FvH4_6g07332

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb6
OG0000154
Physical Location & Seq
Reverse (-)
4407810 .. 4409035
1226 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_6g07332.t1

Sequence Viewer

Length: 1086 bp
ATGGCCAATAGGGTCGAGTTCTCGCAGTGCCTAGTCGGAAAATTTGACGGGAAGGGCAAATTTCAACATTGGAGAGCCCAGATGGAGCTTTTCTTTAAGGAGGCTTGGGATTGTCTCATCATCAATTGCTATGTGGGACAAGATAAGGTGAAAAAGGTTCAGCTCCAGACTTTACGGCGGCAATTTGAGCTTCTTCAGATGGAGAAAAGGGAGAGCAACTCTGATTACTTCTCACGCACCTTGGCGATTGTCAATCAGATGAAAGCCAATGGTGAGGTTTTATCAAATCTACAAGTTGTGGAGAAAATTCTTCGAACTTTGACAGATCGGTTCGAAGGCAAAGTCACAGCGATAGAAGAGTCAAGAGATCTGGCAGCAGTGACGGTTGATGAGTTTATGGGTTCTCTACAAGCCTATAAGCATAGGCTAAATGAGAAGTCAGAGGTTGCAATTGAAGAAGCGTTGGAGACTCGGTTGAGTTTGAAGAAAGAGAGAAACTTGGCGCACTGCAGTGAAGGAAGTTCCCGCTGTGAGGGAGGCTACCGTCGTGACGTAAGAAACCAGAATTCAAGTTACAGAAGAGGATCAAATCATCGGTTTGGAGCAAAAAGAGGAAGAGGCTACAATTGGAGTCAACCACGTGATAAGTCGAGGATACAGTGCTTTAATTGCAAGGAGTATGGCCATTACAAAACAGAGTGCAATCAGAGAAGGAGGTTCGAGGGTCAGGAGTTCCATGCCAAGATTGCAGAGAATGATGTTGACAATGAAGAGAATCTGTTGCTGGCTTTCAACGCGATGAATGGTCGAGAGAAGACAAAGTGGTTCTTGGATACAAGGTGCAGCAACCATATGTGTGGCCATAAGGACTTATTTGCTGAACAGAATGAGTCCATAACATCAGAGATCACATTTGGCAATGCAGCAAAGATGCCGGTGAAAGGAAAAGGCAAAATCTCTATCAAGTTGAAGAAGGGGGAGAACAATAGCATCTCTGATGTGTATTATGTACCTAGTCTTCGCCACAATTTGCTAAGTGTAAGGCAGCTCTCTGAGAAGGGATATGATATGAGGATCTACAGATGA
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 zf-CCHC

Protein Analysis

362

Amino Acids

42.04

Weight (kDa)

9.31

Isoelectric Point (pI)

