FvH4_3g12191

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0000258
Physical Location & Seq
Reverse (-)
7222958 .. 7224317
1360 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g12191.t1

Sequence Viewer

Length: 1266 bp
ATGGCTGCTGCTTTGACCAAAATCCCAGATGTGTCCAAGATCGATGTGTTCAACGGCTCGTTCTTCAAAAGATGGCAAGAAAGGGTCTTCTCTTCTCTTGATGTCATGAACTATGCAGATTATCTCACCAAGGCCAAGCCCGAGGAAGGAAGTGAGGACTATGACAACGCATTGGCCAAGTGGGAGAAAGGTAACAAGGTCTGTAGGCATACCATTCTGAGCACACTTTCAAATGAGCTTTTTGATATCTATTGTACCTTCAAGACTGCTGCTGAAATTTGGGAGGTTCTCAACAAGAAGTATGTGACTGAAGATGCCGGAAGCCAGAAGTATGCAATTGGGAATTTTCTGAAATTTCAGATGGTGGAAGACAAAGATGTTTCACTTCAAATTCATGAGTTTCACAAGATTGTCAATGATTTGAAGACTGAAGGCATTGAGTTACCTGAAGCATTTGTGTCCGGAAGCCTTATTGAAAAACTACCCGAATCATGGAAGGACTACAAGAACAACATGAAACACAAAAAGAAGCATATGAGCCTAGAAGATGCTGTTGTTCATATCCGAATTGACGAAACGAACCGTGTACGAGATAGAGTTGCTCAAGTTGATGAAATGAAGGTAAAAGCTAATGTGATCGAGGAGGGTAAGTTGAAAGGTAAAAATTACAATTCTAGTTACAAATCTTTCACCAAGTATGACAACAAATCTCATCACAAGTTTGTTAAGAATATGAAGCCTACTCACAACACAAATTTCAAAAAGAAGGGGAGTTGTTTTGTTTGTGGAAAACCAGGACACCACGCAAATGAATGCAATAGAAGGAAGGGCAACAACCCACCTGCTCGTGCTAACTTGGTAGAATCAGAAGATGAAGTCATTGCTGCGGTCATTTCTGAAGTCAATGTGGTGACTAGTGCCAAAGATTGGGTGGTAGACTCTAGTGCTACAAGGCACATATGTGCTAATAGGAGTGCCTTTCTCTCATTTATTCCAATAAAAGAAGGTGAGGAGGTCGTCCTTATGGGTGACTCAAGGCCTACCCCAGTTAAGGGTAAAGGAAAAGTGCTTCTCAAACTAACCTCTGGTAAAACCCTTTCACTTAGTGATGTTCTTTATGTTCCAAAAATTCGTCATAATCTTGTTTCTGTTGCTTTGCTTGGTAAAGTGGGGGTAAGGGTTGTTTTTGAATCTGATAAGATTGTTCTGACTAAAAATGGTCAATTTGTGGGGAAAGGGTTTTGCAATCAAGACTTGGTCATGTGA
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

422

Amino Acids

47.53

Weight (kDa)

9.11

Isoelectric Point (pI)

