FvH4_1g25682

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb1
OG0000258
Physical Location & Seq
Reverse (-)
17565742 .. 17567373
1632 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_1g25682.t1

Sequence Viewer

Length: 1548 bp
ATGGATCAACCTGCTGCTGTTGCTGGTGTGAAGAACCACATTGAGAAGCCTTTTGTGTTCAAAGATTTACCTGCTAAAGGTGATATTCCTGATGAAACTATAAAGGCTGTGGAGGCATGGACTCAAAACGAGTTTTTGTGCAAGAATTATATACTGAATGCCTTGGATGATTCTCTATATGATGTTTATCTGTCATTTAAGACTCCTAAAGAGCTATGGGATTCTTTGAACAAGAAGTACAAGTCTGAAGTTGCAAGTGCCAAGAAGTTCATTGTGGGAAAATTCTTGAACTTCAGGATGAGTGACACCTATTCTGTGGTGAAACAAGTGGAGGAACTCCAAGTTACTGCTCATGAATTAAGAGATGAAGGTATGGGGTTGAATGAGACTTTTCTTGTTGCTTCTATTATTGAAAAGTTGCCTCCATCTTGGAAAGATTTTAAGATTTATCTTAAGCACTTATCTGAAAACATGAATCTTGAGCAATTAATTCTCAAGCTTCGTGTGGAAGAAGAAAATCGTAAGAATGAGAGGTCTGATTTTTCCTCTATGGAAGCAAAGGCAAATGTGATTGAAGGAAGTACCTCCAAGCCTAAATTCTTCCAGAATAACAAGAAGGGAAAAGCTGCAAAGAAAGCATTTACTACACCAAAGGCTGCTACCTTCAAGAAGAAGGTTCAAGGTGGATGTTGGGTGTGTGGAAAACCAGGCCATAGAGCCAAGGACTGCCGCCACAAAAAGGAAGGGTCTGCTGAAAATACCAACCAAGCAAACATAGCAGAAAATCATTTTGTTGCTGTTGTATCTGAGGTCAATCTAATGACCAATGCCAATGAATGGTGGGTTGACACAGGTGCATCAAGGCATGTGTGTGCTGATAAAAGTCTGTTTGCTACATATGAACAAGGATCTGGTGGAGAAAATCTCTACATGGGCAATGCTAGCACTGCTGCAGTTGAAGGGAAAGGAAAAGTGATTCTGAAACTTACTTCTGGAAAGGAACTGGCACTCACCAACGTGCTTCATGTGCCTGAGATTAGAAAGAATCTGATTTCTGGCTCTCTTCTTAGCAACAAAGGTTTTAAGCTTGTGTTTGAGTCTGATAAGTTTGTACTCACCAAAGGTGGGATGTATGTAGGAAAAGGCTACCTTGCTGAGGGTCTTTTCAAACTGAATGTACTACCTGTTAATAATATTAATGCAGGCAATAGCACTGCTTCTATCTACTTACTTGACTCAAGTGATTTATGGCATGCAAGGCTAGGCCATGTTAACTATCGCTCTCTACATAGAATGATGAATTTAGGATTGTTACCAAAATACAATCCTAATAATGCTGATAAGAATAAATGTGAGGTCTGCATAGAATCAAAATATGCAACGCATTCTTATAAATCTGTTGAGAAATCAAACGAAGTACTTGGATTGATCCATAGTGATCTATGTGATTTTAAATCAACTCCAAGTCGTGCAGGAAAGAATTATTCTAATATCCACTTAACTTTTGACCCTCCTATAAATAAATTCTGGCTACGCCACTGGTTATAA
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

516

Amino Acids

57.82

Weight (kDa)

9.11

Isoelectric Point (pI)

