGTCCAAAGCATTCAAGAAGCCACAAATTGGAGGCTGCTGGGTGTGTGGAAAACCAGGGCATAGAGCAAAGGAGTGTCGCCTCAAGAAAGATCATGGAGGTGCTAGAGGTTCCGGAAATTCCAACCAAGCAAACCTTGCTGAGTTTGAAAATCAATTCATTGGAGTGATTGAAGCAAATCTGGTTACCAATGTTGTTGATTTGTGGGTTGATACTGGTGCTACAAGGCATGTATGCTCTTCAAGGGAGATGTTCTTTTCATACCAACCAATCAACGATGGAGAATCATTGTTCATGGGGAATGCCACTACTGCAAAGGTGGAAGGAAAAGGGAAGTTAATTCTGAAACTCACTTCCGGGAAAGATCTTGTACTTACTAATGTGTTACATGTGCCTGAAATTTGTAAGAATCTAGTTTCTGGTCCTGTTCTAAGAAACAAAGGATTCAAACTTGTATTCGAATCAGACAAATTTGTTCTCACCAAGGGTGGGATGTATGTAGGAAAGGGTTACCTCTATGAAGGGCTCTTTAAGCTTAATGTTGTACCTACTATGGATGATGGTATTATTAATAATAATAATGCAAGCACTAGCACTGCTTCTATGTCATCCTCATAA
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

465

Amino Acids

51.58

Weight (kDa)

8.86

Isoelectric Point (pI)

31.8

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 57 - 213 1.3e-28 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 328 - 408 3.2e-22 Pol polyprotein, beta-barrel domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