38.75

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 33 - 147 3e-15 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 275 - 355 5e-28 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
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000154)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g02351 FvH4_1g18383 FvH4_1g18442 FvH4_1g19622 FvH4_2g08148 FvH4_2g16312 FvH4_3g06912 FvH4_3g10761 FvH4_3g12332 FvH4_3g12332 FvH4_3g14182 FvH4_3g21021 FvH4_3g35231 FvH4_3g45132 FvH4_4g08663 FvH4_4g30271 FvH4_4g30272 FvH4_4g30901 FvH4_4g30902 FvH4_5g12471 FvH4_5g22951 FvH4_6g07331 FvH4_6g07332 FvH4_6g41872 FvH4_6g43841 FvH4_6g43842 FvH4_6g48811 FvH4_7g03911 FvH4_7g13272 FvH4_7g21181 FvH4_7g29024 FvH4_7g33702
malus_domestica MD00G1037700.v1.1 MD01G1037300.v1.1 MD01G1096700.v1.1 MD01G1101100.v1.1 MD01G1129400.v1.1 MD02G1295200.v1.1 MD03G1131300.v1.1 MD04G1072100.v1.1 MD05G1104800.v1.1 MD07G1028600.v1.1 MD07G1274600.v1.1 MD08G1027200.v1.1 MD09G1044400.v1.1 MD09G1044700.v1.1 MD09G1129500.v1.1 MD09G1238700.v1.1 MD10G1011700.v1.1 MD10G1071400.v1.1 MD10G1108600.v1.1 MD10G1162100.v1.1 MD10G1162300.v1.1 MD11G1016700.v1.1 MD11G1074500.v1.1 MD15G1058600.v1.1 MD15G1383000.v1.1 MD16G1192200.v1.1 MD17G1077400.v1.1 MD17G1077500.v1.1
pyrus_communis pycom01g03520 pycom02g00350 pycom03g09910 pycom03g13960 pycom03g13970 pycom03g19180 pycom04g08410 pycom04g10140 pycom06g03750 pycom07g09240 pycom07g09260 pycom08g20130 pycom09g11020 pycom10g12690 pycom14g04140 pycom14g05710 pycom16g06380 pycom17g05500 pycom808g00140
rosa_chinensis RchiOBHm_Chr1g0316211 RchiOBHm_Chr1g0319901 RchiOBHm_Chr1g0321811 RchiOBHm_Chr1g0329831 RchiOBHm_Chr1g0330721 RchiOBHm_Chr1g0330731 RchiOBHm_Chr1g0368461 RchiOBHm_Chr1g0381111 RchiOBHm_Chr2g0154461 RchiOBHm_Chr2g0164521 RchiOBHm_Chr2g0175301 RchiOBHm_Chr3g0451301 RchiOBHm_Chr3g0453691 RchiOBHm_Chr3g0470191 RchiOBHm_Chr3g0486561 RchiOBHm_Chr4g0409141 RchiOBHm_Chr4g0409151 RchiOBHm_Chr4g0421231 RchiOBHm_Chr4g0440701 RchiOBHm_Chr5g0018211 RchiOBHm_Chr5g0023611 RchiOBHm_Chr5g0045971 RchiOBHm_Chr5g0056061 RchiOBHm_Chr5g0063381 RchiOBHm_Chr5g0064011 RchiOBHm_Chr5g0064021 RchiOBHm_Chr5g0064041 RchiOBHm_Chr6g0259681 RchiOBHm_Chr6g0259691 RchiOBHm_Chr6g0296531 RchiOBHm_Chr7g0186421 RchiOBHm_Chr7g0192321 RchiOBHm_Chr7g0198271 RchiOBHm_Chr7g0198951 RchiOBHm_Chr7g0237911
rosa_laevigata RLG00000026946
rosa_roxburghii Rroxscaffold_1G00014460 Rroxscaffold_1G00014610 Rroxscaffold_1G00028950 Rroxscaffold_1G00052630 Rroxscaffold_2G00104760 Rroxscaffold_2G00138900 Rroxscaffold_2G00145210 Rroxscaffold_3G00220110 Rroxscaffold_4G00297860 Rroxscaffold_4G00321570 Rroxscaffold_5G00332990 Rroxscaffold_5G00360870
rosa_samantha Rh1AG319600 Rh1CG299100 Rh4DG385900 Rh5BG032200
rosa_wichuraiana Rw0G002380 Rw0G003050 Rw0G003940 Rw1G002730 Rw1G003260 Rw1G005490 Rw1G016140 Rw1G016150 Rw1G017930 Rw1G017940 Rw1G022540 Rw1G022630 Rw1G031080 Rw1G039680 Rw2G003340 Rw2G003720 Rw2G006640 Rw2G020790 Rw2G025650 Rw2G028430 Rw2G029550 Rw2G034920 Rw2G040820 Rw2G048420 Rw2G048570 Rw3G010040 Rw3G022790 Rw3G023350 Rw3G025140 Rw3G028810 Rw4G000680 Rw4G003350 Rw4G004640 Rw4G026650 Rw4G034500 Rw5G008490 Rw5G020650 Rw5G023000 Rw5G033610 Rw5G037280 Rw5G046620 Rw5G050250 Rw6G001410 Rw6G005690 Rw6G005820 Rw6G010920 Rw6G022790 Rw6G023940 Rw6G026290 Rw6G028610 Rw6G031260 Rw6G036550 Rw6G036560 Rw7G015300 Rw7G017250 Rw7G018150 Rw7G031960 Rw7G036490

