Rw7G027460

Retrotransposon gag protein

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000128
Physical Location & Seq
Reverse (-)
35506971 .. 35508215
1245 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G027460.1

Sequence Viewer

Length: 1077 bp
ATGGAGAAGCTAGAAATTCAACATGGCGATGACTCAGAAAAAGGTCCGCGTGGTCATAAGAAAGACTCATCTGCTTCATGGTCAATTCAGCAACTTCAAGACATGATTGCCAACACAATCAAAGCTCAATATGGTGGTCCCTCTCAAGATACGCTAACATACTCCAAGCCTTATACTAAGCGGTTAGATCATTTGAGGATGCCAACTAGGTACCAACCTCCCAAGTTTCAACAGTTCGATGGCAAAGAATTGGAGTCTGAATCCATTGACAGCTGGGAGCAAATGGAAAAAGAGTTATTGAATCGCTTCTTCAGTACACGTCGCATTGTGAGCATGTTAGAGCTCACCAACACCAAACAACAGAATGACGAGTCAGCTGTAGAATTCATCAACCGTTGGAGTGCACTAAGCCTCGACTGCAAGGATCGACTCTCACAGTTGTCAGCGGTAGAAATGTGCATTCAAGGCATGCATTGGGACTTACTGTCAATCCTTCAAGGGATAAAGCCTCGCACCTTTGAAGAACTTGCCACTCGAGCTCATGACATGGAACTTAGCATCGCTAGTCATAGTCGAGGAAGAGGTGAAATTGTTGAACCACATAATCAGAAACGTGTCATGGAGTCTTTGGCGATCACAACTCCTGTCAAGATCACAGCACGAGTCAAGTCAAACAACCAAAACAAGTTGGAGCCGACTCATGATCAAACAAGGCGGTGCACTCTTAGAGAGCTAGAAGCTAAAAGTTACCCTTTTCCAGATTCCGATGTTGCTGACATGTTGGAAGATTTGCTTCAAAAGAAAGTAATTAAATTGCCATACTGCAAACGTCCAGAAGAGATGCATCGCATCAATGACCCAAAGTACTGCAAGTACCACTGTGTCATCAGTCACCCGACGGAGAAGTGCTTTGTGTTGAAAGACCTCATCATGAAGCTCGCACAACAAGGAAAAATCTGTTTAGACATTGAGGATGATGTGGCTCAATCAAATCATGCTGCCATCATCTTTGATCAACTCGAAGTAGTGTCGTCCACGCCTTTGCAGGGGGCATGCTACTTGCCTAAATTTTCTTAG
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
Retrotrans_gag

Protein Analysis

358

Amino Acids

41.27

Weight (kDa)

6.47

Isoelectric Point (pI)

49.19

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotrans_gag PF03732 83 - 158 5e-07 Retrotransposon gag protein
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
Loading...
Style Settings
Image
Tree File
Tip: Beautify your tree with professional tools

Download the Full Tree (.nwk) file, then upload it to any of the following tools to customize colors, fonts, annotations, clades, and branch support.

Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0000128)

