FvH4_7g01381

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb7
OG0000258
Physical Location & Seq
Forward (+)
1780908 .. 1782005
1098 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_7g01381.t1

Sequence Viewer

Length: 1032 bp
ATGGATCAATCAATTGCTGTTGGGGTTAAGAACCACATTGAGAAGCCGTTTGTGTTCAAGGGAGTGGACTTCAAACGATGGCAGCAAAATATGCTGTTTTACCTTACAACTCTGAATTTGGCACAAATCATTACTGGGGAGGCTCCTGAAGTGCCAAAAGAGGGTGATATCCCTGCTGCAACGCTCAAGGCTGCTGAGACATGGAACCAAAATGAGTTTCTGTGCAAAAACTACATTCTGAATGCCTTGGATGATGCACTGTATGATGTATATTCCTCATTCAAAACTGCAAAGGAGTTGTGGGAATCTCTGGACAAGAAGTACAAGTCTGAGGTTGCAAGTGCTAAGAAGTTTGTTGTTGGAAAATTTCTGAATTTCAAGATGAGCGACATGCTTTCTGTTGTGAAACAAGTAGAGGAAATTCAGATAATAGTTCATGAGTTACTGGATGAAGATTTCAAGTTACATCTCAAGCATATTACTGAGAGCATGAACCTTGAGCAACTCATACTGAAACTTCGTGTGGAGGAGGAGAATCGCAAAAATGAGAAAGTTGATGCGACTTCTATGGAAGTAAAAGCCAATGTAATTGAAGGTGGCACCTCCAAGCCTAAATTTGCACAAAAGAAGGCTGCTGCAAAGAAGGTTGCTACTGCACCAAAGGCTGCTACCTTTAAGAAAAAGATTCAAGGAGGCTGTTGGGTGTGTGGAAAGCCTGGACACCGAGCCAAGGACTGCCGCCACAGGAAAGATGGAAGTTCTGGAAACACCAACCAAGCACATGTAGCAGTGGATGATATTCAGTTCACTGGGGTTGTATCTGAGGCAAACACAATGACAATTTCCAATGATTGGTGGGTTGACACCGGTGCTTCAAGGCATGTCTGCGCCATGAAAAGCATGTTTGCTACATATGAGCAAGGATCTGGTGGAGAGAACATCTACATGGGAAATGCAAGTACTGCTGCTGTTGAAGGAAAGGGAAAAGTGATACTGAAACTCACTTCTGGAAAGGACTTTTGTGCTCACTGA
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

344

Amino Acids

38.16

Weight (kDa)

8.67

Isoelectric Point (pI)

