FvH4_5g24552

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000258
Physical Location & Seq
Forward (+)
15919406 .. 15931362
11957 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g24552.t1

Sequence Viewer

Length: 1404 bp
ATGGATCAATCAATTGCTGTTGGGGTTAAGAACCACATTGAGAAGCCGTTTGTGTTCAAGGGAGTGGACTTCAAACGATGGCAGCAAAAGATGCTGTTTTACCTTACAACTCTGAATTTGGCACAAATCATTACTGGAGAGGCTCCTGAAGTGCCAAAAGAGGGTGATATCCCTGCTGCAACGCTCAAGGCTGCTGAGACATGGAACCAAAATGAGTTTCTGTGCAAAAACTACATTCTGAATGCCTTGGATGATGCACTGTATGATGTATATTCCTCATTCAAAACTGCAAAGAAGTTGTGGGAATCTCTGGACAAGAAGTACAAGTCTGAGGTTGCAAGTGCTAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTCAAGATGAGCGACATGCTTTCTGTTGTGAAACAAGTAGAGGAAATTCAGATAATAGTTCATGAGTTACTGGATGAAGATTTCAAGTTACATCTTAAGCATATTACTGAGAGCATGAACCTTGAGCAACTCATACTGAAACTTCGTGTGGAGGAGGAGAATCGCAAAAATGAGAAAGTTGATGCGACTTCTATGGAAGTAAAAGCCAATGTAATTGAAGGTGGCATCTCCAAGCCTAAATTTGCACAAAAGAAGGCTGCTGCAAAGAAGGTTGCTACTGCACCAAAGGCTGCTACCTTCAAGAAAAAGATTCAAGGAGGCTGTTGGGTGTGTGGAAAGCCTGGACACCGAGCCAAGGACTGCCGCCACAGGAAAGATGGAAGTTCTGGAAACACCAACCAAGCACATGTAGCAGTGGATGATATGCAGTTCACTGGGGTTGTTATTGTTGACGAGCCTTCTTACTTTGTTGAATTTGTCTTCAAGGCAAACGTGCATAGAAAGAAGAAGCTAGCACAGATAAAAGTAGAAGATATTAACAATGAGGGCACAAATTCAAGAATTGCTTCAATTACCAATGATGAACAACAAGACTATTCTCGAGTGAGATCGACTCACATCAGAGAGTTTGCCCGTTCGACTACATCACGTTCAAACGATGGAGTTGTCCGGGGTTTCGCTCGCTATGATTTACCTAATGCTACCATGAACAATCATGATGAGAACGTGAACAATGTGGCAACCAATAATGATGATGGACATACCAACTACACTGAAGCCGTGAATATCGATGGAGATCAAGGTAGTGACAGTGAGCATGCAAATGGTCATGAGGTGCAACACAACAACGTTCATCGAGTACCAAGAATGAGACGAGAGCGCATTCGCTACAATGCAGCTAGAGATTTCCATGAAGAAAGGGGGGGTCCAAGATTTTCAATTGCCCTCACCAATAACATGCCCATACTGTACAGCATTGTTATTCCATCGAGAGACCTTCAGTTTGTGTTGCATGAAGGGAAATATTGA
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
No domains found.

Protein Analysis

468

Amino Acids

53.05

Weight (kDa)

8.82

Isoelectric Point (pI)