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 797
AciI CCGC 2 cut(s) 178, 526
AclWI GGATC 2 cut(s) 592, 1082
AcoI YGGCCR 3 cut(s) 3, 682, 859
AcsI RAATTY 4 cut(s) 41, 59, 306, 565
AcuI CTGAAG 1 cut(s) 179
AcvI CACGTG 1 cut(s) 641
AfaI GTAC 1 cut(s) 1011
AfiI CCNNNNNNNGG 2 cut(s) 532, 941
AgsI TTSAA 6 cut(s) 65, 455, 484, 570, 793, 970
AleI CACNNNNGTG 1 cut(s) 510
AluBI AGCT 4 cut(s) 88, 163, 190, 1048
AluI AGCT 4 cut(s) 88, 163, 190, 1048
Alw26I GTCTC 2 cut(s) 119, 461
AlwI GGATC 2 cut(s) 592, 1082
AoxI GGCC 3 cut(s) 3, 682, 859
ApeKI GCWGC 4 cut(s) 374, 843, 923, 1045
ApoI RAATTY 4 cut(s) 41, 59, 306, 565
ArsI GACNNNNNNTTYG 2 cut(s) 327, 359
AspLEI GCGC 1 cut(s) 505
AsuHPI GGTGA 3 cut(s) 160, 284, 949
AsuII TTCGAA 2 cut(s) 313, 333
BalI TGGCCA 3 cut(s) 5, 684, 861
BanII GRGCYC 1 cut(s) 79
BarI GAAGNNNNNNTAC 2 cut(s) 1002, 1034
BbrPI CACGTG 1 cut(s) 641
BbsI GAAGAC 2 cut(s) 821, 1010
BbvI GCAGC 4 cut(s) 386, 855, 935, 1057
BccI CCATC 2 cut(s) 76, 193
BceAI ACGGC 1 cut(s) 191
BciVI GTATCC 2 cut(s) 648, 826
BcoDI GTCTC 2 cut(s) 119, 461
BfaI CTAG 2 cut(s) 32, 1014
BfmI CTRYAG 2 cut(s) 508, 1078
BfuI GTATCC 2 cut(s) 648, 826
BglII AGATCT 1 cut(s) 367
BisI GCNGC 5 cut(s) 179, 375, 844, 924, 1046
BlsI GCNGC 5 cut(s) 180, 376, 845, 925, 1047
BmsI GCATC 2 cut(s) 921, 999
BpiI GAAGAC 2 cut(s) 821, 1010
BplI GAGNNNNNCTC 2 cut(s) 203, 235
BpmI CTGGAG 1 cut(s) 149
Bpu14I TTCGAA 2 cut(s) 313, 333
BsaAI YACGTR 1 cut(s) 641
BsaJI CCNNGG 1 cut(s) 240
BsaXI ACNNNNNCTCC 2 cut(s) 458, 488
Bsc4I CCNNNNNNNGG 2 cut(s) 532, 941
Bse118I RCCGGY 1 cut(s) 934
Bse3DI GCAATG 1 cut(s) 925
BseDI CCNNGG 1 cut(s) 240
BseLI CCNNNNNNNGG 2 cut(s) 532, 941
BseMI GCAATG 1 cut(s) 925
BseMII CTCAG 1 cut(s) 1044
BseXI GCAGC 4 cut(s) 386, 855, 935, 1057
BsgI GTGCAG 1 cut(s) 862
Bsh1236I CGCG 1 cut(s) 797
BshFI GGCC 3 cut(s) 5, 684, 861
BsiSI CCGG 1 cut(s) 935
BslFI GGGAC 1 cut(s) 150
BslI CCNNNNNNNGG 2 cut(s) 532, 941
BsmAI GTCTC 2 cut(s) 119, 461
BsmFI GGGAC 1 cut(s) 150
BsnI GGCC 3 cut(s) 5, 684, 861
Bsp119I TTCGAA 2 cut(s) 313, 333
Bsp1286I GDGCHC 1 cut(s) 79
Bsp143I GATC 5 cut(s) 325, 367, 584, 906, 1074
BspACI CCGC 2 cut(s) 178, 526
BspANI GGCC 3 cut(s) 5, 684, 861
BspCNI CTCAG 1 cut(s) 1045
BspFNI CGCG 1 cut(s) 797
BspMAI CTGCAG 1 cut(s) 512
BspPI GGATC 2 cut(s) 592, 1082
BspT104I TTCGAA 2 cut(s) 313, 333
BsrDI GCAATG 1 cut(s) 925
BsrFI RCCGGY 1 cut(s) 934
BssAI RCCGGY 1 cut(s) 934
BssECI CCNNGG 1 cut(s) 240
BssMI GATC 5 cut(s) 325, 367, 584, 906, 1074
BssT1I CCWWGG 1 cut(s) 240
Bst4CI ACNGT 3 cut(s) 385, 545, 660