27.84

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 32 - 152 1.1e-15 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 285 - 338 5.5e-13 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)
AccB1I GGYRCC 1 cut(s) 599
AccB7I CCANNNNNTGG 1 cut(s) 852
AciI CCGC 1 cut(s) 739
AclWI GGATC 2 cut(s) 12, 931
AcsI RAATTY 5 cut(s) 115, 365, 373, 420, 614
AcuI CTGAAG 1 cut(s) 168
AfaI GTAC 2 cut(s) 323, 961
AfiI CCNNNNNNNGG 3 cut(s) 161, 730, 852
AflIII ACRYGT 1 cut(s) 781
AgeI ACCGGT 1 cut(s) 866
AgsI TTSAA 9 cut(s) 58, 73, 283, 379, 460, 593, 689, 876, 974
AjnI CCWGG 1 cut(s) 715
AjuI GAANNNNNNNTTGG 2 cut(s) 201, 233
Alw21I GWGCWC 1 cut(s) 1027
Alw26I GTCTC 1 cut(s) 191
AlwI GGATC 2 cut(s) 12, 931
ApeKI GCWGC 7 cut(s) 82, 176, 191, 632, 635, 665, 965
ApoI RAATTY 5 cut(s) 115, 365, 373, 420, 614
AsiGI ACCGGT 1 cut(s) 866
AspLEI GCGC 1 cut(s) 890
AsuHPI GGTGA 1 cut(s) 176
BanI GGYRCC 1 cut(s) 599
Bbv12I GWGCWC 1 cut(s) 1027
BbvI GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 952
BccI CCATC 2 cut(s) 72, 746
BceAI ACGGC 1 cut(s) 31
BciT130I CCWGG 1 cut(s) 717
BcoDI GTCTC 1 cut(s) 191
BisI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 966
BlsI GCNGC 8 cut(s) 84, 178, 193, 634, 637, 667, 740, 967
BmcAI AGTACT 1 cut(s) 961
Bme1390I CCNGG 1 cut(s) 717
BmiI GGNNCC 3 cut(s) 144, 206, 601
BmrFI CCNGG 1 cut(s) 717
BmrI ACTGGG 2 cut(s) 144, 819
BmsI GCATC 2 cut(s) 244, 547
BmuI ACTGGG 2 cut(s) 144, 819
BpuEI CTTGAG 3 cut(s) 170, 455, 518
BsaJI CCNNGG 2 cut(s) 246, 729
BsaWI WCCGGW 1 cut(s) 866
Bsc4I CCNNNNNNNGG 3 cut(s) 161, 730, 852
Bse118I RCCGGY 1 cut(s) 866
Bse1I ACTGG 3 cut(s) 139, 450, 814
BseBI CCWGG 1 cut(s) 717
BseDI CCNNGG 2 cut(s) 246, 729
BseGI GGATG 3 cut(s) 256, 454, 799
BseLI CCNNNNNNNGG 3 cut(s) 161, 730, 852
BseMII CTCAG 4 cut(s) 186, 321, 474, 813
BseNI ACTGG 3 cut(s) 139, 450, 814
BseRI GAGGAG 2 cut(s) 542, 545
BseXI GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 952
BsgI GTGCAG 1 cut(s) 639
BshNI GGYRCC 1 cut(s) 599
BshTI ACCGGT 1 cut(s) 866
BsiHKAI GWGCWC 1 cut(s) 1027
BsiSI CCGG 1 cut(s) 867
BslI CCNNNNNNNGG 3 cut(s) 161, 730, 852
BsmAI GTCTC 1 cut(s) 191
BsmI GAATGC 1 cut(s) 247
Bsp1286I GDGCHC 1 cut(s) 1027
Bsp143I GATC 2 cut(s) 4, 923
BspACI CCGC 1 cut(s) 739
BspCNI CTCAG 4 cut(s) 187, 322, 475, 814
BspHI TCATGA 1 cut(s) 436
BspLI GGNNCC 3 cut(s) 144, 206, 601
BspPI GGATC 2 cut(s) 12, 931
BspT107I GGYRCC 1 cut(s) 599
BsrFI RCCGGY 1 cut(s) 866
