FvH4_4g27782

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb4
OG0000258
Physical Location & Seq
Forward (+)
28617737 .. 28619072
1336 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_4g27782.t1

Sequence Viewer

Length: 1254 bp
ATGGCATCATTGAAGGAGTTTACAGCAAATTTTGTGAAACTTGATCGCTTTGACGGAGCAAATTTCAGACATTGGCAAAAGAAGTTGCATTTCCTACTATCAAGCTTGAAGGTCGTCTACGTGCTTACAACTCCAAAACCTGTAGAAACAGAAGATGATACCCTTGCTGCACAACGTGAAAGACTGAAGTGGGAACAAGATGATTATGTCTGCAAGGGCCGTATATGCAATTCCATGTCTGATGCCTTATTTGATATCTACCATGAGATGGCTACTGCAAAGGAAATATGGGATGCACTGGAGGCTAAGTATATCTCACATGATGCTACAAGTAAGAAATTTCTGGTCCAAAAGTTCTTCAATTATAACATGACTGATGATAGATCAATTGTTGAACAATTCCATGAGATTATGCATATACACAATCAGTTTAATCAATTCAAAATGCATATGGATGATTCTATAATTGTATATGCAATTATGGATAAACTTCCACCATCTTGGAAGGAATGCAAGAAGAGCCTCAAACATAAGAAAGAGGACATGTCCATAGAGCAGTTGGGGACTCATCTTCGCATAGAAGAAGAATGCAGATCCCGAGAGAAAACTGATGATACTGATTTCTCTTCCAAAGTTCATATGGTTGATGAAGGGCCTAAACATTCAAAAATCAGCCATGGAAATAATAAGAGGAAGGGCAACTTTTCCAAGAAAGGCTTCCAAAGTCAGAATGTAAAGAAGACAAAAGGAGGATGCTTCTTTTGTGGCAAGCCAGGTCATTACAAGAAAGATTGTCGTCATCTCAAGAACAAACAAGGAACTACCAATGAAAAGTATGTGGCAATGATTTCTGAAATAAATATGATGGAGGATATTGAAGCTTGGTGGATAGACTCTGGTGCTACAAAGCATGTCTGCAAGAACAAAGATATGTTCAAAACATATGAACCAAGTGGAGATGACAACGTACTCTACATGGGAAACTCCTCTACTTCTTCTATCAAAGGAAAAGGGACAATTGAATTAGAGTTCACATCAGGAAAAATTCTTACTCTTACTGATGTGTACCATGTTCCAGAAGTTAGAAAGAATTTGGTTTCTGCTAGTCTTTTGAACAAGTCTGGGTTCAAGCTTGTCATGGAATCAAACAAGTTTATTCTGACCAAGGGTGGTACCTTTGTAGGAAAAGGGTATATGTATGATGGAATGTTCAAACTCAATATTAATAAAATAATATGGCAAATCTGGGTTTAA
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

418

Amino Acids

48.33

Weight (kDa)

8.94

Isoelectric Point (pI)

