FvH4_5g31431

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0009688
Physical Location & Seq
Reverse (-)
22366562 .. 22370771
4210 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g31431.t1

Sequence Viewer

Length: 2238 bp
ATGGAGTCGTCGAGTAGGAGTGTCGGCCTTAGCATAGAGCTGCTCAACCAATCAAATTACAAGATGTGGAAATCTTGTATGGAGTCTTATTTGGTTGGTGAAGAGCTATGGGATGTTGTTGGTGGAGCAAATACAGCGAGGCCAGAAAACAATGCAGAAAATACTGAAGCCTTGAAGAAGTGGACGACTATGAATGCAAAGGCAGAATTTGTGCTAAAGAAATCCATTTCGCCTGCATTGTTCGATCATATTATGAAGTGCACCTCAGCTAATGATATATGGGAGACTCTCAACAGGTTATTCAACAAGAAAGATATTGGTCGCCTGCAAATGTTGGAGAACGAGCTAGCAAATTCAAACCAAGGTGATCTTTCAATCTCTCAATTCTTTTTGAAGATTAAAAATCTGTGTTCGGAGATTTCTGTCTTGGATCCAGATGAACCTATTTCTGAAGCTCGTGTTCGAAGGCATATTATTCGACGGCTGAGGAAGGAGTACACTCCTTTTGTTACTTCAATTCAAGGATGGGATCGACAACCCTCCTTGGAAGAGTTTGAGAATCTCCTTTCTTCTCAAGAATCTTTAGCACGTCAAATGGCTGGCATGTCCTTAACCAATGATTCTAACAATACTGGAGAGGCACTATTCACTCATGGAAGGAAGAATTTCGGATTCGAAAAGAAAAAGGAGTTCAAACGGAATGATGGTGTTGGACCCGGAGAAGCTTCCCCTCACCATAAGAAGAAATTGATCAAGTGCCATCGATGTGGCACCCCTGACCATATCAAAAAGTTCTGCCGTGTCAAGATGAACTCCGGAAATTATGTAAGAAAGAATGAAGGCTCTCATGGTTCAAATGTTGCTGAAGGAGAAGACAACTGGGGAAATTGTTTCATGGTTGAGAAGTCATCACACAATGCCTTGGCTTCTATCAATTTTCAGAATGATTGGATCGTTGATTCCGGGTGTGGTCATCACTTGACAGGTGATCAATCCAAGTTCTCAAGTTTGCAGCCGCACAAAGGCAATGAAGCTATGGTAACAGCAAACAACTCCGTCCACAAAGTTGAGAATGAAGGCACTGTCATTATTAATGGTGGAGGTAATGATTCTATCACCTTGAGCAATGTTTTTCATGTTTCCGGTATGAAGAAGAATTTATTTTCAGTACCAAATGTTGTGGATGCTGGCTATGGAGTTTTGTTTGGGCCACATGATGTCAAATTTCTCCGCAATATTAAATGCTTGAAGGCTGATATTGTGCACACCGACAAGAGGGTAAAAGACACATTTGTGTTATCTGCGTCTTCTTCCTATATTGACAAGTTGAGCTGCAATGAGAATGCTTCCTTATGGCACGCAAGGTTGGGGCATGTGAATTTTGACAAGCTGAGAGTTATGGTTCGAAGGAATTTGGTGAACACAAGGAAACAGGGGGGCATTAATTCTGAAAATGAAGAAGAGCATGAAGATGGCAGAGTTCCTCAAGAGCAAAAGCTCACAAATTCAAGGCCAAGAAGAACCATTGTCAAACCGGAGGGTGTTCTGCTATCACAAGAAGGCTATGCTAAGAAGTTGATTGAGAAACATGGGCTGAAACTTAGCAAAAAGCGATCTACTCCTCTAGACACAAGTGAGAAAATAAGGAGGAATGAAGGCTCACTCTTACCGGATCCTAAGTCTTATCGTTCTCTTGTTGGTGGCCTTTTGTATTTGACAATCATAAGGCCGGATATTGCTTTTTCAGTTGGGCTCATAAGCCGCTACTTGCAAGAGCCTCGGAAGCCACATTTAGAAGCAGCAAAGAAGATTCTCAAGTATGTTAACTCGACCATTGATCTTAGTCTGCTTTACAAAAGTGGTGGTGTTTTTCAGTTAAATGGTTATACAAATGCAGACTTTGGAGGAGATTTAGACAATAGGAGGTCTACATCTGGTTATGTGTTTATGTGCAACAATACAAGTGTTTCTTGGTGTAGCAAGAAACAAGATGCAGTGGCTTTATCCACAACTGAAGCAGAGTACAAGGCTGCTACACTTGCTGCACAAGAGCTTGCTTATAATCCGGTGTGTCATGCTAGAACTAAACACATTGAAATTGAGCATCACTTTATTCGGGAGAAGGTTCTTGATGGAACAATCAACAACAGGGAAGTAAGAAGTCAGTTCAATGTTGCAGACATCTTCACTAAGACTCTCTCTAAAGGGTTGTTCGAGTTTCTTCGTGCAAAGCTGTGA
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 zf-CCHC