35.58

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 34 - 198 4.8e-27 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 310 - 390 3.8e-22 Pol polyprotein, beta-barrel 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)
AarI CACCTGC 1 cut(s) 850
Acc36I ACCTGC 1 cut(s) 850
AccB7I CCANNNNNTGG 1 cut(s) 927
AccI GTMKAC 1 cut(s) 936
AccIII TCCGGA 1 cut(s) 461
AciI CCGC 1 cut(s) 887
AcoI YGGCCR 1 cut(s) 174
AcsI RAATTY 6 cut(s) 276, 343, 353, 390, 754, 1128
AcuI CTGAAG 4 cut(s) 330, 450, 468, 918
AdeI CACNNNGTG 1 cut(s) 1106
AfaI GTAC 2 cut(s) 256, 588
AfiI CCNNNNNNNGG 5 cut(s) 146, 492, 927, 1051, 1052
AhlI ACTAGT 1 cut(s) 914
AjnI CCWGG 1 cut(s) 793
AleI CACNNNNGTG 1 cut(s) 960
AluBI AGCT 2 cut(s) 238, 629
AluI AGCT 2 cut(s) 238, 629
Alw21I GWGCWC 1 cut(s) 224
Ama87I CYCGRG 1 cut(s) 140
Aor13HI TCCGGA 1 cut(s) 461
AoxI GGCC 3 cut(s) 132, 174, 1037
ApeKI GCWGC 4 cut(s) 5, 8, 269, 884
ApoI RAATTY 6 cut(s) 276, 343, 353, 390, 754, 1128
AsuHPI GGTGA 5 cut(s) 118, 682, 922, 1019, 1040
AvaI CYCGRG 1 cut(s) 140
BalI TGGCCA 1 cut(s) 176
BauI CACGAG 1 cut(s) 846
BbsI GAAGAC 3 cut(s) 79, 375, 431
Bbv12I GWGCWC 1 cut(s) 224
BbvI GCAGC 2 cut(s) 256, 871
BccI CCATC 2 cut(s) 66, 355
BceAI ACGGC 1 cut(s) 70
BciT130I CCWGG 1 cut(s) 795
BcuI ACTAGT 1 cut(s) 914
BfaI CTAG 4 cut(s) 542, 675, 915, 942
BfmI CTRYAG 1 cut(s) 202
BfuAI ACCTGC 1 cut(s) 850
BisI GCNGC 4 cut(s) 6, 9, 270, 885
BlsI GCNGC 4 cut(s) 7, 10, 271, 886
Bme1390I CCNGG 1 cut(s) 795
BmeT110I CYCGRG 1 cut(s) 140
BmrFI CCNGG 1 cut(s) 795
BmrI ACTGGG 1 cut(s) 1040
BmsI GCATC 2 cut(s) 304, 538
BmuI ACTGGG 1 cut(s) 1040
BpiI GAAGAC 3 cut(s) 79, 375, 431
BpuEI CTTGAG 2 cut(s) 588, 1018
Bsa29I ATCGAT 1 cut(s) 42
BsaJI CCNNGG 2 cut(s) 129, 141
BsaWI WCCGGW 1 cut(s) 461
BsaXI ACNNNNNCTCC 2 cut(s) 635, 665
Bsc4I CCNNNNNNNGG 5 cut(s) 146, 492, 927, 1051, 1052
Bse1I ACTGG 1 cut(s) 1046
Bse3DI GCAATG 1 cut(s) 879
BseAI TCCGGA 1 cut(s) 461
BseBI CCWGG 1 cut(s) 795
BseCI ATCGAT 1 cut(s) 42
BseDI CCNNGG 2 cut(s) 129, 141
BseLI CCNNNNNNNGG 5 cut(s) 146, 492, 927, 1051, 1052
BseMI GCAATG 1 cut(s) 879
BseMII CTCAG 1 cut(s) 209
BseNI ACTGG 1 cut(s) 1046
BseRI GAGGAG 2 cut(s) 656, 1025
BseXI GCAGC 2 cut(s) 256, 871
BshFI GGCC 3 cut(s) 134, 176, 1039
BshVI ATCGAT 1 cut(s) 42
BsiHKAI GWGCWC 1 cut(s) 224
BsiHKCI CYCGRG 1 cut(s) 140
BsiSI CCGG 2 cut(s) 318, 462
BslI CCNNNNNNNGG 5 cut(s) 146, 492, 927, 1051, 1052
BsmI GAATGC 1 cut(s) 818
BsnI GGCC 3 cut(s) 134, 176, 1039
BsoBI CYCGRG 1 cut(s) 140