31.85

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 178 1.2e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 280 - 361 3e-25 Pol polyprotein, beta-barrel domain
gag_pre-integrs PF13976 392 - 458 8e-14 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)
AanI TTATAA 2 cut(s) 1392, 1546
Acc36I ACCTGC 2 cut(s) 19, 79
AccB7I CCANNNNNTGG 1 cut(s) 837
AciI CCGC 1 cut(s) 730
AclWI GGATC 3 cut(s) 12, 916, 1423
AcsI RAATTY 4 cut(s) 281, 596, 1300, 1523
AcuI CTGAAG 2 cut(s) 267, 277
AfaI GTAC 5 cut(s) 239, 583, 1113, 1179, 1419
AfiI CCNNNNNNNGG 5 cut(s) 77, 739, 837, 1125, 1156
AflII CTTAAG 1 cut(s) 452
AjnI CCWGG 1 cut(s) 706
AjuI GAANNNNNNNTTGG 2 cut(s) 581, 613
AleI CACNNNNGTG 1 cut(s) 1016
AluBI AGCT 4 cut(s) 214, 499, 626, 1087
AluI AGCT 4 cut(s) 214, 499, 626, 1087
Alw26I GTCTC 1 cut(s) 380
AlwI GGATC 3 cut(s) 12, 916, 1423
AoxI GGCC 2 cut(s) 709, 1264
ApeKI GCWGC 4 cut(s) 14, 626, 656, 950
ApoI RAATTY 4 cut(s) 281, 596, 1300, 1523
AseI ATTAAT 2 cut(s) 488, 1197
AsuHPI GGTGA 4 cut(s) 92, 331, 1003, 1108
AsuNHI GCTAGC 1 cut(s) 941
BbvCI CCTCAGC 1 cut(s) 1155
BbvI GCAGC 3 cut(s) 613, 643, 937
BccI CCATC 1 cut(s) 433
BciT130I CCWGG 1 cut(s) 708
BcoDI GTCTC 1 cut(s) 380
BfaI CTAG 2 cut(s) 942, 1262
BfmI CTRYAG 1 cut(s) 951
BfrI CTTAAG 1 cut(s) 452
BfuAI ACCTGC 2 cut(s) 19, 79
BisI GCNGC 5 cut(s) 15, 627, 657, 730, 951
BlsI GCNGC 5 cut(s) 16, 628, 658, 731, 952
BmcAI AGTACT 1 cut(s) 1419
Bme1390I CCNGG 1 cut(s) 708
BmrFI CCNGG 1 cut(s) 708
BmsI GCATC 1 cut(s) 866
BmtI GCTAGC 1 cut(s) 945
BplI GAGNNNNNCTC 2 cut(s) 909, 941
Bpu10I CCTNAGC 1 cut(s) 1155
BpuEI CTTGAG 3 cut(s) 479, 500, 1222
BsaBI GATNNNNATC 1 cut(s) 186
BsaJI CCNNGG 2 cut(s) 162, 720
Bsc4I CCNNNNNNNGG 5 cut(s) 77, 739, 837, 1125, 1156
Bse1I ACTGG 2 cut(s) 1008, 1544
Bse3DI GCAATG 1 cut(s) 943
Bse8I GATNNNNATC 1 cut(s) 186
BseBI CCWGG 1 cut(s) 708
BseDI CCNNGG 2 cut(s) 162, 720
BseGI GGATG 4 cut(s) 172, 303, 692, 1134
BseJI GATNNNNATC 1 cut(s) 186
BseLI CCNNNNNNNGG 5 cut(s) 77, 739, 837, 1125, 1156
BseMI GCAATG 1 cut(s) 943
BseMII CTCAG 3 cut(s) 798, 1023, 1146
BseNI ACTGG 2 cut(s) 1008, 1544
BseXI GCAGC 3 cut(s) 613, 643, 937
BsgI GTGCAG 1 cut(s) 1491
BshFI GGCC 2 cut(s) 711, 1266
BslI CCNNNNNNNGG 5 cut(s) 77, 739, 837, 1125, 1156
BsmAI GTCTC 1 cut(s) 380
BsmI GAATGC 2 cut(s) 163, 1384
BsnI GGCC 2 cut(s) 711, 1266
Bsp143I GATC 4 cut(s) 4, 908, 1428, 1438
BspACI CCGC 1 cut(s) 730
BspANI GGCC 2 cut(s) 711, 1266
BspCNI CTCAG 3 cut(s) 799, 1024, 1147
BspHI TCATGA 1 cut(s) 352
BspMAI CTGCAG 1 cut(s) 955
BspMI ACCTGC 2 cut(s) 19, 79
BspOI GCTAGC 1 cut(s) 945
BspPI GGATC 3 cut(s) 12, 916, 1423
BspTI CTTAAG 1 cut(s) 452
BsrDI GCAATG 1 cut(s) 943
BsrI ACTGG 2 cut(s) 1008, 1544
BssECI CCNNGG 2 cut(s) 162, 720