42.05

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 202 1.2e-28 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 295 - 376 2.1e-27 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)
AanI TTATAA 1 cut(s) 366
Acc65I GGTACC 1 cut(s) 1172
AccB1I GGYRCC 1 cut(s) 1172
AccB7I CCANNNNNTGG 1 cut(s) 268
AccI GTMKAC 1 cut(s) 117
AclWI GGATC 1 cut(s) 588
AcsI RAATTY 5 cut(s) 28, 61, 338, 1044, 1090
AcuI CTGAAG 1 cut(s) 206
AdeI CACNNNGTG 1 cut(s) 176
AfaI GTAC 3 cut(s) 969, 1067, 1174
AfiI CCNNNNNNNGG 1 cut(s) 268
AflIII ACRYGT 1 cut(s) 543
AjnI CCWGG 1 cut(s) 772
AjuI GAANNNNNNNTTGG 2 cut(s) 701, 733
AluBI AGCT 3 cut(s) 105, 881, 1132
AluI AGCT 3 cut(s) 105, 881, 1132
AlwI GGATC 1 cut(s) 588
Ama87I CYCGRG 1 cut(s) 597
AoxI GGCC 2 cut(s) 217, 653
ApeKI GCWGC 1 cut(s) 167
ApoI RAATTY 5 cut(s) 28, 61, 338, 1044, 1090
AseI ATTAAT 1 cut(s) 1224
Asp700I GAANNNNTTC 1 cut(s) 716
Asp718I GGTACC 1 cut(s) 1172
AspS9I GGNCC 3 cut(s) 217, 346, 653
AvaI CYCGRG 1 cut(s) 597
AvaII GGWCC 1 cut(s) 346
BaeI ACNNNNGTAYC 2 cut(s) 1164, 1197
BanI GGYRCC 1 cut(s) 1172
BarI GAAGNNNNNNTAC 2 cut(s) 101, 133
BbsI GAAGAC 1 cut(s) 746
BbvI GCAGC 1 cut(s) 154
BccI CCATC 4 cut(s) 262, 505, 859, 1196
BceAI ACGGC 1 cut(s) 204
BciT130I CCWGG 1 cut(s) 774
BfaI CTAG 1 cut(s) 1104
BfmI CTRYAG 1 cut(s) 141
BisI GCNGC 1 cut(s) 168
BlsI GCNGC 1 cut(s) 169
Bme1390I CCNGG 1 cut(s) 774
Bme18I GGWCC 1 cut(s) 346
BmeT110I CYCGRG 1 cut(s) 597
BmgT120I GGNCC 3 cut(s) 217, 346, 653
BmiI GGNNCC 1 cut(s) 1174
BmrFI CCNGG 1 cut(s) 774
BmsI GCATC 5 cut(s) 14, 232, 283, 313, 743
BpiI GAAGAC 1 cut(s) 746
BpmI CTGGAG 1 cut(s) 320
BpuEI CTTGAG 1 cut(s) 788
BsaAI YACGTR 1 cut(s) 121
BsaJI CCNNGG 2 cut(s) 676, 1164
BsaXI ACNNNNNCTCC 2 cut(s) 293, 323
Bsc4I CCNNNNNNNGG 1 cut(s) 268
Bse1I ACTGG 1 cut(s) 303
Bse3DI GCAATG 1 cut(s) 849
BseBI CCWGG 1 cut(s) 774
BseDI CCNNGG 2 cut(s) 676, 1164
BseGI GGATG 3 cut(s) 298, 460, 758
BseLI CCNNNNNNNGG 1 cut(s) 268
BseMI GCAATG 1 cut(s) 849
BseNI ACTGG 1 cut(s) 303
BseRI GAGGAG 1 cut(s) 976
BseXI GCAGC 1 cut(s) 154
BsgI GTGCAG 1 cut(s) 153
BshFI GGCC 2 cut(s) 219, 655
BshNI GGYRCC 1 cut(s) 1172
BsiHKCI CYCGRG 1 cut(s) 597
BslFI GGGAC 2 cut(s) 577, 1027
BslI CCNNNNNNNGG 1 cut(s) 268
BsmFI GGGAC 2 cut(s) 577, 1027
BsmI GAATGC 2 cut(s) 515, 593
BsnI GGCC 2 cut(s) 219, 655
BsoBI CYCGRG 1 cut(s) 597
Bsp143I GATC 3 cut(s) 43, 383, 593
Bsp19I CCATGG 1 cut(s) 676
BspANI GGCC 2 cut(s) 219, 655
BspLI GGNNCC 1 cut(s) 1174
BspPI GGATC 1 cut(s) 588
BspQI GCTCTTC 1 cut(s) 512