Species Orthologous Gene IDs
fragaria_vesca FvH4_1g28082 FvH4_2g15191 FvH4_2g31621 FvH4_3g07261 FvH4_3g22806 FvH4_3g26703 FvH4_3g26704 FvH4_3g31360 FvH4_4g01161 FvH4_4g22271 FvH4_4g25732 FvH4_5g00242 FvH4_5g28911 FvH4_5g32461 FvH4_6g13112 FvH4_6g53790 FvH4_6g53791 FvH4_7g03661 FvH4_7g04125 FvH4_7g04126
pyrus_communis pycom01g01950 pycom01g01960 pycom01g03260 pycom01g07760 pycom01g11430 pycom01g23980 pycom02g15030 pycom02g18630 pycom03g12320 pycom03g18810 pycom03g19250 pycom04g05010 pycom04g06520 pycom04g06680 pycom04g09630 pycom04g09640 pycom05g06850 pycom05g07540 pycom05g08940 pycom06g04300 pycom06g05750 pycom06g06960 pycom06g19690 pycom07g08750 pycom07g10700 pycom07g10910 pycom07g27480 pycom07g27790 pycom07g27800 pycom08g13620 pycom09g03540 pycom09g03550 pycom09g09870 pycom09g13480 pycom09g14360 pycom09g14890 pycom09g14930 pycom09g15760 pycom10g02190 pycom10g05270 pycom10g06810 pycom10g06830 pycom10g08060 pycom10g08520 pycom11g02350 pycom11g14170 pycom11g15050 pycom11g19270 pycom11g20160 pycom11g22420 pycom12g08620 pycom12g08630 pycom12g10440 pycom12g16590 pycom133g00190 pycom13g20730 pycom13g22230 pycom13g22670 pycom13g23230 pycom13g23250 pycom13g24880 pycom13g25300 pycom13g28040 pycom13g29010 pycom14g07570 pycom14g18650 pycom15g04500 pycom15g09310 pycom15g27210 pycom15g30810 pycom15g34920 pycom16g16040 pycom16g17260 pycom16g17940 pycom16g20990 pycom16g23470 pycom16g24160 pycom16g24720 pycom16g25910 pycom16g25920 pycom16g26370 pycom17g03310 pycom17g12670 pycom17g17530 pycom17g25090 pycom17g27300 pycom17g27310 pycom420g00140 pycom420g00160 pycom420g00320 pycom505g00220 pycom520g00740 pycom520g01010 pycom520g01020 pycom576g00060 pycom675g00040
rosa_laevigata RLG00000022630
rosa_multiflora Rmu_co7993280.1_g000001 Rmu_co8054704.1_g000001 Rmu_co8148394.1_g000001 Rmu_co8243015.1_g000001 Rmu_co8272095.1_g000001 Rmu_co8282359.1_g000001 Rmu_co8334783.1_g000001 Rmu_co8404405.1_g000001 Rmu_sc0000161.1_g000030 Rmu_sc0000418.1_g000026 Rmu_sc0000488.1_g000015 Rmu_sc0000706.1_g000041 Rmu_sc0000720.1_g000013 Rmu_sc0000776.1_g000022 Rmu_sc0000948.1_g000017 Rmu_sc0001167.1_g000045 Rmu_sc0001167.1_g000047 Rmu_sc0001211.1_g000054 Rmu_sc0001241.1_g000019 Rmu_sc0001307.1_g000021 Rmu_sc0001438.1_g000043 Rmu_sc0001468.1_g000032 Rmu_sc0001851.1_g000020 Rmu_sc0002026.1_g000023 Rmu_sc0002811.1_g000016 Rmu_sc0002958.1_g000002 Rmu_sc0002958.1_g000003 Rmu_sc0003745.1_g000010 Rmu_sc0004234.1_g000006 Rmu_sc0004234.1_g000008 Rmu_sc0005035.1_g000001 Rmu_sc0005320.1_g000010 Rmu_sc0005866.1_g000006 Rmu_sc0006139.1_g000009 Rmu_sc0006504.1_g000008 Rmu_sc0006695.1_g000049 Rmu_sc0006695.1_g000050 Rmu_sc0006981.1_g000001 Rmu_sc0007108.1_g000012 Rmu_sc0007355.1_g000001 Rmu_sc0007873.1_g000015 Rmu_sc0007961.1_g000003 Rmu_sc0008991.1_g000005 Rmu_sc0009528.1_g000009 Rmu_sc0013299.1_g000003 Rmu_sc0013532.1_g000015 Rmu_sc0015524.1_g000001 Rmu_sc0015793.1_g000001 Rmu_sc0015817.1_g000006 Rmu_sc0015930.1_g000003 Rmu_sc0015930.1_g000006 Rmu_sc0016952.1_g000002 Rmu_sc0016952.1_g000003 Rmu_sc0018715.1_g000003 Rmu_sc0018715.1_g000005 Rmu_sc0023934.1_g000003 Rmu_sc0023989.1_g000002 Rmu_sc0023989.1_g000003 Rmu_sc0028612.1_g000001 Rmu_sc0029049.1_g000001 Rmu_sc0029639.1_g000001 Rmu_sc0035263.1_g000001 Rmu_sc0037892.1_g000001 Rmu_ssc0000170.1_g000024 Rmu_ssc0000233.1_g000057 Rmu_ssc0000259.1_g000055 Rmu_ssc0000259.1_g000057
rosa_roxburghii Rroxscaffold_4G00287780 Rroxscaffold_4G00325290 Rroxscaffold_5G00333910 Rroxscaffold_7G00211350
rosa_rugosa Rorug01G0056300 Rorug04G0149000 Rorug07G0222000
rosa_samantha Rh1AG072900 Rh1CG072000
rosa_wichuraiana Rw0G003630 Rw0G005250 Rw0G020770 Rw0G023770 Rw1G005460 Rw1G005980 Rw1G007190 Rw1G011350 Rw1G022520 Rw1G028660 Rw2G018620 Rw2G019490 Rw4G006910 Rw4G013020 Rw4G023970 Rw5G044650 Rw6G006590 Rw6G012210 Rw6G023750 Rw7G027370 Rw7G027460 Rw7G035570

