FvH4_2g20162

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb2
OG0000258
Physical Location & Seq
Reverse (-)
16963231 .. 16966170
2940 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_2g20162.t1

Sequence Viewer

Length: 1023 bp
ATGATTCCCATAAAACTACGAGTGCATACCGAGTCGACCCAAAACCCTGAACCTAAAGCCCGGCAATGGCTTGTGATGGATCAATCTGTATCTGTTCTGAAAAATCATGTTGAGAGACCCGAGAAATTCAAGGGGTCGGATTTCAAATGCTGGCAACAGAAGATGTTGTTCTATTTGACAATACTTCATGTGGCAAATGTTCTCACTGCCGAGGCTCCAAAGGCTCTGCCGGAAGGAGAAGGGGAGAATGCTCCAACGGATGCTCAAAGGGCCGAAAATCTGAAGGCTATTGAAACTTGGAACAACAATGAGTATAGTTGCAGAAACTACATCCTCAATGCCTTGGACAATTCCTTGTATGATATCTATTCTACCTTCAAGACGGCAAGGGAATTGTGGGAATCATTGGAGAACAAGTACAAGACTGAAGTTGCTTGTTCCAAGAAGTTTGTCATTGGCAAGTTTCTGAATTTCAAGATGAGCGATGCCAAGTCTGTTGTCAAGCAAGTGGAGGAACTCCAAGTCATTGTTCATGAGTTAGATATGGAAGGTATGGGTCTTAACCCGAATTTCCTTGTTGGTTCTATTATTGAGAAGTTACCTCCTTCATGGAAAGATTTCAAAATATATCTGAAACATCTAACCGAGGATATGAATTTTGAGCAATTGGTTCTTAAACTTCGAGTTGAAGAGGATAACCGGAAGAATGAAAGGGTTGATGCTATTTCCTTGAAGCCAACTGCAAATATGGTTGGAGGAAGTCCATCAAAGGTCAAGTTTCAGAAAAACAAAGGCAAAGGTGTTGCTGCCAAGCCTCTTTTTATTACTGGAAAGAACCCTCTCGTCCCACAAAAGTCCAAAGCATTCAAGAAGCCACAAATTGGAGGCTGTTGGGTGTGTGGAAAACCAGGGCATAGAGCAAAGGAGTGTCGCCTCAAGAAAGATCATGGAGGTGCTGGAGGTTCTGGAAATTCCAACCAAGCAAACCTTGTTGAGTCTGACAAAATCAATTCATTGGAGTGA
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

341

Amino Acids

38.39

Weight (kDa)

9.18

Isoelectric Point (pI)