Protein Analysis

746

Amino Acids

83.8

Weight (kDa)

9.13

Isoelectric Point (pI)

42.43

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
DUF4219 PF13961 15 - 40 1.2e-09 Domain of unknown function (DUF4219)
Retrotran_gag_2 PF14223 27 - 193 3.8e-20 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 317 - 398 1.8e-18 Pol polyprotein, beta-barrel domain
gag_pre-integrs PF13976 445 - 475 3e-07 GAG-pre-integrase 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

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 2061
AccB1I GGYRCC 1 cut(s) 770
AccI GTMKAC 1 cut(s) 1928
AccIII TCCGGA 1 cut(s) 815
AciI CCGC 3 cut(s) 1016, 1231, 1762
AclWI GGATC 6 cut(s) 425, 438, 537, 959, 1667, 1680
AcsI RAATTY 8 cut(s) 206, 352, 664, 1156, 1223, 1378, 1411, 1504
AcuI CTGAAG 4 cut(s) 186, 471, 885, 2034
AfaI GTAC 3 cut(s) 497, 1170, 2024
AfiI CCNNNNNNNGG 2 cut(s) 1022, 1275
AjiI CACGTC 1 cut(s) 590
AleI CACNNNNGTG 1 cut(s) 1292
Alw21I GWGCWC 2 cut(s) 263, 1266
Alw26I GTCTC 1 cut(s) 278
Alw44I GTGCAC 2 cut(s) 259, 1262
AlwI GGATC 6 cut(s) 425, 438, 537, 959, 1667, 1680
Aor13HI TCCGGA 1 cut(s) 815
AoxI GGCC 6 cut(s) 25, 140, 1208, 1511, 1702, 1727
ApaLI GTGCAC 2 cut(s) 259, 1262
ApeKI GCWGC 6 cut(s) 40, 1012, 1332, 1799, 2030, 2042
ApoI RAATTY 8 cut(s) 206, 352, 664, 1156, 1223, 1378, 1411, 1504
AseI ATTAAT 2 cut(s) 1092, 1443
Asp700I GAANNNNTTC 1 cut(s) 665
AspS9I GGNCC 2 cut(s) 713, 1208
AsuC2I CCSGG 2 cut(s) 717, 964
AsuHPI GGTGA 6 cut(s) 110, 377, 725, 998, 1108, 1429
AsuII TTCGAA 3 cut(s) 463, 675, 1405
AsuNHI GCTAGC 1 cut(s) 346
AvaII GGWCC 1 cut(s) 713
BaeGI GKGCMC 2 cut(s) 263, 1266
BamHI GGATCC 2 cut(s) 430, 1672
BanI GGYRCC 1 cut(s) 770
BanII GRGCYC 1 cut(s) 1755
BauI CACGAG 1 cut(s) 456
BbsI GAAGAC 2 cut(s) 879, 1299
Bbv12I GWGCWC 2 cut(s) 263, 1266
BbvCI CCTCAGC 2 cut(s) 265, 485
BbvI GCAGC 6 cut(s) 27, 1024, 1319, 1811, 2017, 2029
BccI CCATC 5 cut(s) 519, 698, 768, 1466, 2126
BceAI ACGGC 2 cut(s) 497, 783
BcgI CGANNNNNNTGC 4 cut(s) 458, 492, 1760, 1794
BclI TGATCA 2 cut(s) 750, 988
BcnI CCSGG 2 cut(s) 717, 964