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)
AccB7I CCANNNNNTGG 1 cut(s) 806
AccIII TCCGGA 1 cut(s) 890
AclWI GGATC 1 cut(s) 12
AcoI YGGCCR 1 cut(s) 195
AcsI RAATTY 7 cut(s) 50, 394, 493, 580, 895, 1176, 1247
AcuI CTGAAG 2 cut(s) 227, 372
AfaI GTAC 3 cut(s) 344, 1149, 1323
AfiI CCNNNNNNNGG 2 cut(s) 806, 1266
AflIII ACRYGT 1 cut(s) 1165
AjnI CCWGG 1 cut(s) 832
AjuI GAANNNNNNNTTGG 2 cut(s) 438, 470
AluBI AGCT 1 cut(s) 1312
AluI AGCT 1 cut(s) 1312
Alw26I GTCTC 2 cut(s) 34, 212
AlwI GGATC 1 cut(s) 12
Ama87I CYCGRG 1 cut(s) 44
Aor13HI TCCGGA 1 cut(s) 890
AoxI GGCC 2 cut(s) 195, 696
ApeKI GCWGC 2 cut(s) 731, 813
ApoI RAATTY 7 cut(s) 50, 394, 493, 580, 895, 1176, 1247
AseI ATTAAT 1 cut(s) 1347
Asp700I GAANNNNTTC 1 cut(s) 542
AspS9I GGNCC 1 cut(s) 1199
AsuC2I CCSGG 1 cut(s) 1135
AsuHPI GGTGA 1 cut(s) 1249
AsuII TTCGAA 1 cut(s) 1236
AvaI CYCGRG 1 cut(s) 44
AvaII GGWCC 1 cut(s) 1199
BanII GRGCYC 1 cut(s) 1305
BbvI GCAGC 2 cut(s) 718, 800
BccI CCATC 3 cut(s) 697, 1049, 1331
BceAI ACGGC 1 cut(s) 324
BciT130I CCWGG 1 cut(s) 834
BcnI CCSGG 1 cut(s) 1135
BcoDI GTCTC 2 cut(s) 34, 212
BfaI CTAG 3 cut(s) 882, 1190, 1368
BglII AGATCT 1 cut(s) 1141
BisI GCNGC 2 cut(s) 732, 814
BlsI GCNGC 2 cut(s) 733, 815
Bme1390I CCNGG 2 cut(s) 834, 1135
Bme18I GGWCC 1 cut(s) 1199
BmeT110I CYCGRG 1 cut(s) 44
BmgT120I GGNCC 1 cut(s) 1199
BmiI GGNNCC 3 cut(s) 141, 660, 889
BmrFI CCNGG 2 cut(s) 834, 1135
BmsI GCATC 3 cut(s) 175, 400, 634
Bpu14I TTCGAA 1 cut(s) 1236
BpuEI CTTGAG 1 cut(s) 845
BpuMI CCSGG 1 cut(s) 1135
BsaI GGTCTC 1 cut(s) 34
BsaJI CCNNGG 6 cut(s) 135, 267, 570, 654, 833, 1260
BsaWI WCCGGW 2 cut(s) 624, 890
BsaXI ACNNNNNCTCC 2 cut(s) 326, 356
Bsc4I CCNNNNNNNGG 2 cut(s) 806, 1266
Bse1I ACTGG 1 cut(s) 997
BseAI TCCGGA 1 cut(s) 890
BseBI CCWGG 1 cut(s) 834
BseDI CCNNGG 6 cut(s) 135, 267, 570, 654, 833, 1260
BseGI GGATG 5 cut(s) 190, 255, 1275, 1339, 1385
BseLI CCNNNNNNNGG 2 cut(s) 806, 1266
BseMII CTCAG 1 cut(s) 909
BseNI ACTGG 1 cut(s) 997
BseXI GCAGC 2 cut(s) 718, 800
BseYI CCCAGC 1 cut(s) 816
BshFI GGCC 2 cut(s) 197, 698
BsiHKCI CYCGRG 1 cut(s) 44
BsiSI CCGG 4 cut(s) 155, 625, 891, 1134
BslI CCNNNNNNNGG 2 cut(s) 806, 1266
BsmAI GTCTC 2 cut(s) 34, 212
BsmI GAATGC 3 cut(s) 178, 788, 1084
BsnI GGCC 2 cut(s) 197, 698
Bso31I GGTCTC 1 cut(s) 34
BsoBI CYCGRG 1 cut(s) 44
Bsp119I TTCGAA 1 cut(s) 1236
Bsp1286I GDGCHC 1 cut(s) 1305
Bsp13I TCCGGA 1 cut(s) 890
Bsp143I GATC 3 cut(s) 4, 868, 1141
BspANI GGCC 2 cut(s) 197, 698
BspCNI CTCAG 1 cut(s) 910
BspEI TCCGGA 1 cut(s) 890
BspHI TCATGA 1 cut(s) 457
BspLI GGNNCC 3 cut(s) 141, 660, 889
BspPI GGATC 1 cut(s) 12
BspQI GCTCTTC 1 cut(s) 1021
BspT104I TTCGAA 1 cut(s) 1236
BspTNI GGTCTC 1 cut(s) 34
BsrI ACTGG 1 cut(s) 997
BssECI CCNNGG 6 cut(s) 135, 267, 570, 654, 833, 1260
BssMI GATC 3 cut(s) 4, 868, 1141
BssT1I CCWWGG 3 cut(s) 267, 654, 1260