Bst6I CTCTTC 4 cut(s) 351, 574, 610, 765
BstBAI YACGTR 1 cut(s) 641
BstBI TTCGAA 2 cut(s) 313, 333
BstC8I GCNNGC 1 cut(s) 786
BstDEI CTNAG 2 cut(s) 1034, 1053
BstFNI CGCG 1 cut(s) 797
BstHHI GCGC 1 cut(s) 505
BstKTI GATC 5 cut(s) 328, 370, 587, 909, 1077
BstMAI GTCTC 2 cut(s) 119, 461
BstMBI GATC 5 cut(s) 325, 367, 584, 906, 1074
BstMWI GCNNNNNNNGC 4 cut(s) 187, 669, 746, 794
BstSFI CTRYAG 2 cut(s) 508, 1078
BstUI CGCG 1 cut(s) 797
BstV1I GCAGC 4 cut(s) 386, 855, 935, 1057
BstV2I GAAGAC 2 cut(s) 821, 1010
BstX2I RGATCY 2 cut(s) 367, 1074
BstXI CCANNNNNNTGG 1 cut(s) 857
BstYI RGATCY 2 cut(s) 367, 1074
BsuI GTATCC 2 cut(s) 648, 826
BsuRI GGCC 3 cut(s) 5, 684, 861
BtgZI GCGATG 1 cut(s) 812
BtsI GCAGTG 4 cut(s) 32, 384, 505, 517
BtsIMutI CAGTG 5 cut(s) 32, 384, 505, 517, 665
Cac8I GCNNGC 1 cut(s) 786
CfoI GCGC 1 cut(s) 505
Cfr10I RCCGGY 1 cut(s) 934
Csp6I GTAC 1 cut(s) 1010
CviAII CATG 1 cut(s) 737
CviQI GTAC 1 cut(s) 1010
DdeI CTNAG 2 cut(s) 1034, 1053
DpnI GATC 5 cut(s) 327, 369, 586, 908, 1076
DpnII GATC 5 cut(s) 325, 367, 584, 906, 1074
EaeI YGGCCR 3 cut(s) 3, 682, 859
Eam1104I CTCTTC 4 cut(s) 351, 574, 610, 765
EarI CTCTTC 4 cut(s) 351, 574, 610, 765
Eco130I CCWWGG 1 cut(s) 240
Eco24I GRGCYC 1 cut(s) 79
Eco57I CTGAAG 1 cut(s) 179
Eco72I CACGTG 1 cut(s) 641
EcoRI GAATTC 1 cut(s) 565
EcoT14I CCWWGG 1 cut(s) 240
EcoT38I GRGCYC 1 cut(s) 79
ErhI CCWWGG 1 cut(s) 240
FaeI CATG 1 cut(s) 740
FalI AAGNNNNNCTT 2 cut(s) 812, 844
FaqI GGGAC 1 cut(s) 150
FatI CATG 1 cut(s) 736
FauI CCCGC 1 cut(s) 533
FauNDI CATATG 1 cut(s) 852
Fnu4HI GCNGC 5 cut(s) 179, 375, 844, 924, 1046
FriOI GRGCYC 1 cut(s) 79
Fsp4HI GCNGC 5 cut(s) 179, 375, 844, 924, 1046
FspBI CTAG 2 cut(s) 32, 1014
GlaI GCGC 1 cut(s) 504
GluI GCNGC 5 cut(s) 179, 375, 844, 924, 1046
GsuI CTGGAG 1 cut(s) 149
HaeIII GGCC 3 cut(s) 5, 684, 861
HapII CCGG 1 cut(s) 935
HhaI GCGC 1 cut(s) 505
Hin1II CATG 1 cut(s) 740
Hin6I GCGC 1 cut(s) 503
HinP1I GCGC 1 cut(s) 503
HincII GTYRAC 2 cut(s) 635, 763
HindII GTYRAC 2 cut(s) 635, 763
HinfI GANTC 5 cut(s) 359, 469, 631, 775, 890
HpaII CCGG 1 cut(s) 935
HphI GGTGA 3 cut(s) 160, 284, 949
Hpy166II GTNNAC 2 cut(s) 635, 763
Hpy188I TCNGA 9 cut(s) 38, 198, 223, 258, 442, 708, 904, 997, 1054
Hpy188III TCNNGA 5 cut(s) 166, 363, 548, 728, 809
Hpy8I GTNNAC 2 cut(s) 635, 763
Hpy99I CGWCG 1 cut(s) 549
HpyAV CCTTC 6 cut(s) 46, 329, 509, 705, 967, 1051
HpyCH4III ACNGT 3 cut(s) 385, 545, 660
HpyCH4IV ACGT 2 cut(s) 552, 640
HpyCH4V TGCA 7 cut(s) 449, 510, 672, 702, 749, 843, 923
HpyF10VI GCNNNNNNNGC 4 cut(s) 187, 669, 746, 794
HpyF3I CTNAG 2 cut(s) 1034, 1053