BcoDI GTCTC 1 cut(s) 278
BfaI CTAG 3 cut(s) 347, 1625, 2079
BisI GCNGC 8 cut(s) 41, 1013, 1016, 1333, 1762, 1800, 2031, 2043
BlsI GCNGC 8 cut(s) 42, 1014, 1017, 1334, 1763, 1801, 2032, 2044
Bme1390I CCNGG 2 cut(s) 717, 964
Bme18I GGWCC 1 cut(s) 713
BmgBI CACGTC 1 cut(s) 590
BmgT120I GGNCC 2 cut(s) 713, 1208
BmiI GGNNCC 4 cut(s) 432, 715, 772, 1674
BmrFI CCNGG 2 cut(s) 717, 964
BmrI ACTGGG 1 cut(s) 889
BmsI GCATC 3 cut(s) 1174, 1981, 2113
BmtI GCTAGC 1 cut(s) 350
BmuI ACTGGG 1 cut(s) 889
BpiI GAAGAC 2 cut(s) 879, 1299
BpmI CTGGAG 1 cut(s) 654
Bpu10I CCTNAGC 3 cut(s) 29, 265, 485
Bpu14I TTCGAA 3 cut(s) 463, 675, 1405
BpuEI CTTGAG 5 cut(s) 558, 988, 1141, 1470, 1799
BpuMI CCSGG 2 cut(s) 717, 964
Bsa29I ATCGAT 1 cut(s) 763
BsaJI CCNNGG 4 cut(s) 361, 543, 921, 1778
BsaWI WCCGGW 5 cut(s) 815, 1142, 1534, 1669, 2065
Bsc4I CCNNNNNNNGG 2 cut(s) 1022, 1275
Bse1I ACTGG 2 cut(s) 637, 884
Bse3DI GCAATG 3 cut(s) 1033, 1132, 1342
BseAI TCCGGA 1 cut(s) 815
BseCI ATCGAT 1 cut(s) 763
BseDI CCNNGG 4 cut(s) 361, 543, 921, 1778
BseGI GGATG 3 cut(s) 118, 530, 1189
BseLI CCNNNNNNNGG 2 cut(s) 1022, 1275
BseMI GCAATG 3 cut(s) 1033, 1132, 1342
BseMII CTCAG 3 cut(s) 279, 476, 1382
BseNI ACTGG 2 cut(s) 637, 884
BseRI GAGGAG 2 cut(s) 1611, 1920
BseSI GKGCMC 2 cut(s) 263, 1266
BseXI GCAGC 6 cut(s) 27, 1024, 1319, 1811, 2017, 2029
BsgI GTGCAG 1 cut(s) 2028
BshFI GGCC 6 cut(s) 27, 142, 1210, 1513, 1704, 1729
BshNI GGYRCC 1 cut(s) 770
BshVI ATCGAT 1 cut(s) 763
BsiHKAI GWGCWC 2 cut(s) 263, 1266
BsiSI CCGG 8 cut(s) 717, 816, 963, 1143, 1535, 1670, 1730, 2066
BslI CCNNNNNNNGG 2 cut(s) 1022, 1275
BsmAI GTCTC 1 cut(s) 278
BsmI GAATGC 2 cut(s) 199, 1348
BsnI GGCC 6 cut(s) 27, 142, 1210, 1513, 1704, 1729
Bsp119I TTCGAA 3 cut(s) 463, 675, 1405
Bsp1286I GDGCHC 3 cut(s) 263, 1266, 1755
Bsp13I TCCGGA 1 cut(s) 815
BspACI CCGC 3 cut(s) 1016, 1231, 1762
BspANI GGCC 6 cut(s) 27, 142, 1210, 1513, 1704, 1729
BspCNI CTCAG 3 cut(s) 278, 477, 1383
BspDI ATCGAT 1 cut(s) 763
BspEI TCCGGA 1 cut(s) 815
BspLI GGNNCC 4 cut(s) 432, 715, 772, 1674
BspOI GCTAGC 1 cut(s) 350