33.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 155 5.9e-15 gag-polypeptide of LTR copia-type
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)
AciI CCGC 1 cut(s) 739
AclI AACGTT 1 cut(s) 1224
AclWI GGATC 1 cut(s) 12
AcsI RAATTY 7 cut(s) 115, 365, 373, 420, 614, 848, 928
AcuI CTGAAG 3 cut(s) 168, 1170, 1358
AfaI GTAC 3 cut(s) 323, 1236, 1346
AfiI CCNNNNNNNGG 2 cut(s) 161, 730
AflII CTTAAG 1 cut(s) 470
AflIII ACRYGT 1 cut(s) 781
AjnI CCWGG 1 cut(s) 715
AjuI GAANNNNNNNTTGG 2 cut(s) 201, 233
AluBI AGCT 2 cut(s) 886, 1274
AluI AGCT 2 cut(s) 886, 1274
Alw26I GTCTC 3 cut(s) 191, 1240, 1362
AlwI GGATC 1 cut(s) 12
Ama87I CYCGRG 1 cut(s) 975
ApeKI GCWGC 7 cut(s) 82, 176, 191, 632, 635, 665, 1271
ApoI RAATTY 7 cut(s) 115, 365, 373, 420, 614, 848, 928
ArsI GACNNNNNNTTYG 2 cut(s) 1361, 1393
Asp700I GAANNNNTTC 1 cut(s) 940
AspLEI GCGC 1 cut(s) 1257
AspS9I GGNCC 1 cut(s) 1301
AsuC2I CCSGG 1 cut(s) 1046
AsuHPI GGTGA 2 cut(s) 176, 1315
AsuNHI GCTAGC 1 cut(s) 886
AvaI CYCGRG 1 cut(s) 975
AvaII GGWCC 1 cut(s) 1301
BaeGI GKGCMC 1 cut(s) 926
BbsI GAAGAC 1 cut(s) 847
BbvI GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 1283
BccI CCATC 6 cut(s) 72, 746, 1028, 1124, 1160, 1369
BceAI ACGGC 2 cut(s) 31, 1139
BciT130I CCWGG 1 cut(s) 717
BcnI CCSGG 1 cut(s) 1046
BcoDI GTCTC 3 cut(s) 191, 1240, 1362
BfaI CTAG 2 cut(s) 887, 1275
BfrI CTTAAG 1 cut(s) 470
BisI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 1272
BlsI GCNGC 8 cut(s) 84, 178, 193, 634, 637, 667, 740, 1273
Bme1390I CCNGG 2 cut(s) 717, 1046
Bme18I GGWCC 1 cut(s) 1301
BmeT110I CYCGRG 1 cut(s) 975
BmgT120I GGNCC 1 cut(s) 1301
BmiI GGNNCC 3 cut(s) 144, 206, 1302
BmrFI CCNGG 2 cut(s) 717, 1046
BmrI ACTGGG 1 cut(s) 819
BmsI GCATC 4 cut(s) 81, 244, 547, 609
BmtI GCTAGC 1 cut(s) 890
BmuI ACTGGG 1 cut(s) 819
BpiI GAAGAC 1 cut(s) 847
BplI GAGNNNNNCTC 2 cut(s) 973, 1005
BpmI CTGGAG 1 cut(s) 156
BpuEI CTTGAG 2 cut(s) 170, 518
BpuMI CCSGG 1 cut(s) 1046
Bsa29I ATCGAT 1 cut(s) 1164
BsaBI GATNNNNATC 1 cut(s) 1170
BsaI GGTCTC 1 cut(s) 1362
BsaJI CCNNGG 3 cut(s) 246, 729, 1045
Bsc4I CCNNNNNNNGG 2 cut(s) 161, 730
Bse1I ACTGG 3 cut(s) 139, 450, 814
Bse8I GATNNNNATC 1 cut(s) 1170
BseBI CCWGG 1 cut(s) 717
BseCI ATCGAT 1 cut(s) 1164
BseDI CCNNGG 3 cut(s) 246, 729, 1045