BssMI GATC 4 cut(s) 4, 908, 1428, 1438
BssT1I CCWWGG 2 cut(s) 162, 720
Bst2UI CCWGG 1 cut(s) 708
Bst6I CTCTTC 1 cut(s) 1068
BstAFI CTTAAG 1 cut(s) 452
BstC8I GCNNGC 3 cut(s) 943, 1204, 1254
BstDEI CTNAG 4 cut(s) 807, 1032, 1067, 1155
BstENI CCTNNNNNAGG 2 cut(s) 75, 1154
BstF5I GGATG 4 cut(s) 172, 303, 692, 1134
BstKTI GATC 4 cut(s) 7, 911, 1431, 1441
BstMAI GTCTC 1 cut(s) 380
BstMBI GATC 4 cut(s) 4, 908, 1428, 1438
BstMWI GCNNNNNNNGC 8 cut(s) 20, 113, 635, 776, 942, 947, 1027, 1258
BstNI CCWGG 1 cut(s) 708
BstNSI RCATGY 2 cut(s) 869, 1256
BstSCI CCNGG 1 cut(s) 706
BstSFI CTRYAG 1 cut(s) 951
BstV1I GCAGC 3 cut(s) 613, 643, 937
BstX2I RGATCY 1 cut(s) 908
BstYI RGATCY 1 cut(s) 908
BsuRI GGCC 2 cut(s) 711, 1266
BtsCI GGATG 4 cut(s) 172, 303, 692, 1134
BtsI GCAGTG 2 cut(s) 945, 1212
BtsIMutI CAGTG 3 cut(s) 945, 1212, 1537
BveI ACCTGC 2 cut(s) 19, 79
Cac8I GCNNGC 3 cut(s) 943, 1204, 1254
CciI TCATGA 1 cut(s) 352
Csp6I GTAC 5 cut(s) 238, 582, 1112, 1178, 1418
CviAII CATG 8 cut(s) 117, 353, 472, 866, 931, 1025, 1253, 1268
CviQI GTAC 5 cut(s) 238, 582, 1112, 1178, 1418
DdeI CTNAG 4 cut(s) 807, 1032, 1067, 1155
DpnI GATC 4 cut(s) 6, 910, 1430, 1440
DpnII GATC 4 cut(s) 4, 908, 1428, 1438
DraI TTTAAA 1 cut(s) 1453
Eam1104I CTCTTC 1 cut(s) 1068
EarI CTCTTC 1 cut(s) 1068
Eco130I CCWWGG 2 cut(s) 162, 720
Eco57I CTGAAG 2 cut(s) 267, 277
EcoNI CCTNNNNNAGG 2 cut(s) 75, 1154
EcoRII CCWGG 1 cut(s) 706
EcoT14I CCWWGG 2 cut(s) 162, 720
ErhI CCWWGG 2 cut(s) 162, 720
FaeI CATG 8 cut(s) 120, 356, 475, 869, 934, 1028, 1256, 1271
FalI AAGNNNNNCTT 2 cut(s) 1134, 1166
FatI CATG 8 cut(s) 116, 352, 471, 865, 930, 1024, 1252, 1267
FauNDI CATATG 1 cut(s) 898
Fnu4HI GCNGC 5 cut(s) 15, 627, 657, 730, 951
FokI GGATG 4 cut(s) 179, 310, 699, 1141
Fsp4HI GCNGC 5 cut(s) 15, 627, 657, 730, 951
FspBI CTAG 2 cut(s) 942, 1262
GluI GCNGC 5 cut(s) 15, 627, 657, 730, 951
HaeIII GGCC 2 cut(s) 711, 1266
Hin1II CATG 8 cut(s) 120, 356, 475, 869, 934, 1028, 1256, 1271
HincII GTYRAC 2 cut(s) 847, 1273
HindII GTYRAC 2 cut(s) 847, 1273
HindIII AAGCTT 2 cut(s) 497, 1085
HpaI GTTAAC 1 cut(s) 1273
HphI GGTGA 4 cut(s) 92, 331, 1003, 1108
Hpy166II GTNNAC 2 cut(s) 847, 1273
Hpy188I TCNGA 7 cut(s) 247, 466, 538, 808, 981, 1050, 1102
Hpy188III TCNNGA 8 cut(s) 89, 286, 295, 353, 479, 604, 667, 993
Hpy8I GTNNAC 2 cut(s) 847, 1273
HpyAV CCTTC 7 cut(s) 362, 569, 610, 667, 673, 737, 953
HpyCH4IV ACGT 1 cut(s) 1017
HpyF10VI GCNNNNNNNGC 8 cut(s) 20, 113, 635, 776, 942, 947, 1027, 1258
HpyF3I CTNAG 4 cut(s) 807, 1032, 1067, 1155
HpySE526I ACGT 1 cut(s) 1017
Hsp92II CATG 8 cut(s) 120, 356, 475, 869, 934, 1028, 1256, 1271
KspAI GTTAAC 1 cut(s) 1273
Kzo9I GATC 4 cut(s) 4, 908, 1428, 1438
Lsp1109I GCAGC 3 cut(s) 613, 643, 937
LweI GCATC 1 cut(s) 866