BspPI GGATC 6 cut(s) 425, 438, 537, 959, 1667, 1680
BspQI GCTCTTC 2 cut(s) 96, 1455
BspT104I TTCGAA 3 cut(s) 463, 675, 1405
BspT107I GGYRCC 1 cut(s) 770
BsrDI GCAATG 3 cut(s) 1033, 1132, 1342
BsrI ACTGG 2 cut(s) 637, 884
BssECI CCNNGG 4 cut(s) 361, 543, 921, 1778
BssSI CACGAG 1 cut(s) 456
BssT1I CCWWGG 3 cut(s) 361, 543, 921
Bst2BI CACGAG 1 cut(s) 456
Bst4CI ACNGT 1 cut(s) 1084
Bst6I CTCTTC 3 cut(s) 96, 543, 1455
BstBI TTCGAA 3 cut(s) 463, 675, 1405
BstC8I GCNNGC 7 cut(s) 234, 326, 348, 601, 1189, 1359, 2055
BstDEI CTNAG 9 cut(s) 29, 265, 485, 1391, 1569, 1601, 1677, 1841, 2190
BstF5I GGATG 3 cut(s) 118, 530, 1189
BstMAI GTCTC 1 cut(s) 278
BstMWI GCNNNNNNNGC 3 cut(s) 134, 1783, 2039
BstNSI RCATGY 2 cut(s) 607, 1376
BstSCI CCNGG 2 cut(s) 715, 962
BstSLI GKGCMC 2 cut(s) 263, 1266
BstV1I GCAGC 6 cut(s) 27, 1024, 1319, 1811, 2017, 2029
BstV2I GAAGAC 2 cut(s) 879, 1299
BstX2I RGATCY 2 cut(s) 430, 1672
BstXI CCANNNNNNTGG 1 cut(s) 767
BstYI RGATCY 2 cut(s) 430, 1672
Bsu15I ATCGAT 1 cut(s) 763
BsuRI GGCC 6 cut(s) 27, 142, 1210, 1513, 1704, 1729
BsuTUI ATCGAT 1 cut(s) 763
BtrI CACGTC 1 cut(s) 590
BtsCI GGATG 3 cut(s) 118, 530, 1189
BtsI GCAGTG 1 cut(s) 2001
BtsIMutI CAGTG 2 cut(s) 1080, 2001
Cac8I GCNNGC 7 cut(s) 234, 326, 348, 601, 1189, 1359, 2055
Cfr13I GGNCC 2 cut(s) 713, 1208
ClaI ATCGAT 1 cut(s) 763
CseI GACGC 1 cut(s) 1293
Csp6I GTAC 3 cut(s) 496, 1169, 2023
CspCI CAANNNNNGTGG 4 cut(s) 1161, 1196, 1843, 1878
CviQI GTAC 3 cut(s) 496, 1169, 2023
DdeI CTNAG 9 cut(s) 29, 265, 485, 1391, 1569, 1601, 1677, 1841, 2190
Eam1104I CTCTTC 3 cut(s) 96, 543, 1455
EarI CTCTTC 3 cut(s) 96, 543, 1455
Eco130I CCWWGG 3 cut(s) 361, 543, 921
Eco24I GRGCYC 1 cut(s) 1755
Eco47I GGWCC 1 cut(s) 713
Eco57I CTGAAG 4 cut(s) 186, 471, 885, 2034
EcoT14I CCWWGG 3 cut(s) 361, 543, 921
EcoT38I GRGCYC 1 cut(s) 1755
ErhI CCWWGG 3 cut(s) 361, 543, 921
FalI AAGNNNNNCTT 4 cut(s) 354, 386, 1954, 1986
FbaI TGATCA 2 cut(s) 750, 988
FblI GTMKAC 1 cut(s) 1928
Fnu4HI GCNGC 8 cut(s) 41, 1013, 1016, 1333, 1762, 1800, 2031, 2043
FokI GGATG 3 cut(s) 125, 537, 1196