BseGI GGATG 3 cut(s) 256, 454, 799
BseJI GATNNNNATC 1 cut(s) 1170
BseLI CCNNNNNNNGG 2 cut(s) 161, 730
BseMII CTCAG 3 cut(s) 186, 321, 474
BseNI ACTGG 3 cut(s) 139, 450, 814
BseRI GAGGAG 2 cut(s) 542, 545
BseSI GKGCMC 1 cut(s) 926
BseXI GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 1283
BsgI GTGCAG 1 cut(s) 639
BshVI ATCGAT 1 cut(s) 1164
BsiHKCI CYCGRG 1 cut(s) 975
BsiSI CCGG 1 cut(s) 1045
BslI CCNNNNNNNGG 2 cut(s) 161, 730
BsmAI GTCTC 3 cut(s) 191, 1240, 1362
BsmBI CGTCTC 1 cut(s) 1240
BsmI GAATGC 2 cut(s) 247, 1257
Bso31I GGTCTC 1 cut(s) 1362
BsoBI CYCGRG 1 cut(s) 975
Bsp1286I GDGCHC 1 cut(s) 926
Bsp1407I TGTACA 1 cut(s) 1344
Bsp143I GATC 3 cut(s) 4, 983, 1171
BspACI CCGC 1 cut(s) 739
BspCNI CTCAG 3 cut(s) 187, 322, 475
BspDI ATCGAT 1 cut(s) 1164
BspHI TCATGA 3 cut(s) 436, 1090, 1204
BspLI GGNNCC 3 cut(s) 144, 206, 1302
BspOI GCTAGC 1 cut(s) 890
BspPI GGATC 1 cut(s) 12
BspTI CTTAAG 1 cut(s) 470
BspTNI GGTCTC 1 cut(s) 1362
BsrGI TGTACA 1 cut(s) 1344
BsrI ACTGG 3 cut(s) 139, 450, 814
BssECI CCNNGG 3 cut(s) 246, 729, 1045
BssMI GATC 3 cut(s) 4, 983, 1171
BssT1I CCWWGG 2 cut(s) 246, 729
Bst2UI CCWGG 1 cut(s) 717
Bst4CI ACNGT 3 cut(s) 261, 1187, 1344
BstAFI CTTAAG 1 cut(s) 470
BstAPI GCANNNNNTGC 1 cut(s) 91
BstAUI TGTACA 1 cut(s) 1344
BstC8I GCNNGC 3 cut(s) 888, 1057, 1194
BstDEI CTNAG 4 cut(s) 195, 330, 345, 483
BstF5I GGATG 3 cut(s) 256, 454, 799
BstHHI GCGC 1 cut(s) 1257
BstKTI GATC 3 cut(s) 7, 986, 1174
BstMAI GTCTC 3 cut(s) 191, 1240, 1362
BstMBI GATC 3 cut(s) 4, 983, 1171
BstMWI GCNNNNNNNGC 3 cut(s) 91, 662, 785
BstNI CCWGG 1 cut(s) 717
BstNSI RCATGY 4 cut(s) 394, 785, 1196, 1336
BstSCI CCNGG 2 cut(s) 715, 1044
BstSLI GKGCMC 1 cut(s) 926
BstV1I GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 1283
BstV2I GAAGAC 1 cut(s) 847
Bsu15I ATCGAT 1 cut(s) 1164
BsuTUI ATCGAT 1 cut(s) 1164
BtsCI GGATG 3 cut(s) 256, 454, 799
BtsI GCAGTG 1 cut(s) 795
BtsIMutI CAGTG 5 cut(s) 257, 795, 807, 1146, 1192
Cac8I GCNNGC 3 cut(s) 888, 1057, 1194
CciI TCATGA 3 cut(s) 436, 1090, 1204
CfoI GCGC 1 cut(s) 1257
Cfr13I GGNCC 1 cut(s) 1301
ClaI ATCGAT 1 cut(s) 1164
Csp6I GTAC 3 cut(s) 322, 1235, 1345
CviQI GTAC 3 cut(s) 322, 1235, 1345
DdeI CTNAG 4 cut(s) 195, 330, 345, 483
DpnI GATC 3 cut(s) 6, 985, 1173