MaeI CTAG 2 cut(s) 942, 1262
MaeII ACGT 1 cut(s) 1017
MaeIII GTNAC 3 cut(s) 302, 343, 1311
MalI GATC 4 cut(s) 6, 910, 1430, 1440
MboI GATC 4 cut(s) 4, 908, 1428, 1438
MboII GAAGA 6 cut(s) 43, 521, 524, 592, 682, 1055
MflI RGATCY 1 cut(s) 908
MluCI AATT 9 cut(s) 145, 281, 356, 485, 489, 596, 1300, 1480, 1523
MlyI GAGTC 4 cut(s) 115, 196, 1106, 1229
MslI CAYNNNNRTG 2 cut(s) 870, 1016
MspCI CTTAAG 1 cut(s) 452
MspR9I CCNGG 1 cut(s) 708
Mva1269I GAATGC 2 cut(s) 163, 1384
MvaI CCWGG 1 cut(s) 708
MwoI GCNNNNNNNGC 8 cut(s) 20, 113, 635, 776, 942, 947, 1027, 1258
NdeI CATATG 1 cut(s) 898
NdeII GATC 4 cut(s) 4, 908, 1428, 1438
NheI GCTAGC 1 cut(s) 941
NlaIII CATG 8 cut(s) 120, 356, 475, 869, 934, 1028, 1256, 1271
NmuCI GTSAC 1 cut(s) 302
NspI RCATGY 2 cut(s) 869, 1256
OliI CACNNNNGTG 1 cut(s) 1016
PaeI GCATGC 1 cut(s) 1256
PagI TCATGA 1 cut(s) 352
PctI GAATGC 2 cut(s) 163, 1384
PfeI GAWTC 6 cut(s) 170, 221, 475, 976, 1045, 1367
PflMI CCANNNNNTGG 1 cut(s) 837
PkrI GCNGC 5 cut(s) 16, 628, 658, 731, 952
PleI GAGTC 4 cut(s) 115, 196, 1105, 1229
PpsI GAGTC 4 cut(s) 115, 196, 1105, 1229
PshBI ATTAAT 2 cut(s) 488, 1197
PsiI TTATAA 2 cut(s) 1392, 1546
Psp6I CCWGG 1 cut(s) 706
PspGI CCWGG 1 cut(s) 706
PsrI GAACNNNNNNTAC 2 cut(s) 221, 253
PstI CTGCAG 1 cut(s) 955
PsuI RGATCY 1 cut(s) 908
RsaI GTAC 5 cut(s) 239, 583, 1113, 1179, 1419
RsaNI GTAC 5 cut(s) 238, 582, 1112, 1178, 1418
RseI CAYNNNNRTG 2 cut(s) 870, 1016
SatI GCNGC 5 cut(s) 15, 627, 657, 730, 951
Sau3AI GATC 4 cut(s) 4, 908, 1428, 1438
ScaI AGTACT 1 cut(s) 1419
SchI GAGTC 4 cut(s) 115, 196, 1106, 1229
ScrFI CCNGG 1 cut(s) 708
SfaNI GCATC 1 cut(s) 866
SfcI CTRYAG 1 cut(s) 951
SmiMI CAYNNNNRTG 2 cut(s) 870, 1016
SmlI CTYRAG 4 cut(s) 452, 479, 494, 1237
SmoI CTYRAG 4 cut(s) 452, 479, 494, 1237
SphI GCATGC 1 cut(s) 1256
Sse9I AATT 9 cut(s) 145, 281, 356, 485, 489, 596, 1300, 1480, 1523
SsiI CCGC 1 cut(s) 730
SspI AATATT 1 cut(s) 1195
SspMI CTAG 2 cut(s) 942, 1262
StyD4I CCNGG 1 cut(s) 706
StyI CCWWGG 2 cut(s) 162, 720
TaiI ACGT 1 cut(s) 1020
TasI AATT 9 cut(s) 145, 281, 356, 485, 489, 596, 1300, 1480, 1523
TatI WGTACW 4 cut(s) 237, 1111, 1177, 1417
TauI GCSGC 1 cut(s) 732
TfiI GAWTC 6 cut(s) 170, 221, 475, 976, 1045, 1367
TscAI CASTG 3 cut(s) 952, 1219, 1544
TseFI GTSAC 1 cut(s) 302
TseI GCWGC 4 cut(s) 14, 626, 656, 950
Tsp45I GTSAC 1 cut(s) 302
TspDTI ATGAA 9 cut(s) 108, 259, 369, 381, 488, 849, 915, 1013, 1313
TspRI CASTG 3 cut(s) 952, 1219, 1544
Van91I CCANNNNNTGG 1 cut(s) 837
Vha464I CTTAAG 1 cut(s) 452
VspI ATTAAT 2 cut(s) 488, 1197
XagI CCTNNNNNAGG 2 cut(s) 75, 1154
XapI RAATTY 4 cut(s) 281, 596, 1300, 1523
XceI RCATGY 2 cut(s) 869, 1256
XspI CTAG 2 cut(s) 942, 1262
ZrmI AGTACT 1 cut(s) 1419
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.