FriOI GRGCYC 1 cut(s) 1755
Fsp4HI GCNGC 8 cut(s) 41, 1013, 1016, 1333, 1762, 1800, 2031, 2043
FspBI CTAG 3 cut(s) 347, 1625, 2079
GluI GCNGC 8 cut(s) 41, 1013, 1016, 1333, 1762, 1800, 2031, 2043
GsuI CTGGAG 1 cut(s) 654
HaeIII GGCC 6 cut(s) 27, 142, 1210, 1513, 1704, 1729
HapII CCGG 8 cut(s) 717, 816, 963, 1143, 1535, 1670, 1730, 2066
HgaI GACGC 1 cut(s) 1293
HincII GTYRAC 1 cut(s) 1825
HindII GTYRAC 1 cut(s) 1825
HindIII AAGCTT 1 cut(s) 723
HpaI GTTAAC 1 cut(s) 1825
HpaII CCGG 8 cut(s) 717, 816, 963, 1143, 1535, 1670, 1730, 2066
HphI GGTGA 6 cut(s) 110, 377, 725, 998, 1108, 1429
Hpy166II GTNNAC 8 cut(s) 183, 261, 498, 1060, 1264, 1420, 1825, 1929
Hpy188I TCNGA 6 cut(s) 415, 451, 671, 942, 1450, 1782
Hpy188III TCNNGA 8 cut(s) 434, 575, 805, 816, 1487, 1625, 2117, 2129
Hpy8I GTNNAC 8 cut(s) 183, 261, 498, 1060, 1264, 1420, 1825, 1929
Hpy99I CGWCG 2 cut(s) 13, 483
HpyCH4III ACNGT 1 cut(s) 1084
HpyCH4IV ACGT 1 cut(s) 589
HpyF10VI GCNNNNNNNGC 3 cut(s) 134, 1783, 2039
HpyF3I CTNAG 9 cut(s) 29, 265, 485, 1391, 1569, 1601, 1677, 1841, 2190
HpySE526I ACGT 1 cut(s) 589
Kpn2I TCCGGA 1 cut(s) 815
Ksp22I TGATCA 2 cut(s) 750, 988
KspAI GTTAAC 1 cut(s) 1825
LguI GCTCTTC 2 cut(s) 96, 1455
LmnI GCTCC 1 cut(s) 125
Lsp1109I GCAGC 6 cut(s) 27, 1024, 1319, 1811, 2017, 2029
LweI GCATC 3 cut(s) 1174, 1981, 2113
MaeI CTAG 3 cut(s) 347, 1625, 2079
MaeII ACGT 1 cut(s) 589
MaeIII GTNAC 2 cut(s) 508, 1039
MflI RGATCY 2 cut(s) 430, 1672
MhlI GDGCHC 3 cut(s) 263, 1266, 1755
MlyI GAGTC 4 cut(s) 14, 92, 280, 2188
MmeI TCCRAC 2 cut(s) 315, 691
MroI TCCGGA 1 cut(s) 815
MroXI GAANNNNTTC 1 cut(s) 665
MseI TTAA 7 cut(s) 399, 611, 1092, 1239, 1443, 1824, 1877
MslI CAYNNNNRTG 3 cut(s) 765, 1292, 1470
MspI CCGG 8 cut(s) 717, 816, 963, 1143, 1535, 1670, 1730, 2066
MspR9I CCNGG 2 cut(s) 717, 964
Mva1269I GAATGC 2 cut(s) 199, 1348
MwoI GCNNNNNNNGC 3 cut(s) 134, 1783, 2039
NciI CCSGG 2 cut(s) 717, 964
NheI GCTAGC 1 cut(s) 346
NlaIV GGNNCC 4 cut(s) 432, 715, 772, 1674
NspI RCATGY 2 cut(s) 607, 1376
NspV TTCGAA 3 cut(s) 463, 675, 1405
OliI CACNNNNGTG 1 cut(s) 1292