DpnII GATC 3 cut(s) 4, 983, 1171
Eco130I CCWWGG 2 cut(s) 246, 729
Eco31I GGTCTC 1 cut(s) 1362
Eco32I GATATC 1 cut(s) 169
Eco47I GGWCC 1 cut(s) 1301
Eco57I CTGAAG 3 cut(s) 168, 1170, 1358
Eco88I CYCGRG 1 cut(s) 975
EcoRII CCWGG 1 cut(s) 715
EcoRV GATATC 1 cut(s) 169
EcoT14I CCWWGG 2 cut(s) 246, 729
ErhI CCWWGG 2 cut(s) 246, 729
Esp3I CGTCTC 1 cut(s) 1240
FalI AAGNNNNNCTT 2 cut(s) 925, 957
Fnu4HI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 1272
FokI GGATG 3 cut(s) 263, 461, 806
Fsp4HI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 1272
FspBI CTAG 2 cut(s) 887, 1275
GlaI GCGC 1 cut(s) 1256
GluI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 1272
GsuI CTGGAG 1 cut(s) 156
HapII CCGG 1 cut(s) 1045
HhaI GCGC 1 cut(s) 1257
Hin6I GCGC 1 cut(s) 1255
HinP1I GCGC 1 cut(s) 1255
HincII GTYRAC 1 cut(s) 826
HindII GTYRAC 1 cut(s) 826
HinfI GANTC 4 cut(s) 305, 535, 685, 988
HpaII CCGG 1 cut(s) 1045
HphI GGTGA 2 cut(s) 176, 1315
Hpy166II GTNNAC 4 cut(s) 67, 807, 826, 1105
Hpy188I TCNGA 6 cut(s) 114, 240, 331, 372, 426, 998
Hpy8I GTNNAC 4 cut(s) 67, 807, 826, 1105
HpyAV CCTTC 7 cut(s) 587, 622, 637, 682, 843, 1382, 1385
HpyCH4III ACNGT 3 cut(s) 261, 1187, 1344
HpyCH4IV ACGT 4 cut(s) 867, 1024, 1101, 1224
HpyF10VI GCNNNNNNNGC 3 cut(s) 91, 662, 785
HpyF3I CTNAG 4 cut(s) 195, 330, 345, 483
HpySE526I ACGT 4 cut(s) 867, 1024, 1101, 1224
HspAI GCGC 1 cut(s) 1255
Kzo9I GATC 3 cut(s) 4, 983, 1171
LmnI GCTCC 1 cut(s) 148
Lsp1109I GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 1283
LweI GCATC 4 cut(s) 81, 244, 547, 609
MaeI CTAG 2 cut(s) 887, 1275
MaeII ACGT 4 cut(s) 867, 1024, 1101, 1224
MaeIII GTNAC 3 cut(s) 441, 462, 1181
MalI GATC 3 cut(s) 6, 985, 1173
MboI GATC 3 cut(s) 4, 983, 1171
MboII GAAGA 5 cut(s) 464, 847, 892, 917, 1301
MfeI CAATTG 2 cut(s) 12, 1314
MhlI GDGCHC 1 cut(s) 926
MlyI GAGTC 1 cut(s) 982
MmeI TCCRAC 1 cut(s) 340
MroXI GAANNNNTTC 1 cut(s) 940
MseI TTAA 3 cut(s) 27, 471, 912
MslI CAYNNNNRTG 1 cut(s) 1197
MspCI CTTAAG 1 cut(s) 470
MspI CCGG 1 cut(s) 1045
MspR9I CCNGG 2 cut(s) 717, 1046
MunI CAATTG 2 cut(s) 12, 1314
Mva1269I GAATGC 2 cut(s) 247, 1257
MvaI CCWGG 1 cut(s) 717
MwoI GCNNNNNNNGC 3 cut(s) 91, 662, 785
NciI CCSGG 1 cut(s) 1046
NdeII GATC 3 cut(s) 4, 983, 1171