Bsp1286I GDGCHC 1 cut(s) 224
Bsp13I TCCGGA 1 cut(s) 461
Bsp143I GATC 2 cut(s) 39, 636
BspACI CCGC 1 cut(s) 887
BspANI GGCC 3 cut(s) 134, 176, 1039
BspCNI CTCAG 1 cut(s) 210
BspDI ATCGAT 1 cut(s) 42
BspEI TCCGGA 1 cut(s) 461
BspHI TCATGA 2 cut(s) 105, 394
BspMI ACCTGC 1 cut(s) 850
BsrDI GCAATG 1 cut(s) 879
BsrI ACTGG 1 cut(s) 1046
BssECI CCNNGG 2 cut(s) 129, 141
BssMI GATC 2 cut(s) 39, 636
BssSI CACGAG 1 cut(s) 846
BssT1I CCWWGG 1 cut(s) 129
Bst2BI CACGAG 1 cut(s) 846
Bst2UI CCWGG 1 cut(s) 795
Bst4CI ACNGT 1 cut(s) 584
Bst6I CTCTTC 1 cut(s) 97
BstDEI CTNAG 2 cut(s) 218, 1103
BstKTI GATC 2 cut(s) 42, 639
BstMBI GATC 2 cut(s) 39, 636
BstNI CCWGG 1 cut(s) 795
BstSCI CCNGG 1 cut(s) 793
BstSFI CTRYAG 1 cut(s) 202
BstV1I GCAGC 2 cut(s) 256, 871
BstV2I GAAGAC 3 cut(s) 79, 375, 431
Bsu15I ATCGAT 1 cut(s) 42
BsuRI GGCC 3 cut(s) 134, 176, 1039
BsuTUI ATCGAT 1 cut(s) 42
BveI ACCTGC 1 cut(s) 850
CciI TCATGA 2 cut(s) 105, 394
ClaI ATCGAT 1 cut(s) 42
Csp6I GTAC 2 cut(s) 255, 587
CviAII CATG 5 cut(s) 106, 395, 492, 514, 1261
CviQI GTAC 2 cut(s) 255, 587
DdeI CTNAG 2 cut(s) 218, 1103
DpnI GATC 2 cut(s) 41, 638
DpnII GATC 2 cut(s) 39, 636
DraIII CACNNNGTG 1 cut(s) 1106
EaeI YGGCCR 1 cut(s) 174
Eam1104I CTCTTC 1 cut(s) 97
EarI CTCTTC 1 cut(s) 97
Eco130I CCWWGG 1 cut(s) 129
Eco147I AGGCCT 1 cut(s) 1039
Eco32I GATATC 1 cut(s) 247
Eco57I CTGAAG 4 cut(s) 330, 450, 468, 918
Eco88I CYCGRG 1 cut(s) 140
EcoRII CCWGG 1 cut(s) 793
EcoRV GATATC 1 cut(s) 247
EcoT14I CCWWGG 1 cut(s) 129
ErhI CCWWGG 1 cut(s) 129
FaeI CATG 5 cut(s) 109, 398, 495, 517, 1264
FatI CATG 5 cut(s) 105, 394, 491, 513, 1260
FauNDI CATATG 2 cut(s) 534, 959
FblI GTMKAC 1 cut(s) 936
Fnu4HI GCNGC 4 cut(s) 6, 9, 270, 885
Fsp4HI GCNGC 4 cut(s) 6, 9, 270, 885
FspBI CTAG 4 cut(s) 542, 675, 915, 942
GluI GCNGC 4 cut(s) 6, 9, 270, 885
HaeIII GGCC 3 cut(s) 134, 176, 1039
HapII CCGG 2 cut(s) 318, 462
Hin1II CATG 5 cut(s) 109, 398, 495, 517, 1264
HinfI GANTC 5 cut(s) 488, 863, 938, 1031, 1190
HpaII CCGG 2 cut(s) 318, 462
HphI GGTGA 5 cut(s) 118, 682, 922, 1019, 1040
Hpy166II GTNNAC 2 cut(s) 587, 937
Hpy188I TCNGA 8 cut(s) 219, 351, 360, 566, 868, 898, 1195, 1209
Hpy188III TCNNGA 6 cut(s) 98, 106, 262, 395, 462, 1250
Hpy8I GTNNAC 2 cut(s) 587, 937
HpyAV CCTTC 9 cut(s) 140, 268, 425, 490, 613, 760, 816, 820, 998
HpyCH4III ACNGT 1 cut(s) 584
HpyCH4V TGCA 4 cut(s) 116, 335, 816, 1245
HpyF3I CTNAG 2 cut(s) 218, 1103
Hsp92II CATG 5 cut(s) 109, 398, 495, 517, 1264
Kpn2I TCCGGA 1 cut(s) 461
Kzo9I GATC 2 cut(s) 39, 636