PciSI GCTCTTC 2 cut(s) 96, 1455
PctI GAATGC 2 cut(s) 199, 1348
PdmI GAANNNNTTC 1 cut(s) 665
PfeI GAWTC 7 cut(s) 559, 578, 620, 672, 959, 1109, 1810
PkrI GCNGC 8 cut(s) 42, 1014, 1017, 1334, 1763, 1801, 2032, 2044
PleI GAGTC 4 cut(s) 13, 91, 280, 2188
PpsI GAGTC 4 cut(s) 13, 91, 280, 2188
PshBI ATTAAT 2 cut(s) 1092, 1443
PsiI TTATAA 1 cut(s) 2061
PspN4I GGNNCC 4 cut(s) 432, 715, 772, 1674
PspPI GGNCC 2 cut(s) 713, 1208
PsuI RGATCY 2 cut(s) 430, 1672
RsaI GTAC 3 cut(s) 497, 1170, 2024
RsaNI GTAC 3 cut(s) 496, 1169, 2023
RseI CAYNNNNRTG 3 cut(s) 765, 1292, 1470
SapI GCTCTTC 2 cut(s) 96, 1455
SaqAI TTAA 7 cut(s) 399, 611, 1092, 1239, 1443, 1824, 1877
SatI GCNGC 8 cut(s) 41, 1013, 1016, 1333, 1762, 1800, 2031, 2043
Sau96I GGNCC 2 cut(s) 713, 1208
SchI GAGTC 4 cut(s) 14, 92, 280, 2188
ScrFI CCNGG 2 cut(s) 717, 964
SduI GDGCHC 3 cut(s) 263, 1266, 1755
SfaNI GCATC 3 cut(s) 1174, 1981, 2113
SfuI TTCGAA 3 cut(s) 463, 675, 1405
SinI GGWCC 1 cut(s) 713
SmiMI CAYNNNNRTG 3 cut(s) 765, 1292, 1470
SmlI CTYRAG 5 cut(s) 573, 1003, 1120, 1485, 1814
SmoI CTYRAG 5 cut(s) 573, 1003, 1120, 1485, 1814
SsiI CCGC 3 cut(s) 1016, 1231, 1762
SspI AATATT 1 cut(s) 1237
SspMI CTAG 3 cut(s) 347, 1625, 2079
StyD4I CCNGG 2 cut(s) 715, 962
StyI CCWWGG 3 cut(s) 361, 543, 921
TaaI ACNGT 1 cut(s) 1084
TaiI ACGT 1 cut(s) 592
TatI WGTACW 2 cut(s) 495, 2022
TauI GCSGC 2 cut(s) 1018, 1764
TfiI GAWTC 7 cut(s) 559, 578, 620, 672, 959, 1109, 1810
Tru1I TTAA 7 cut(s) 399, 611, 1092, 1239, 1443, 1824, 1877
Tru9I TTAA 7 cut(s) 399, 611, 1092, 1239, 1443, 1824, 1877
TscAI CASTG 2 cut(s) 1087, 2001
TseI GCWGC 6 cut(s) 40, 1012, 1332, 1799, 2030, 2042
TspGWI ACGGA 2 cut(s) 712, 1045
TspRI CASTG 2 cut(s) 1087, 2001
VneI GTGCAC 2 cut(s) 259, 1262
VpaK11BI GGWCC 1 cut(s) 713
VspI ATTAAT 2 cut(s) 1092, 1443
XapI RAATTY 8 cut(s) 206, 352, 664, 1156, 1223, 1378, 1411, 1504
XbaI TCTAGA 1 cut(s) 1624
XceI RCATGY 2 cut(s) 607, 1376
XmiI GTMKAC 1 cut(s) 1928
XmnI GAANNNNTTC 1 cut(s) 665
XspI CTAG 3 cut(s) 347, 1625, 2079
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.