NheI GCTAGC 1 cut(s) 886
NlaIV GGNNCC 3 cut(s) 144, 206, 1302
NmuCI GTSAC 1 cut(s) 1181
NspI RCATGY 4 cut(s) 394, 785, 1196, 1336
PaeI GCATGC 1 cut(s) 1196
PaeR7I CTCGAG 1 cut(s) 975
PagI TCATGA 3 cut(s) 436, 1090, 1204
PciI ACATGT 1 cut(s) 781
PctI GAATGC 2 cut(s) 247, 1257
PdmI GAANNNNTTC 1 cut(s) 940
PfeI GAWTC 3 cut(s) 305, 535, 685
PkrI GCNGC 8 cut(s) 84, 178, 193, 634, 637, 667, 740, 1273
PleI GAGTC 1 cut(s) 982
PpsI GAGTC 1 cut(s) 982
PscI ACATGT 1 cut(s) 781
Psp1406I AACGTT 1 cut(s) 1224
Psp6I CCWGG 1 cut(s) 715
PspGI CCWGG 1 cut(s) 715
PspN4I GGNNCC 3 cut(s) 144, 206, 1302
PspPI GGNCC 1 cut(s) 1301
RsaI GTAC 3 cut(s) 323, 1236, 1346
RsaNI GTAC 3 cut(s) 322, 1235, 1345
RseI CAYNNNNRTG 1 cut(s) 1197
SaqAI TTAA 3 cut(s) 27, 471, 912
SatI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 1272
Sau3AI GATC 3 cut(s) 4, 983, 1171
Sau96I GGNCC 1 cut(s) 1301
SchI GAGTC 1 cut(s) 982
ScrFI CCNGG 2 cut(s) 717, 1046
SduI GDGCHC 1 cut(s) 926
SfaNI GCATC 4 cut(s) 81, 244, 547, 609
Sfr274I CTCGAG 1 cut(s) 975
SinI GGWCC 1 cut(s) 1301
SlaI CTCGAG 1 cut(s) 975
SmiMI CAYNNNNRTG 1 cut(s) 1197
SmlI CTYRAG 4 cut(s) 185, 470, 497, 975
SmoI CTYRAG 4 cut(s) 185, 470, 497, 975
SphI GCATGC 1 cut(s) 1196
SsiI CCGC 1 cut(s) 739
SspI AATATT 1 cut(s) 1400
SspMI CTAG 2 cut(s) 887, 1275
StyD4I CCNGG 2 cut(s) 715, 1044
StyI CCWWGG 2 cut(s) 246, 729
TaaI ACNGT 3 cut(s) 261, 1187, 1344
TaiI ACGT 4 cut(s) 870, 1027, 1104, 1227
TaqI TCGA 6 cut(s) 976, 986, 1013, 1164, 1231, 1364
TatI WGTACW 2 cut(s) 321, 1344
TauI GCSGC 1 cut(s) 741
TfiI GAWTC 3 cut(s) 305, 535, 685
Tru1I TTAA 3 cut(s) 27, 471, 912
Tru9I TTAA 3 cut(s) 27, 471, 912
TscAI CASTG 5 cut(s) 264, 795, 814, 1153, 1192
TseFI GTSAC 1 cut(s) 1181
TseI GCWGC 7 cut(s) 82, 176, 191, 632, 635, 665, 1271
Tsp45I GTSAC 1 cut(s) 1181
TspDTI ATGAA 8 cut(s) 425, 465, 506, 972, 1097, 1217, 1302, 1404
TspRI CASTG 5 cut(s) 264, 795, 814, 1153, 1192
Vha464I CTTAAG 1 cut(s) 470
VpaK11BI GGWCC 1 cut(s) 1301
XapI RAATTY 7 cut(s) 115, 365, 373, 420, 614, 848, 928
XceI RCATGY 4 cut(s) 394, 785, 1196, 1336
XcmI CCANNNNNNNNNTGG 1 cut(s) 749
XhoI CTCGAG 1 cut(s) 975
XmnI GAANNNNTTC 1 cut(s) 940
XspI CTAG 2 cut(s) 887, 1275
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.