BsrI ACTGG 3 cut(s) 139, 450, 814
BssAI RCCGGY 1 cut(s) 866
BssECI CCNNGG 2 cut(s) 246, 729
BssMI GATC 2 cut(s) 4, 923
BssT1I CCWWGG 2 cut(s) 246, 729
Bst2UI CCWGG 1 cut(s) 717
Bst4CI ACNGT 1 cut(s) 261
BstAPI GCANNNNNTGC 2 cut(s) 91, 962
BstDEI CTNAG 5 cut(s) 195, 330, 345, 483, 822
BstF5I GGATG 3 cut(s) 256, 454, 799
BstHHI GCGC 1 cut(s) 890
BstKTI GATC 2 cut(s) 7, 926
BstMAI GTCTC 1 cut(s) 191
BstMBI GATC 2 cut(s) 4, 923
BstMWI GCNNNNNNNGC 4 cut(s) 91, 662, 785, 962
BstNI CCWGG 1 cut(s) 717
BstNSI RCATGY 4 cut(s) 394, 785, 884, 904
BstSCI CCNGG 1 cut(s) 715
BstV1I GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 952
BstX2I RGATCY 1 cut(s) 923
BstYI RGATCY 1 cut(s) 923
BtsCI GGATG 3 cut(s) 256, 454, 799
BtsI GCAGTG 1 cut(s) 795
BtsIMutI CAGTG 4 cut(s) 257, 795, 807, 1027
CciI TCATGA 1 cut(s) 436
CfoI GCGC 1 cut(s) 890
Cfr10I RCCGGY 1 cut(s) 866
Csp6I GTAC 2 cut(s) 322, 960
CspAI ACCGGT 1 cut(s) 866
CviAII CATG 9 cut(s) 201, 391, 437, 490, 782, 881, 892, 901, 946
CviQI GTAC 2 cut(s) 322, 960
DdeI CTNAG 5 cut(s) 195, 330, 345, 483, 822
DpnI GATC 2 cut(s) 6, 925
DpnII GATC 2 cut(s) 4, 923
Eco130I CCWWGG 2 cut(s) 246, 729
Eco32I GATATC 1 cut(s) 169
Eco57I CTGAAG 1 cut(s) 168
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
FaeI CATG 9 cut(s) 204, 394, 440, 493, 785, 884, 895, 904, 949
FatI CATG 9 cut(s) 200, 390, 436, 489, 781, 880, 891, 900, 945
FauNDI CATATG 1 cut(s) 913
Fnu4HI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 966
FokI GGATG 3 cut(s) 263, 461, 806
Fsp4HI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 966
GlaI GCGC 1 cut(s) 889
GluI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 966
HapII CCGG 1 cut(s) 867
HhaI GCGC 1 cut(s) 890
Hin1II CATG 9 cut(s) 204, 394, 440, 493, 785, 884, 895, 904, 949
Hin6I GCGC 1 cut(s) 888
HinP1I GCGC 1 cut(s) 888
HincII GTYRAC 1 cut(s) 862
HindII GTYRAC 1 cut(s) 862
HinfI GANTC 3 cut(s) 305, 535, 685
HpaII CCGG 1 cut(s) 867
HphI GGTGA 1 cut(s) 176
Hpy166II GTNNAC 3 cut(s) 67, 807, 862
Hpy188I TCNGA 6 cut(s) 114, 240, 331, 372, 426, 823
Hpy188III TCNNGA 6 cut(s) 146, 311, 379, 437, 762, 1008
Hpy8I GTNNAC 3 cut(s) 67, 807, 862
HpyAV CCTTC 4 cut(s) 587, 622, 637, 968
HpyCH4III ACNGT 1 cut(s) 261
HpyCH4V TGCA 9 cut(s) 179, 225, 257, 290, 338, 620, 638, 656, 956
HpyF10VI GCNNNNNNNGC 4 cut(s) 91, 662, 785, 962
HpyF3I CTNAG 5 cut(s) 195, 330, 345, 483, 822
Hsp92II CATG 9 cut(s) 204, 394, 440, 493, 785, 884, 895, 904, 949
HspAI GCGC 1 cut(s) 888