BspT107I GGYRCC 1 cut(s) 1172
BsrDI GCAATG 1 cut(s) 849
BsrI ACTGG 1 cut(s) 303
BssECI CCNNGG 2 cut(s) 676, 1164
BssMI GATC 3 cut(s) 43, 383, 593
BssT1I CCWWGG 2 cut(s) 676, 1164
Bst2UI CCWGG 1 cut(s) 774
Bst6I CTCTTC 2 cut(s) 512, 631
BstBAI YACGTR 1 cut(s) 121
BstC8I GCNNGC 1 cut(s) 770
BstDEI CTNAG 1 cut(s) 306
BstDSI CCRYGG 1 cut(s) 676
BstF5I GGATG 3 cut(s) 298, 460, 758
BstKTI GATC 3 cut(s) 46, 386, 596
BstMBI GATC 3 cut(s) 43, 383, 593
BstMWI GCNNNNNNNGC 3 cut(s) 225, 302, 519
BstNI CCWGG 1 cut(s) 774
BstNSI RCATGY 2 cut(s) 547, 914
BstSCI CCNGG 1 cut(s) 772
BstSFI CTRYAG 1 cut(s) 141
BstV1I GCAGC 1 cut(s) 154
BstV2I GAAGAC 1 cut(s) 746
BstX2I RGATCY 1 cut(s) 593
BstXI CCANNNNNNTGG 1 cut(s) 501
BstYI RGATCY 1 cut(s) 593
BsuRI GGCC 2 cut(s) 219, 655
BtgI CCRYGG 1 cut(s) 676
BtsCI GGATG 3 cut(s) 298, 460, 758
BtsIMutI CAGTG 1 cut(s) 296
Cac8I GCNNGC 1 cut(s) 770
Cfr13I GGNCC 3 cut(s) 217, 346, 653
Csp6I GTAC 3 cut(s) 968, 1066, 1173
CviQI GTAC 3 cut(s) 968, 1066, 1173
DdeI CTNAG 1 cut(s) 306
DpnI GATC 3 cut(s) 45, 385, 595
DpnII GATC 3 cut(s) 43, 383, 593
DraIII CACNNNGTG 1 cut(s) 176
Eam1104I CTCTTC 2 cut(s) 512, 631
EarI CTCTTC 2 cut(s) 512, 631
Eco130I CCWWGG 2 cut(s) 676, 1164
Eco32I GATATC 1 cut(s) 256
Eco47I GGWCC 1 cut(s) 346
Eco57I CTGAAG 1 cut(s) 206
Eco88I CYCGRG 1 cut(s) 597
EcoO109I RGGNCCY 1 cut(s) 653
EcoRII CCWGG 1 cut(s) 772
EcoRV GATATC 1 cut(s) 256
EcoT14I CCWWGG 2 cut(s) 676, 1164
EcoT22I ATGCAT 2 cut(s) 417, 450
ErhI CCWWGG 2 cut(s) 676, 1164
FalI AAGNNNNNCTT 4 cut(s) 686, 718, 701, 733
FaqI GGGAC 2 cut(s) 577, 1027
FauNDI CATATG 3 cut(s) 450, 639, 943
FblI GTMKAC 1 cut(s) 117
Fnu4HI GCNGC 1 cut(s) 168
FokI GGATG 3 cut(s) 305, 467, 765
Fsp4HI GCNGC 1 cut(s) 168
FspBI CTAG 1 cut(s) 1104
GluI GCNGC 1 cut(s) 168
GsuI CTGGAG 1 cut(s) 320
HaeIII GGCC 2 cut(s) 219, 655
HindIII AAGCTT 3 cut(s) 103, 879, 1130
HinfI GANTC 4 cut(s) 458, 565, 893, 1142
Hpy166II GTNNAC 4 cut(s) 21, 118, 1032, 1066
Hpy188I TCNGA 5 cut(s) 68, 241, 729, 853, 1161
Hpy188III TCNNGA 4 cut(s) 597, 805, 1038, 1076
Hpy8I GTNNAC 4 cut(s) 21, 118, 1032, 1066
HpyAV CCTTC 5 cut(s) 7, 103, 499, 644, 688
HpyCH4IV ACGT 3 cut(s) 120, 175, 966
HpyF10VI GCNNNNNNNGC 3 cut(s) 225, 302, 519
HpyF3I CTNAG 1 cut(s) 306
HpySE526I ACGT 3 cut(s) 120, 175, 966
KpnI GGTACC 1 cut(s) 1176
Kzo9I GATC 3 cut(s) 43, 383, 593
LguI GCTCTTC 1 cut(s) 512
LmnI GCTCC 1 cut(s) 56
Lsp1109I GCAGC 1 cut(s) 154
LweI GCATC 5 cut(s) 14, 232, 283, 313, 743
MaeI CTAG 1 cut(s) 1104