34.78

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 81 - 238 3.3e-28 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)
AccB7I CCANNNNNTGG 1 cut(s) 881
AccI GTMKAC 1 cut(s) 35
AclWI GGATC 1 cut(s) 87
AcsI RAATTY 5 cut(s) 125, 469, 568, 655, 970
AcuI CTGAAG 2 cut(s) 302, 447
AfaI GTAC 1 cut(s) 419
AfiI CCNNNNNNNGG 2 cut(s) 66, 881
AgsI TTSAA 9 cut(s) 130, 145, 293, 379, 475, 622, 689, 733, 868
AjnI CCWGG 1 cut(s) 907
AjuI GAANNNNNNNTTGG 2 cut(s) 513, 545
Alw26I GTCTC 1 cut(s) 109
AlwI GGATC 1 cut(s) 87
Ama87I CYCGRG 1 cut(s) 119
AoxI GGCC 1 cut(s) 270
ApeKI GCWGC 1 cut(s) 806
ApoI RAATTY 5 cut(s) 125, 469, 568, 655, 970
Asp700I GAANNNNTTC 1 cut(s) 617
AspS9I GGNCC 1 cut(s) 270
AsuC2I CCSGG 1 cut(s) 61
AvaI CYCGRG 1 cut(s) 119
BbvI GCAGC 1 cut(s) 793
BccI CCATC 2 cut(s) 70, 772
BceAI ACGGC 1 cut(s) 399
BciT130I CCWGG 1 cut(s) 909
BcnI CCSGG 1 cut(s) 61
BcoDI GTCTC 1 cut(s) 109
BisI GCNGC 1 cut(s) 807
BlsI GCNGC 1 cut(s) 808
Bme1390I CCNGG 2 cut(s) 61, 909
BmeT110I CYCGRG 1 cut(s) 119
BmgT120I GGNCC 1 cut(s) 270
BmiI GGNNCC 1 cut(s) 216
BmrFI CCNGG 2 cut(s) 61, 909
BmsI GCATC 3 cut(s) 250, 475, 709
BpmI CTGGAG 1 cut(s) 978
BpuEI CTTGAG 1 cut(s) 920
BpuMI CCSGG 1 cut(s) 61
BsaI GGTCTC 1 cut(s) 109
BsaJI CCNNGG 4 cut(s) 210, 342, 645, 908
BsaWI WCCGGW 1 cut(s) 699
BsaXI ACNNNNNCTCC 2 cut(s) 401, 431
Bsc4I CCNNNNNNNGG 2 cut(s) 66, 881
Bse1I ACTGG 1 cut(s) 832
Bse3DI GCAATG 1 cut(s) 71
BseBI CCWGG 1 cut(s) 909
BseDI CCNNGG 4 cut(s) 210, 342, 645, 908
BseGI GGATG 2 cut(s) 265, 330
BseLI CCNNNNNNNGG 2 cut(s) 66, 881
BseMI GCAATG 1 cut(s) 71
BseNI ACTGG 1 cut(s) 832
BseXI GCAGC 1 cut(s) 793
BshFI GGCC 1 cut(s) 272
BsiHKCI CYCGRG 1 cut(s) 119
BsiSI CCGG 3 cut(s) 61, 230, 700
BslFI GGGAC 1 cut(s) 830
BslI CCNNNNNNNGG 2 cut(s) 66, 881
BsmAI GTCTC 1 cut(s) 109
BsmFI GGGAC 1 cut(s) 830
BsmI GAATGC 2 cut(s) 253, 863
BsnI GGCC 1 cut(s) 272
Bso31I GGTCTC 1 cut(s) 109
BsoBI CYCGRG 1 cut(s) 119
Bsp143I GATC 2 cut(s) 79, 943
BspANI GGCC 1 cut(s) 272
BspHI TCATGA 1 cut(s) 532
BspLI GGNNCC 1 cut(s) 216
BspPI GGATC 1 cut(s) 87
BspTNI GGTCTC 1 cut(s) 109
BsrDI GCAATG 1 cut(s) 71
BsrI ACTGG 1 cut(s) 832
BssECI CCNNGG 4 cut(s) 210, 342, 645, 908
BssMI GATC 2 cut(s) 79, 943
BssT1I CCWWGG 1 cut(s) 342
Bst2UI CCWGG 1 cut(s) 909
Bst6I CTCTTC 1 cut(s) 684
BstC8I GCNNGC 1 cut(s) 152
BstF5I GGATG 2 cut(s) 265, 330
BstKTI GATC 2 cut(s) 82, 946
BstMAI GTCTC 1 cut(s) 109
BstMBI GATC 2 cut(s) 79, 943
BstMWI GCNNNNNNNGC 2 cut(s) 221, 269
BstNI CCWGG 1 cut(s) 909
BstSCI CCNGG 2 cut(s) 59, 907
BstV1I GCAGC 1 cut(s) 793
BsuRI GGCC 1 cut(s) 272
BtgZI GCGATG 1 cut(s) 498
BtsCI GGATG 2 cut(s) 265, 330
BtsI GCAGTG 1 cut(s) 204
BtsIMutI CAGTG 1 cut(s) 204
Cac8I GCNNGC 1 cut(s) 152
CciI TCATGA 1 cut(s) 532
Cfr13I GGNCC 1 cut(s) 270
Csp6I GTAC 1 cut(s) 418
CviAII CATG 5 cut(s) 107, 188, 533, 609, 947
CviQI GTAC 1 cut(s) 418
DpnI GATC 2 cut(s) 81, 945
DpnII GATC 2 cut(s) 79, 943
Eam1104I CTCTTC 1 cut(s) 684
EarI CTCTTC 1 cut(s) 684
Eco130I CCWWGG 1 cut(s) 342
Eco31I GGTCTC 1 cut(s) 109
Eco32I GATATC 1 cut(s) 364
Eco57I CTGAAG 2 cut(s) 302, 447
