FvH4_5g32801

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb5
OG0000258
Physical Location & Seq
Reverse (-)
23685944 .. 23691942
5999 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_5g32801.t1

Sequence Viewer

Length: 999 bp
ATGGATCAATATGTGTCTGTTCTGAAAAATCATGTTGAGAGACCCGAGAAATTCAAGGGGTCGGATTTCAAACGCTGGCAACAGAAGATGTTGTTCTATTTAACAACACTTCATGTGGCAAATGTTCTCACTGCCGAGGCTCCAAAGGCTCTGCCGGAAGGAGAAGGGGAGAATGCTCCAACGGATGCTCAAAGGGCCGAAAATTTGAAGGCTATTGAGACTTGGAACAACAATGAGTATAGTTGCAGAAACTACATCCTCAATGCCTTGGACGATTCCTTAAGTTTGTCATTGGCAAGTTTCAAGATGAGCGATGCCAAGTCTGTTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTAGATGTGGAAGGTATGGGTTTTAACCCGAATTTCCTTGTTGGTTCTATTATTGAGAAGTTACCTCCTTCATGGAAAGATTTCAAAATATATCTGAAACATCTAACCGAGGATATGAATTTTGAGCAATTGGTTCTTAAACTTCGAGTTGAAGAGGATAACCGGAAGAATGAAAGGGCTGATGCTATTTCCTTGGAGCCAACTGCAAATATGGTTGGAGGAAGTCCATCAAAGGCCAAGTTTAAGAAAAATAAAGGCAAAGGTGTTGCTGCCAAGCCTCTTTTTATTGCTGGAAAGAACCTTCTCTCCTCACAAAAGTCCAAAGCATTCAAGAAGCCACAAATTGGAGGCTGCTGGGTGTGTGGAAAACCAGGGCATAGAGCAAAGGAGTGTCGCCTTAAGAAAGATCATGGAGGTGCTGGAGGTTCTGGAAATTCCAACCAAGCAAACCTTGCTGAGTCTGAAAATCAATTCATTGGAGTGATTGAAGCAAATCTGGCGTTGAGGCAGGGCAGCGATATAAGGGTGTGCACGCAGGTTGACGTCTTTGTGACTGAGTGGAAGTGGTGGATAGATCCAAACGGTTTTGTGCAAAGGGCGGCTCAGGTTTTAGGAGGCCAAACTGATGGTTGA
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

333

Amino Acids

36.92

Weight (kDa)

8.63

Isoelectric Point (pI)