Kzo9I GATC 2 cut(s) 4, 923
LmnI GCTCC 1 cut(s) 148
Lsp1109I GCAGC 7 cut(s) 94, 163, 178, 619, 622, 652, 952
LweI GCATC 2 cut(s) 244, 547
MaeIII GTNAC 2 cut(s) 441, 462
MalI GATC 2 cut(s) 6, 925
MboI GATC 2 cut(s) 4, 923
MboII GAAGA 1 cut(s) 464
MfeI CAATTG 1 cut(s) 12
MflI RGATCY 1 cut(s) 923
MhlI GDGCHC 1 cut(s) 1027
MluCI AATT 8 cut(s) 12, 115, 365, 373, 420, 588, 614, 840
MmeI TCCRAC 1 cut(s) 340
MseI TTAA 2 cut(s) 27, 675
MslI CAYNNNNRTG 1 cut(s) 944
MspI CCGG 1 cut(s) 867
MspR9I CCNGG 1 cut(s) 717
MunI CAATTG 1 cut(s) 12
Mva1269I GAATGC 1 cut(s) 247
MvaI CCWGG 1 cut(s) 717
MwoI GCNNNNNNNGC 4 cut(s) 91, 662, 785, 962
NdeI CATATG 1 cut(s) 913
NdeII GATC 2 cut(s) 4, 923
NlaIII CATG 9 cut(s) 204, 394, 440, 493, 785, 884, 895, 904, 949
NlaIV GGNNCC 3 cut(s) 144, 206, 601
NspI RCATGY 4 cut(s) 394, 785, 884, 904
PagI TCATGA 1 cut(s) 436
PciI ACATGT 1 cut(s) 781
PctI GAATGC 1 cut(s) 247
PfeI GAWTC 3 cut(s) 305, 535, 685
PflMI CCANNNNNTGG 1 cut(s) 852
PinAI ACCGGT 1 cut(s) 866
PkrI GCNGC 8 cut(s) 84, 178, 193, 634, 637, 667, 740, 967
PscI ACATGT 1 cut(s) 781
Psp6I CCWGG 1 cut(s) 715
PspGI CCWGG 1 cut(s) 715
PspN4I GGNNCC 3 cut(s) 144, 206, 601
PsuI RGATCY 1 cut(s) 923
RsaI GTAC 2 cut(s) 323, 961
RsaNI GTAC 2 cut(s) 322, 960
RseI CAYNNNNRTG 1 cut(s) 944
SaqAI TTAA 2 cut(s) 27, 675
SatI GCNGC 8 cut(s) 83, 177, 192, 633, 636, 666, 739, 966
Sau3AI GATC 2 cut(s) 4, 923
ScaI AGTACT 1 cut(s) 961
ScrFI CCNGG 1 cut(s) 717
SduI GDGCHC 1 cut(s) 1027
SetI ASST 7 cut(s) 105, 336, 498, 598, 605, 648, 674
SfaNI GCATC 2 cut(s) 244, 547
SgrAI CRCCGGYG 1 cut(s) 866
SmiMI CAYNNNNRTG 1 cut(s) 944
SmlI CTYRAG 3 cut(s) 185, 470, 497
SmoI CTYRAG 3 cut(s) 185, 470, 497
Sse9I AATT 8 cut(s) 12, 115, 365, 373, 420, 588, 614, 840
SsiI CCGC 1 cut(s) 739
StyD4I CCNGG 1 cut(s) 715
StyI CCWWGG 2 cut(s) 246, 729
TaaI ACNGT 1 cut(s) 261
TasI AATT 8 cut(s) 12, 115, 365, 373, 420, 588, 614, 840
TatI WGTACW 2 cut(s) 321, 959
TauI GCSGC 1 cut(s) 741
TfiI GAWTC 3 cut(s) 305, 535, 685
Tru1I TTAA 2 cut(s) 27, 675
Tru9I TTAA 2 cut(s) 27, 675
TscAI CASTG 3 cut(s) 264, 795, 814
TseI GCWGC 7 cut(s) 82, 176, 191, 632, 635, 665, 965
TspDTI ATGAA 4 cut(s) 425, 465, 506, 908
TspRI CASTG 3 cut(s) 264, 795, 814
Van91I CCANNNNNTGG 1 cut(s) 852
XapI RAATTY 5 cut(s) 115, 365, 373, 420, 614
XceI RCATGY 4 cut(s) 394, 785, 884, 904
XcmI CCANNNNNNNNNTGG 1 cut(s) 749
ZrmI AGTACT 1 cut(s) 961
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.