Eco88I CYCGRG 1 cut(s) 119
EcoRII CCWGG 1 cut(s) 907
EcoRV GATATC 1 cut(s) 364
EcoT14I CCWWGG 1 cut(s) 342
ErhI CCWWGG 1 cut(s) 342
FaeI CATG 5 cut(s) 110, 191, 536, 612, 950
FalI AAGNNNNNCTT 2 cut(s) 972, 1004
FaqI GGGAC 1 cut(s) 830
FatI CATG 5 cut(s) 106, 187, 532, 608, 946
FblI GTMKAC 1 cut(s) 35
Fnu4HI GCNGC 1 cut(s) 807
FokI GGATG 2 cut(s) 272, 317
Fsp4HI GCNGC 1 cut(s) 807
GluI GCNGC 1 cut(s) 807
GsuI CTGGAG 1 cut(s) 978
HaeIII GGCC 1 cut(s) 272
HapII CCGG 3 cut(s) 61, 230, 700
Hin1II CATG 5 cut(s) 110, 191, 536, 612, 950
HincII GTYRAC 1 cut(s) 36
HindII GTYRAC 1 cut(s) 36
HinfI GANTC 4 cut(s) 4, 32, 401, 995
HpaII CCGG 3 cut(s) 61, 230, 700
Hpy166II GTNNAC 1 cut(s) 36
Hpy188I TCNGA 7 cut(s) 99, 139, 282, 468, 633, 783, 1000
Hpy188III TCNNGA 6 cut(s) 379, 475, 533, 868, 937, 966
Hpy8I GTNNAC 1 cut(s) 36
HpyAV CCTTC 6 cut(s) 227, 233, 277, 385, 542, 615
HpyCH4V TGCA 3 cut(s) 25, 321, 743
HpyF10VI GCNNNNNNNGC 2 cut(s) 221, 269
Hsp92II CATG 5 cut(s) 110, 191, 536, 612, 950
Kzo9I GATC 2 cut(s) 79, 943
LmnI GCTCC 2 cut(s) 220, 256
Lsp1109I GCAGC 1 cut(s) 793
LweI GCATC 3 cut(s) 250, 475, 709
MaeIII GTNAC 1 cut(s) 597
MalI GATC 2 cut(s) 81, 945
MboI GATC 2 cut(s) 79, 943
MboII GAAGA 3 cut(s) 172, 701, 715
MfeI CAATTG 1 cut(s) 665
MlyI GAGTC 2 cut(s) 41, 1004
MmeI TCCRAC 4 cut(s) 117, 278, 733, 999
MroXI GAANNNNTTC 1 cut(s) 617
MseI TTAA 2 cut(s) 561, 675
MslI CAYNNNNRTG 2 cut(s) 951, 1018
MspI CCGG 3 cut(s) 61, 230, 700
MspR9I CCNGG 2 cut(s) 61, 909
MunI CAATTG 1 cut(s) 665
Mva1269I GAATGC 2 cut(s) 253, 863
MvaI CCWGG 1 cut(s) 909
MwoI GCNNNNNNNGC 2 cut(s) 221, 269
NciI CCSGG 1 cut(s) 61
NdeII GATC 2 cut(s) 79, 943
NlaIII CATG 5 cut(s) 110, 191, 536, 612, 950
NlaIV GGNNCC 1 cut(s) 216
NmeAIII GCCGAG 1 cut(s) 235
PagI TCATGA 1 cut(s) 532
PctI GAATGC 2 cut(s) 253, 863
PdmI GAANNNNTTC 1 cut(s) 617
PfeI GAWTC 2 cut(s) 4, 401
PflMI CCANNNNNTGG 1 cut(s) 881
PkrI GCNGC 1 cut(s) 808
PleI GAGTC 2 cut(s) 40, 1003
PpsI GAGTC 2 cut(s) 40, 1003
Psp6I CCWGG 1 cut(s) 907
PspGI CCWGG 1 cut(s) 907
PspN4I GGNNCC 1 cut(s) 216
PspPI GGNCC 1 cut(s) 270
RsaI GTAC 1 cut(s) 419
RsaNI GTAC 1 cut(s) 418
RseI CAYNNNNRTG 2 cut(s) 951, 1018
SalI GTCGAC 1 cut(s) 34
SaqAI TTAA 2 cut(s) 561, 675
SatI GCNGC 1 cut(s) 807
Sau3AI GATC 2 cut(s) 79, 943
Sau96I GGNCC 1 cut(s) 270
SchI GAGTC 2 cut(s) 41, 1004
ScrFI CCNGG 2 cut(s) 61, 909
SetI ASST 9 cut(s) 55, 377, 553, 604, 774, 802, 955, 964, 990
SfaNI GCATC 3 cut(s) 250, 475, 709
SmiMI CAYNNNNRTG 2 cut(s) 951, 1018
SmlI CTYRAG 1 cut(s) 935
SmoI CTYRAG 1 cut(s) 935
StyD4I CCNGG 2 cut(s) 59, 907
StyI CCWWGG 1 cut(s) 342
TaqI TCGA 2 cut(s) 35, 682
TatI WGTACW 1 cut(s) 417
TfiI GAWTC 2 cut(s) 4, 401
Tru1I TTAA 2 cut(s) 561, 675
Tru9I TTAA 2 cut(s) 561, 675
TscAI CASTG 1 cut(s) 211
TseI GCWGC 1 cut(s) 806
TspDTI ATGAA 6 cut(s) 176, 521, 597, 668, 723, 1002
TspGWI ACGGA 1 cut(s) 272
TspRI CASTG 1 cut(s) 211
Van91I CCANNNNNTGG 1 cut(s) 881
XapI RAATTY 5 cut(s) 125, 469, 568, 655, 970
XmiI GTMKAC 1 cut(s) 35
XmnI GAANNNNTTC 1 cut(s) 617
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.