Lsp1109I GCAGC 2 cut(s) 256, 871
LweI GCATC 2 cut(s) 304, 538
MaeI CTAG 4 cut(s) 542, 675, 915, 942
MaeIII GTNAC 6 cut(s) 191, 304, 441, 677, 910, 1028
MalI GATC 2 cut(s) 41, 638
MboI GATC 2 cut(s) 39, 636
MboII GAAGA 8 cut(s) 55, 79, 84, 323, 380, 436, 557, 881
MfeI CAATTG 1 cut(s) 336
MhlI GDGCHC 1 cut(s) 224
MlsI TGGCCA 1 cut(s) 176
MluNI TGGCCA 1 cut(s) 176
MlyI GAGTC 2 cut(s) 932, 1025
MnlI CCTC 8 cut(s) 136, 148, 277, 634, 637, 1003, 1006, 1093
Mox20I TGGCCA 1 cut(s) 176
MroI TCCGGA 1 cut(s) 461
MscI TGGCCA 1 cut(s) 176
MseI TTAA 2 cut(s) 726, 1050
MslI CAYNNNNRTG 2 cut(s) 807, 960
Msp20I TGGCCA 1 cut(s) 176
MspI CCGG 2 cut(s) 318, 462
MspR9I CCNGG 1 cut(s) 795
MunI CAATTG 1 cut(s) 336
Mva1269I GAATGC 1 cut(s) 818
MvaI CCWGG 1 cut(s) 795
NdeI CATATG 2 cut(s) 534, 959
NdeII GATC 2 cut(s) 39, 636
NlaIII CATG 5 cut(s) 109, 398, 495, 517, 1264
NmuCI GTSAC 3 cut(s) 304, 910, 1028
OliI CACNNNNGTG 1 cut(s) 960
PagI TCATGA 2 cut(s) 105, 394
PaqCI CACCTGC 1 cut(s) 850
PceI AGGCCT 1 cut(s) 1039
PctI GAATGC 1 cut(s) 818
PfeI GAWTC 3 cut(s) 488, 863, 1190
PflFI GACNNNGTC 1 cut(s) 1256
PflMI CCANNNNNTGG 1 cut(s) 927
PkrI GCNGC 4 cut(s) 7, 10, 271, 886
PleI GAGTC 2 cut(s) 932, 1025
PpsI GAGTC 2 cut(s) 932, 1025
Psp6I CCWGG 1 cut(s) 793
PspGI CCWGG 1 cut(s) 793
PsyI GACNNNGTC 1 cut(s) 1256
RsaI GTAC 2 cut(s) 256, 588
RsaNI GTAC 2 cut(s) 255, 587
RseI CAYNNNNRTG 2 cut(s) 807, 960
SaqAI TTAA 2 cut(s) 726, 1050
SatI GCNGC 4 cut(s) 6, 9, 270, 885
Sau3AI GATC 2 cut(s) 39, 636
SchI GAGTC 2 cut(s) 932, 1025
ScrFI CCNGG 1 cut(s) 795
SduI GDGCHC 1 cut(s) 224
SfaNI GCATC 2 cut(s) 304, 538
SfcI CTRYAG 1 cut(s) 202
SmiMI CAYNNNNRTG 2 cut(s) 807, 960
SmlI CTYRAG 2 cut(s) 603, 1033
SmoI CTYRAG 2 cut(s) 603, 1033
SpeI ACTAGT 1 cut(s) 914
SseBI AGGCCT 1 cut(s) 1039
SsiI CCGC 1 cut(s) 887
SspMI CTAG 4 cut(s) 542, 675, 915, 942
StuI AGGCCT 1 cut(s) 1039
StyD4I CCNGG 1 cut(s) 793
StyI CCWWGG 1 cut(s) 129
TaaI ACNGT 1 cut(s) 584
TaqI TCGA 2 cut(s) 42, 639
TfiI GAWTC 3 cut(s) 488, 863, 1190
Tru1I TTAA 2 cut(s) 726, 1050
Tru9I TTAA 2 cut(s) 726, 1050
TseFI GTSAC 3 cut(s) 304, 910, 1028
TseI GCWGC 4 cut(s) 5, 8, 269, 884
Tsp45I GTSAC 3 cut(s) 304, 910, 1028
TspDTI ATGAA 9 cut(s) 122, 383, 530, 548, 627, 632, 749, 825, 888
Tth111I GACNNNGTC 1 cut(s) 1256
Van91I CCANNNNNTGG 1 cut(s) 927
XapI RAATTY 6 cut(s) 276, 343, 353, 390, 754, 1128
XcmI CCANNNNNNNNNTGG 1 cut(s) 928
XmiI GTMKAC 1 cut(s) 936
XspI CTAG 4 cut(s) 542, 675, 915, 942
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.