HpySE526I ACGT 2 cut(s) 552, 640
Hsp92II CATG 1 cut(s) 740
HspAI GCGC 1 cut(s) 503
Kzo9I GATC 5 cut(s) 325, 367, 584, 906, 1074
LmnI GCTCC 3 cut(s) 85, 168, 602
LpnPI CCDG 7 cut(s) 92, 179, 356, 575, 713, 770, 948
Lsp1109I GCAGC 4 cut(s) 386, 855, 935, 1057
LweI GCATC 2 cut(s) 921, 999
MaeI CTAG 2 cut(s) 32, 1014
MaeII ACGT 2 cut(s) 552, 640
MaeIII GTNAC 4 cut(s) 343, 379, 548, 572
MalI GATC 5 cut(s) 327, 369, 586, 908, 1076
MboI GATC 5 cut(s) 325, 367, 584, 906, 1074
MfeI CAATTG 3 cut(s) 124, 450, 625
MflI RGATCY 2 cut(s) 367, 1074
MhlI GDGCHC 1 cut(s) 79
MlsI TGGCCA 3 cut(s) 5, 684, 861
MluNI TGGCCA 3 cut(s) 5, 684, 861
MlyI GAGTC 4 cut(s) 368, 463, 640, 899
MmeI TCCRAC 2 cut(s) 16, 444
Mox20I TGGCCA 3 cut(s) 5, 684, 861
MscI TGGCCA 3 cut(s) 5, 684, 861
MseI TTAA 2 cut(s) 96, 666
MslI CAYNNNNRTG 2 cut(s) 510, 855
Msp20I TGGCCA 3 cut(s) 5, 684, 861
MspA1I CMGCKG 1 cut(s) 528
MspI CCGG 1 cut(s) 935
MunI CAATTG 3 cut(s) 124, 450, 625
MvnI CGCG 1 cut(s) 797
MwoI GCNNNNNNNGC 4 cut(s) 187, 669, 746, 794
NdeI CATATG 1 cut(s) 852
NdeII GATC 5 cut(s) 325, 367, 584, 906, 1074
NlaIII CATG 1 cut(s) 740
NmuCI GTSAC 3 cut(s) 343, 379, 548
NspV TTCGAA 2 cut(s) 313, 333
OliI CACNNNNGTG 1 cut(s) 510
PfeI GAWTC 1 cut(s) 775
PkrI GCNGC 5 cut(s) 180, 376, 845, 925, 1047
PleI GAGTC 4 cut(s) 367, 463, 639, 898
PmaCI CACGTG 1 cut(s) 641
PmlI CACGTG 1 cut(s) 641
PpsI GAGTC 4 cut(s) 367, 463, 639, 898
Ppu21I YACGTR 1 cut(s) 641
PspCI CACGTG 1 cut(s) 641
PstI CTGCAG 1 cut(s) 512
PsuI RGATCY 2 cut(s) 367, 1074
RsaI GTAC 1 cut(s) 1011
RsaNI GTAC 1 cut(s) 1010
RseI CAYNNNNRTG 2 cut(s) 510, 855
SaqAI TTAA 2 cut(s) 96, 666
SatI GCNGC 5 cut(s) 179, 375, 844, 924, 1046
Sau3AI GATC 5 cut(s) 325, 367, 584, 906, 1074
SchI GAGTC 4 cut(s) 368, 463, 640, 899
SduI GDGCHC 1 cut(s) 79
SfaNI GCATC 2 cut(s) 921, 999
SfcI CTRYAG 2 cut(s) 508, 1078
SfuI TTCGAA 2 cut(s) 313, 333
SmiMI CAYNNNNRTG 2 cut(s) 510, 855
SsiI CCGC 2 cut(s) 178, 526
SspMI CTAG 2 cut(s) 32, 1014
StyI CCWWGG 1 cut(s) 240
TaaI ACNGT 3 cut(s) 385, 545, 660
TaiI ACGT 2 cut(s) 555, 643
TaqI TCGA 6 cut(s) 15, 313, 333, 650, 720, 808
TauI GCSGC 1 cut(s) 181
TfiI GAWTC 1 cut(s) 775
Tru1I TTAA 2 cut(s) 96, 666
Tru9I TTAA 2 cut(s) 96, 666
TscAI CASTG 5 cut(s) 32, 384, 512, 517, 665
TseFI GTSAC 3 cut(s) 343, 379, 548
TseI GCWGC 4 cut(s) 374, 843, 923, 1045
Tsp45I GTSAC 3 cut(s) 343, 379, 548
TspDTI ATGAA 3 cut(s) 275, 783, 815
TspRI CASTG 5 cut(s) 32, 384, 512, 517, 665
XapI RAATTY 4 cut(s) 41, 59, 306, 565
XspI CTAG 2 cut(s) 32, 1014
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.