33.59

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 97 - 181 4.8e-12 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)
AatII GACGTC 1 cut(s) 912
Acc36I ACCTGC 1 cut(s) 892
AccB7I CCANNNNNTGG 1 cut(s) 710
AciI CCGC 1 cut(s) 965
AclWI GGATC 2 cut(s) 12, 935
AcsI RAATTY 5 cut(s) 50, 202, 397, 484, 799
AcyI GRCGYC 1 cut(s) 909
AfiI CCNNNNNNNGG 1 cut(s) 710
AflII CTTAAG 2 cut(s) 280, 764
AgsI TTSAA 8 cut(s) 55, 70, 208, 304, 451, 518, 697, 854
AjnI CCWGG 1 cut(s) 736
AjuI GAANNNNNNNTTGG 2 cut(s) 342, 374
AloI GAACNNNNNNTCC 2 cut(s) 656, 688
Alw21I GWGCWC 1 cut(s) 899
Alw26I GTCTC 2 cut(s) 34, 212
Alw44I GTGCAC 1 cut(s) 895
AlwI GGATC 2 cut(s) 12, 935
Ama87I CYCGRG 1 cut(s) 44
AoxI GGCC 3 cut(s) 195, 600, 982
ApaLI GTGCAC 1 cut(s) 895
ApeKI GCWGC 3 cut(s) 635, 717, 879
ApoI RAATTY 5 cut(s) 50, 202, 397, 484, 799
Asp700I GAANNNNTTC 1 cut(s) 446
AspS9I GGNCC 1 cut(s) 195
AvaI CYCGRG 1 cut(s) 44
BaeGI GKGCMC 1 cut(s) 899
Bbv12I GWGCWC 1 cut(s) 899
BbvI GCAGC 3 cut(s) 622, 704, 891
BccI CCATC 2 cut(s) 601, 986
BciT130I CCWGG 1 cut(s) 738
BcoDI GTCTC 2 cut(s) 34, 212
BfrI CTTAAG 2 cut(s) 280, 764
BfuAI ACCTGC 1 cut(s) 892
BisI GCNGC 4 cut(s) 636, 718, 880, 966
BlsI GCNGC 4 cut(s) 637, 719, 881, 967
Bme1390I CCNGG 1 cut(s) 738
BmeT110I CYCGRG 1 cut(s) 44
BmgT120I GGNCC 1 cut(s) 195
BmiI GGNNCC 2 cut(s) 141, 564
BmrFI CCNGG 1 cut(s) 738
BmsI GCATC 3 cut(s) 175, 304, 538
BpmI CTGGAG 1 cut(s) 807
Bpu10I CCTNAGC 1 cut(s) 969
BsaHI GRCGYC 1 cut(s) 909
BsaI GGTCTC 1 cut(s) 34
BsaJI CCNNGG 5 cut(s) 135, 267, 474, 558, 737
BsaWI WCCGGW 1 cut(s) 528
BsaXI ACNNNNNCTCC 2 cut(s) 656, 686
Bsc4I CCNNNNNNNGG 1 cut(s) 710
BseBI CCWGG 1 cut(s) 738
BseDI CCNNGG 5 cut(s) 135, 267, 474, 558, 737
BseGI GGATG 2 cut(s) 190, 255
BseLI CCNNNNNNNGG 1 cut(s) 710
BseMII CTCAG 3 cut(s) 813, 912, 983
BseRI GAGGAG 1 cut(s) 664
BseSI GKGCMC 1 cut(s) 899
BseXI GCAGC 3 cut(s) 622, 704, 891
BseYI CCCAGC 1 cut(s) 720
BshFI GGCC 3 cut(s) 197, 602, 984
BsiHKAI GWGCWC 1 cut(s) 899
BsiHKCI CYCGRG 1 cut(s) 44
BsiSI CCGG 2 cut(s) 155, 529
BslI CCNNNNNNNGG 1 cut(s) 710
BsmAI GTCTC 2 cut(s) 34, 212
BsmI GAATGC 2 cut(s) 178, 692
BsnI GGCC 3 cut(s) 197, 602, 984
Bso31I GGTCTC 1 cut(s) 34
BsoBI CYCGRG 1 cut(s) 44
Bsp1286I GDGCHC 1 cut(s) 899
Bsp143I GATC 3 cut(s) 4, 772, 940
BspACI CCGC 1 cut(s) 965
BspANI GGCC 3 cut(s) 197, 602, 984
BspCNI CTCAG 3 cut(s) 814, 913, 982
BspHI TCATGA 1 cut(s) 361
BspLI GGNNCC 2 cut(s) 141, 564
BspMI ACCTGC 1 cut(s) 892
BspPI GGATC 2 cut(s) 12, 935
BspTI CTTAAG 2 cut(s) 280, 764