MaeII ACGT 3 cut(s) 120, 175, 966
MalI GATC 3 cut(s) 45, 385, 595
MboI GATC 3 cut(s) 43, 383, 593
MboII GAAGA 9 cut(s) 164, 349, 529, 563, 593, 596, 618, 751, 987
MfeI CAATTG 2 cut(s) 387, 1017
MflI RGATCY 1 cut(s) 593
MlyI GAGTC 2 cut(s) 559, 887
MnlI CCTC 7 cut(s) 295, 532, 533, 684, 743, 862, 997
Mph1103I ATGCAT 2 cut(s) 417, 450
MroXI GAANNNNTTC 1 cut(s) 716
MseI TTAA 3 cut(s) 432, 1224, 1252
MslI CAYNNNNRTG 1 cut(s) 453
MspR9I CCNGG 1 cut(s) 774
MunI CAATTG 2 cut(s) 387, 1017
Mva1269I GAATGC 2 cut(s) 515, 593
MvaI CCWGG 1 cut(s) 774
MwoI GCNNNNNNNGC 3 cut(s) 225, 302, 519
NcoI CCATGG 1 cut(s) 676
NdeI CATATG 3 cut(s) 450, 639, 943
NdeII GATC 3 cut(s) 43, 383, 593
NlaIV GGNNCC 1 cut(s) 1174
NsiI ATGCAT 2 cut(s) 417, 450
NspI RCATGY 2 cut(s) 547, 914
PciI ACATGT 1 cut(s) 543
PciSI GCTCTTC 1 cut(s) 512
PctI GAATGC 2 cut(s) 515, 593
PdmI GAANNNNTTC 1 cut(s) 716
PfeI GAWTC 2 cut(s) 458, 1142
PflMI CCANNNNNTGG 1 cut(s) 268
PkrI GCNGC 1 cut(s) 169
PleI GAGTC 2 cut(s) 559, 887
PpsI GAGTC 2 cut(s) 559, 887
Ppu21I YACGTR 1 cut(s) 121
PscI ACATGT 1 cut(s) 543
PshBI ATTAAT 1 cut(s) 1224
PsiI TTATAA 1 cut(s) 366
Psp6I CCWGG 1 cut(s) 772
PspGI CCWGG 1 cut(s) 772
PspN4I GGNNCC 1 cut(s) 1174
PspPI GGNCC 3 cut(s) 217, 346, 653
PsuI RGATCY 1 cut(s) 593
RsaI GTAC 3 cut(s) 969, 1067, 1174
RsaNI GTAC 3 cut(s) 968, 1066, 1173
RseI CAYNNNNRTG 1 cut(s) 453
SapI GCTCTTC 1 cut(s) 512
SaqAI TTAA 3 cut(s) 432, 1224, 1252
SatI GCNGC 1 cut(s) 168
Sau3AI GATC 3 cut(s) 43, 383, 593
Sau96I GGNCC 3 cut(s) 217, 346, 653
SchI GAGTC 2 cut(s) 559, 887
ScrFI CCNGG 1 cut(s) 774
SfaNI GCATC 5 cut(s) 14, 232, 283, 313, 743
SfcI CTRYAG 1 cut(s) 141
SinI GGWCC 1 cut(s) 346
SmiMI CAYNNNNRTG 1 cut(s) 453
SmlI CTYRAG 1 cut(s) 803
SmoI CTYRAG 1 cut(s) 803
SspI AATATT 1 cut(s) 1222
SspMI CTAG 1 cut(s) 1104
StyD4I CCNGG 1 cut(s) 772
StyI CCWWGG 2 cut(s) 676, 1164
TaiI ACGT 3 cut(s) 123, 178, 969
TfiI GAWTC 2 cut(s) 458, 1142
Tru1I TTAA 3 cut(s) 432, 1224, 1252
Tru9I TTAA 3 cut(s) 432, 1224, 1252
TscAI CASTG 1 cut(s) 303
TseI GCWGC 1 cut(s) 167
TspDTI ATGAA 4 cut(s) 626, 663, 843, 960
TspGWI ACGGA 1 cut(s) 69
TspRI CASTG 1 cut(s) 303
Van91I CCANNNNNTGG 1 cut(s) 268
VpaK11BI GGWCC 1 cut(s) 346
VspI ATTAAT 1 cut(s) 1224
XapI RAATTY 5 cut(s) 28, 61, 338, 1044, 1090
XceI RCATGY 2 cut(s) 547, 914
XcmI CCANNNNNNNNNTGG 2 cut(s) 556, 637
XmiI GTMKAC 1 cut(s) 117
XmnI GAANNNNTTC 1 cut(s) 716
XspI CTAG 1 cut(s) 1104
Zsp2I ATGCAT 2 cut(s) 417, 450
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.