Bst2UI CCWGG 1 cut(s) 834
Bst6I CTCTTC 2 cut(s) 609, 1021
BstAPI GCANNNNNTGC 1 cut(s) 914
BstBI TTCGAA 1 cut(s) 1236
BstC8I GCNNGC 2 cut(s) 77, 1363
BstDEI CTNAG 2 cut(s) 918, 1208
BstEII GGTNACC 2 cut(s) 961, 1286
BstF5I GGATG 5 cut(s) 190, 255, 1275, 1339, 1385
BstKTI GATC 3 cut(s) 7, 871, 1144
BstMAI GTCTC 2 cut(s) 34, 212
BstMBI GATC 3 cut(s) 4, 868, 1141
BstMWI GCNNNNNNNGC 5 cut(s) 146, 194, 914, 1088, 1309
BstNI CCWGG 1 cut(s) 834
BstNSI RCATGY 2 cut(s) 1010, 1169
BstPI GGTNACC 2 cut(s) 961, 1286
BstSCI CCNGG 2 cut(s) 832, 1133
BstV1I GCAGC 2 cut(s) 718, 800
BstX2I RGATCY 1 cut(s) 1141
BstYI RGATCY 1 cut(s) 1141
BsuRI GGCC 2 cut(s) 197, 698
BtgZI GCGATG 1 cut(s) 423
BtsCI GGATG 5 cut(s) 190, 255, 1275, 1339, 1385
BtsI GCAGTG 2 cut(s) 129, 1371
BtsIMutI CAGTG 2 cut(s) 129, 1371
Cac8I GCNNGC 2 cut(s) 77, 1363
CciI TCATGA 1 cut(s) 457
Cfr13I GGNCC 1 cut(s) 1199
Csp6I GTAC 3 cut(s) 343, 1148, 1322
CviAII CATG 8 cut(s) 32, 113, 458, 534, 872, 1007, 1072, 1166
CviQI GTAC 3 cut(s) 343, 1148, 1322
DdeI CTNAG 2 cut(s) 918, 1208
DpnI GATC 3 cut(s) 6, 870, 1143
DpnII GATC 3 cut(s) 4, 868, 1141
EaeI YGGCCR 1 cut(s) 195
Eam1104I CTCTTC 2 cut(s) 609, 1021
EarI CTCTTC 2 cut(s) 609, 1021
Eco130I CCWWGG 3 cut(s) 267, 654, 1260
Eco24I GRGCYC 1 cut(s) 1305
Eco31I GGTCTC 1 cut(s) 34
Eco32I GATATC 1 cut(s) 289
Eco47I GGWCC 1 cut(s) 1199
Eco57I CTGAAG 2 cut(s) 227, 372
Eco88I CYCGRG 1 cut(s) 44
Eco91I GGTNACC 2 cut(s) 961, 1286
EcoO65I GGTNACC 2 cut(s) 961, 1286
EcoRII CCWGG 1 cut(s) 832
EcoRV GATATC 1 cut(s) 289
EcoT14I CCWWGG 3 cut(s) 267, 654, 1260
EcoT38I GRGCYC 1 cut(s) 1305
ErhI CCWWGG 3 cut(s) 267, 654, 1260
FaeI CATG 8 cut(s) 35, 116, 461, 537, 875, 1010, 1075, 1169
FalI AAGNNNNNCTT 2 cut(s) 897, 929
FatI CATG 8 cut(s) 31, 112, 457, 533, 871, 1006, 1071, 1165
Fnu4HI GCNGC 2 cut(s) 732, 814
FokI GGATG 5 cut(s) 197, 242, 1282, 1346, 1372
FriOI GRGCYC 1 cut(s) 1305
Fsp4HI GCNGC 2 cut(s) 732, 814
FspBI CTAG 3 cut(s) 882, 1190, 1368
GluI GCNGC 2 cut(s) 732, 814
GsaI CCCAGC 1 cut(s) 820
HaeIII GGCC 2 cut(s) 197, 698
HapII CCGG 4 cut(s) 155, 625, 891, 1134
Hin1II CATG 8 cut(s) 35, 116, 461, 537, 875, 1010, 1075, 1169
HindIII AAGCTT 1 cut(s) 1310
HinfI GANTC 6 cut(s) 275, 326, 1061, 1186, 1221, 1238
HpaII CCGG 4 cut(s) 155, 625, 891, 1134
HphI GGTGA 1 cut(s) 1249
Hpy188I TCNGA 7 cut(s) 24, 64, 207, 558, 708, 1122, 1243
Hpy188III TCNNGA 5 cut(s) 400, 458, 793, 862, 891
HpyAV CCTTC 7 cut(s) 152, 158, 202, 467, 540, 1094, 1292
HpyCH4V TGCA 4 cut(s) 246, 668, 1091, 1361
HpyF10VI GCNNNNNNNGC 5 cut(s) 146, 194, 914, 1088, 1309
HpyF3I CTNAG 2 cut(s) 918, 1208
Hsp92II CATG 8 cut(s) 35, 116, 461, 537, 875, 1010, 1075, 1169
Kpn2I TCCGGA 1 cut(s) 890
Kzo9I GATC 3 cut(s) 4, 868, 1141
LguI GCTCTTC 1 cut(s) 1021
LmnI GCTCC 3 cut(s) 145, 181, 658
Lsp1109I GCAGC 2 cut(s) 718, 800