BspTNI GGTCTC 1 cut(s) 34
BssECI CCNNGG 5 cut(s) 135, 267, 474, 558, 737
BssMI GATC 3 cut(s) 4, 772, 940
BssNI GRCGYC 1 cut(s) 909
BssT1I CCWWGG 2 cut(s) 267, 558
Bst2UI CCWGG 1 cut(s) 738
Bst4CI ACNGT 1 cut(s) 950
Bst6I CTCTTC 1 cut(s) 513
BstACI GRCGYC 1 cut(s) 909
BstAFI CTTAAG 2 cut(s) 280, 764
BstAPI GCANNNNNTGC 1 cut(s) 818
BstC8I GCNNGC 2 cut(s) 77, 899
BstDEI CTNAG 3 cut(s) 822, 921, 969
BstF5I GGATG 2 cut(s) 190, 255
BstKTI GATC 3 cut(s) 7, 775, 943
BstMAI GTCTC 2 cut(s) 34, 212
BstMBI GATC 3 cut(s) 4, 772, 940
BstMWI GCNNNNNNNGC 4 cut(s) 146, 194, 818, 863
BstNI CCWGG 1 cut(s) 738
BstSCI CCNGG 1 cut(s) 736
BstSLI GKGCMC 1 cut(s) 899
BstV1I GCAGC 3 cut(s) 622, 704, 891
BstX2I RGATCY 1 cut(s) 940
BstXI CCANNNNNNTGG 1 cut(s) 992
BstYI RGATCY 1 cut(s) 940
BsuRI GGCC 3 cut(s) 197, 602, 984
BtgZI GCGATG 1 cut(s) 327
BtsCI GGATG 2 cut(s) 190, 255
BtsI GCAGTG 1 cut(s) 129
BtsIMutI CAGTG 1 cut(s) 129
BveI ACCTGC 1 cut(s) 892
Cac8I GCNNGC 2 cut(s) 77, 899
CciI TCATGA 1 cut(s) 361
Cfr13I GGNCC 1 cut(s) 195
CviAII CATG 5 cut(s) 32, 113, 362, 438, 776
DdeI CTNAG 3 cut(s) 822, 921, 969
DpnI GATC 3 cut(s) 6, 774, 942
DpnII GATC 3 cut(s) 4, 772, 940
Eam1104I CTCTTC 1 cut(s) 513
EarI CTCTTC 1 cut(s) 513
Eco130I CCWWGG 2 cut(s) 267, 558
Eco31I GGTCTC 1 cut(s) 34
Eco88I CYCGRG 1 cut(s) 44
EcoRII CCWGG 1 cut(s) 736
EcoT14I CCWWGG 2 cut(s) 267, 558
ErhI CCWWGG 2 cut(s) 267, 558
FaeI CATG 5 cut(s) 35, 116, 365, 441, 779
FalI AAGNNNNNCTT 2 cut(s) 801, 833
FatI CATG 5 cut(s) 31, 112, 361, 437, 775
Fnu4HI GCNGC 4 cut(s) 636, 718, 880, 966
FokI GGATG 2 cut(s) 197, 242
Fsp4HI GCNGC 4 cut(s) 636, 718, 880, 966
GluI GCNGC 4 cut(s) 636, 718, 880, 966
GsaI CCCAGC 1 cut(s) 724
GsuI CTGGAG 1 cut(s) 807
HaeIII GGCC 3 cut(s) 197, 602, 984
HapII CCGG 2 cut(s) 155, 529
Hin1I GRCGYC 1 cut(s) 909
Hin1II CATG 5 cut(s) 35, 116, 365, 441, 779
HincII GTYRAC 1 cut(s) 907
HindII GTYRAC 1 cut(s) 907
HinfI GANTC 2 cut(s) 275, 824
HpaII CCGG 2 cut(s) 155, 529
Hpy166II GTNNAC 2 cut(s) 897, 907
Hpy188I TCNGA 4 cut(s) 24, 64, 462, 829
Hpy188III TCNNGA 4 cut(s) 304, 362, 697, 795
Hpy8I GTNNAC 2 cut(s) 897, 907
HpyAV CCTTC 6 cut(s) 152, 158, 202, 371, 444, 677
HpyCH4III ACNGT 1 cut(s) 950
HpyCH4IV ACGT 1 cut(s) 909
HpyCH4V TGCA 4 cut(s) 246, 572, 897, 958
HpyF10VI GCNNNNNNNGC 4 cut(s) 146, 194, 818, 863
HpyF3I CTNAG 3 cut(s) 822, 921, 969
HpySE526I ACGT 1 cut(s) 909
Hsp92I GRCGYC 1 cut(s) 909
Hsp92II CATG 5 cut(s) 35, 116, 365, 441, 779
Kzo9I GATC 3 cut(s) 4, 772, 940
LmnI GCTCC 3 cut(s) 145, 181, 562
Lsp1109I GCAGC 3 cut(s) 622, 704, 891
LweI GCATC 3 cut(s) 175, 304, 538
MaeII ACGT 1 cut(s) 909
MaeIII GTNAC 2 cut(s) 426, 916
MalI GATC 3 cut(s) 6, 774, 942
MboI GATC 3 cut(s) 4, 772, 940
MboII GAAGA 3 cut(s) 97, 530, 544
MfeI CAATTG 1 cut(s) 494
MflI RGATCY 1 cut(s) 940
MhlI GDGCHC 1 cut(s) 899
MluCI AATT 8 cut(s) 50, 202, 397, 484, 494, 708, 799, 836
MlyI GAGTC 1 cut(s) 833
MmeI TCCRAC 4 cut(s) 42, 203, 562, 828
MroXI GAANNNNTTC 1 cut(s) 446
MseI TTAA 6 cut(s) 101, 281, 390, 504, 609, 765
MslI CAYNNNNRTG 2 cut(s) 780, 845
MspCI CTTAAG 2 cut(s) 280, 764
MspI CCGG 2 cut(s) 155, 529
MspR9I CCNGG 1 cut(s) 738
MunI CAATTG 1 cut(s) 494
Mva1269I GAATGC 2 cut(s) 178, 692
MvaI CCWGG 1 cut(s) 738
MwoI GCNNNNNNNGC 4 cut(s) 146, 194, 818, 863
NdeII GATC 3 cut(s) 4, 772, 940
NlaIII CATG 5 cut(s) 35, 116, 365, 441, 779
NlaIV GGNNCC 2 cut(s) 141, 564
NmeAIII GCCGAG 1 cut(s) 160
NmuCI GTSAC 1 cut(s) 916
PagI TCATGA 1 cut(s) 361
PctI GAATGC 2 cut(s) 178, 692
PdmI GAANNNNTTC 1 cut(s) 446
PfeI GAWTC 1 cut(s) 275
PflMI CCANNNNNTGG 1 cut(s) 710
PkrI GCNGC 4 cut(s) 637, 719, 881, 967
PleI GAGTC 1 cut(s) 832
PpsI GAGTC 1 cut(s) 832
Psp6I CCWGG 1 cut(s) 736
PspFI CCCAGC 1 cut(s) 720
PspGI CCWGG 1 cut(s) 736
PspN4I GGNNCC 2 cut(s) 141, 564
PspPI GGNCC 1 cut(s) 195
PsuI RGATCY 1 cut(s) 940
RseI CAYNNNNRTG 2 cut(s) 780, 845
SaqAI TTAA 6 cut(s) 101, 281, 390, 504, 609, 765
SatI GCNGC 4 cut(s) 636, 718, 880, 966
Sau3AI GATC 3 cut(s) 4, 772, 940
Sau96I GGNCC 1 cut(s) 195
SchI GAGTC 1 cut(s) 833
ScrFI CCNGG 1 cut(s) 738
SduI GDGCHC 1 cut(s) 899
SfaNI GCATC 3 cut(s) 175, 304, 538
SmiMI CAYNNNNRTG 2 cut(s) 780, 845
SmlI CTYRAG 2 cut(s) 280, 764
SmoI CTYRAG 2 cut(s) 280, 764
Sse9I AATT 8 cut(s) 50, 202, 397, 484, 494, 708, 799, 836
SsiI CCGC 1 cut(s) 965
StyD4I CCNGG 1 cut(s) 736
StyI CCWWGG 2 cut(s) 267, 558
TaaI ACNGT 1 cut(s) 950
TaiI ACGT 1 cut(s) 912
TaqI TCGA 1 cut(s) 511
TasI AATT 8 cut(s) 50, 202, 397, 484, 494, 708, 799, 836
TauI GCSGC 1 cut(s) 968
TfiI GAWTC 1 cut(s) 275
Tru1I TTAA 6 cut(s) 101, 281, 390, 504, 609, 765
Tru9I TTAA 6 cut(s) 101, 281, 390, 504, 609, 765
TscAI CASTG 1 cut(s) 136
TseFI GTSAC 1 cut(s) 916
TseI GCWGC 3 cut(s) 635, 717, 879
Tsp45I GTSAC 1 cut(s) 916
TspDTI ATGAA 6 cut(s) 101, 350, 426, 497, 552, 829
TspGWI ACGGA 1 cut(s) 197
TspRI CASTG 1 cut(s) 136
Van91I CCANNNNNTGG 1 cut(s) 710
Vha464I CTTAAG 2 cut(s) 280, 764
VneI GTGCAC 1 cut(s) 895
XapI RAATTY 5 cut(s) 50, 202, 397, 484, 799
XmnI GAANNNNTTC 1 cut(s) 446
ZraI GACGTC 1 cut(s) 910
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.