LweI GCATC 3 cut(s) 175, 400, 634
MaeI CTAG 3 cut(s) 882, 1190, 1368
MaeIII GTNAC 4 cut(s) 522, 961, 1161, 1286
MalI GATC 3 cut(s) 6, 870, 1143
MboI GATC 3 cut(s) 4, 868, 1141
MboII GAAGA 4 cut(s) 97, 626, 640, 1008
MfeI CAATTG 1 cut(s) 590
MflI RGATCY 1 cut(s) 1141
MhlI GDGCHC 1 cut(s) 1305
MmeI TCCRAC 4 cut(s) 42, 203, 658, 924
MroI TCCGGA 1 cut(s) 890
MroXI GAANNNNTTC 1 cut(s) 542
MseI TTAA 7 cut(s) 303, 486, 600, 1115, 1308, 1314, 1347
MslI CAYNNNNRTG 2 cut(s) 876, 941
MspI CCGG 4 cut(s) 155, 625, 891, 1134
MspR9I CCNGG 2 cut(s) 834, 1135
MunI CAATTG 1 cut(s) 590
Mva1269I GAATGC 3 cut(s) 178, 788, 1084
MvaI CCWGG 1 cut(s) 834
MwoI GCNNNNNNNGC 5 cut(s) 146, 194, 914, 1088, 1309
NciI CCSGG 1 cut(s) 1135
NdeII GATC 3 cut(s) 4, 868, 1141
NlaIII CATG 8 cut(s) 35, 116, 461, 537, 875, 1010, 1075, 1169
NlaIV GGNNCC 3 cut(s) 141, 660, 889
NmeAIII GCCGAG 1 cut(s) 160
NspI RCATGY 2 cut(s) 1010, 1169
NspV TTCGAA 1 cut(s) 1236
PagI TCATGA 1 cut(s) 457
PciI ACATGT 1 cut(s) 1165
PciSI GCTCTTC 1 cut(s) 1021
PctI GAATGC 3 cut(s) 178, 788, 1084
PdmI GAANNNNTTC 1 cut(s) 542
PfeI GAWTC 6 cut(s) 275, 326, 1061, 1186, 1221, 1238
PflMI CCANNNNNTGG 1 cut(s) 806
PfoI TCCNGGA 1 cut(s) 1133
PkrI GCNGC 2 cut(s) 733, 815
PscI ACATGT 1 cut(s) 1165
PshBI ATTAAT 1 cut(s) 1347
Psp6I CCWGG 1 cut(s) 832
PspEI GGTNACC 2 cut(s) 961, 1286
PspFI CCCAGC 1 cut(s) 816
PspGI CCWGG 1 cut(s) 832
PspN4I GGNNCC 3 cut(s) 141, 660, 889
PspPI GGNCC 1 cut(s) 1199
PsuI RGATCY 1 cut(s) 1141
RsaI GTAC 3 cut(s) 344, 1149, 1323
RsaNI GTAC 3 cut(s) 343, 1148, 1322
RseI CAYNNNNRTG 2 cut(s) 876, 941
SapI GCTCTTC 1 cut(s) 1021
SaqAI TTAA 7 cut(s) 303, 486, 600, 1115, 1308, 1314, 1347
SatI GCNGC 2 cut(s) 732, 814
Sau3AI GATC 3 cut(s) 4, 868, 1141
Sau96I GGNCC 1 cut(s) 1199
ScrFI CCNGG 2 cut(s) 834, 1135
SduI GDGCHC 1 cut(s) 1305
SfaNI GCATC 3 cut(s) 175, 400, 634
SfuI TTCGAA 1 cut(s) 1236
SinI GGWCC 1 cut(s) 1199
SmiMI CAYNNNNRTG 2 cut(s) 876, 941
SmlI CTYRAG 1 cut(s) 860
SmoI CTYRAG 1 cut(s) 860
SspMI CTAG 3 cut(s) 882, 1190, 1368
StyD4I CCNGG 2 cut(s) 832, 1133
StyI CCWWGG 3 cut(s) 267, 654, 1260
TaqI TCGA 2 cut(s) 607, 1236
TatI WGTACW 2 cut(s) 342, 1147
TfiI GAWTC 6 cut(s) 275, 326, 1061, 1186, 1221, 1238
Tru1I TTAA 7 cut(s) 303, 486, 600, 1115, 1308, 1314, 1347
Tru9I TTAA 7 cut(s) 303, 486, 600, 1115, 1308, 1314, 1347
TscAI CASTG 2 cut(s) 136, 1378
TseI GCWGC 2 cut(s) 731, 813
TspDTI ATGAA 9 cut(s) 101, 446, 522, 593, 648, 925, 1026, 1060, 1311
TspGWI ACGGA 1 cut(s) 197
TspRI CASTG 2 cut(s) 136, 1378
Van91I CCANNNNNTGG 1 cut(s) 806
VpaK11BI GGWCC 1 cut(s) 1199
VspI ATTAAT 1 cut(s) 1347
XapI RAATTY 7 cut(s) 50, 394, 493, 580, 895, 1176, 1247
XceI RCATGY 2 cut(s) 1010, 1169
XmnI GAANNNNTTC 1 cut(s) 542
XspI CTAG 3 cut(s) 882, 1190, 1368
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.