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc65I GGTACC 1 cut(s) 210
AccB1I GGYRCC 1 cut(s) 210
AccII CGCG 1 cut(s) 49
AciI CCGC 4 cut(s) 47, 181, 446, 715
AclWI GGATC 1 cut(s) 432
AcsI RAATTY 3 cut(s) 15, 383, 1067
AcuI CTGAAG 1 cut(s) 295
AfaI GTAC 4 cut(s) 212, 316, 866, 875
AfiI CCNNNNNNNGG 1 cut(s) 1046
AflIII ACRYGT 3 cut(s) 317, 613, 777
AhdI GACNNNNNGTC 1 cut(s) 484
AjiI CACGTC 1 cut(s) 320
AluBI AGCT 9 cut(s) 10, 125, 273, 343, 377, 539, 733, 740, 937
AluI AGCT 9 cut(s) 10, 125, 273, 343, 377, 539, 733, 740, 937
Alw21I GWGCWC 4 cut(s) 345, 406, 541, 722
Alw44I GTGCAC 2 cut(s) 402, 718
AlwI GGATC 1 cut(s) 432
Ama87I CYCGRG 1 cut(s) 534
ApaLI GTGCAC 2 cut(s) 402, 718
ApeKI GCWGC 1 cut(s) 998
ApoI RAATTY 3 cut(s) 15, 383, 1067
Asp700I GAANNNNTTC 1 cut(s) 305
Asp718I GGTACC 1 cut(s) 210
AspS9I GGNCC 2 cut(s) 44, 137
AsuHPI GGTGA 3 cut(s) 337, 596, 884
AvaI CYCGRG 1 cut(s) 534
AvaII GGWCC 2 cut(s) 44, 137
BaeGI GKGCMC 2 cut(s) 406, 722
BanI GGYRCC 1 cut(s) 210
BanII GRGCYC 2 cut(s) 345, 541
BauI CACGAG 1 cut(s) 660
Bbv12I GWGCWC 4 cut(s) 345, 406, 541, 722
BbvI GCAGC 1 cut(s) 985
BccI CCATC 2 cut(s) 233, 1010
BclI TGATCA 2 cut(s) 703, 1012
BfaI CTAG 4 cut(s) 11, 207, 564, 734
BfmI CTRYAG 1 cut(s) 378
BisI GCNGC 1 cut(s) 999
BlsI GCNGC 1 cut(s) 1000
BmcAI AGTACT 1 cut(s) 866
Bme18I GGWCC 2 cut(s) 44, 137
BmeRI GACNNNNNGTC 1 cut(s) 484
BmeT110I CYCGRG 1 cut(s) 534
BmgBI CACGTC 1 cut(s) 320
BmgT120I GGNCC 2 cut(s) 44, 137
BmiI GGNNCC 3 cut(s) 139, 212, 693
BmsI GCATC 5 cut(s) 189, 567, 831, 853, 858
BpuEI CTTGAG 1 cut(s) 129
Bsc4I CCNNNNNNNGG 1 cut(s) 1046
BseGI GGATG 2 cut(s) 204, 979
BseLI CCNNNNNNNGG 1 cut(s) 1046
BseMII CTCAG 1 cut(s) 48
BseSI GKGCMC 2 cut(s) 406, 722
BseXI GCAGC 1 cut(s) 985
BseYI CCCAGC 1 cut(s) 273
Bsh1236I CGCG 1 cut(s) 49
BshNI GGYRCC 1 cut(s) 210
BsiHKAI GWGCWC 4 cut(s) 345, 406, 541, 722
BsiHKCI CYCGRG 1 cut(s) 534
BslFI GGGAC 2 cut(s) 123, 491
BslI CCNNNNNNNGG 1 cut(s) 1046
BsmFI GGGAC 2 cut(s) 123, 491
BsmI GAATGC 1 cut(s) 459
BsoBI CYCGRG 1 cut(s) 534
Bsp1286I GDGCHC 4 cut(s) 345, 406, 541, 722
Bsp143I GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
BspACI CCGC 4 cut(s) 47, 181, 446, 715
BspCNI CTCAG 1 cut(s) 47
BspFNI CGCG 1 cut(s) 49
BspHI TCATGA 3 cut(s) 541, 700, 930
BspLI GGNNCC 3 cut(s) 139, 212, 693
BspPI GGATC 1 cut(s) 432
BspT107I GGYRCC 1 cut(s) 210
BssMI GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
BssSI CACGAG 1 cut(s) 660
Bst2BI CACGAG 1 cut(s) 660
Bst4CI ACNGT 5 cut(s) 234, 395, 438, 486, 881
Bst6I CTCTTC 2 cut(s) 574, 831
BstC8I GCNNGC 3 cut(s) 470, 939, 1054
BstDEI CTNAG 6 cut(s) 34, 177, 407, 554, 725, 1074
BstF5I GGATG 2 cut(s) 204, 979
BstFNI CGCG 1 cut(s) 49
BstKTI GATC 6 cut(s) 190, 427, 636, 654, 706, 1015
BstMBI GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
BstMWI GCNNNNNNNGC 4 cut(s) 330, 417, 465, 536
BstNSI RCATGY 4 cut(s) 337, 472, 781, 1056
BstSFI CTRYAG 1 cut(s) 378
BstSLI GKGCMC 2 cut(s) 406, 722
BstUI CGCG 1 cut(s) 49
BstV1I GCAGC 1 cut(s) 985
BtgZI GCGATG 3 cut(s) 42, 544, 830
BtrI CACGTC 1 cut(s) 320
BtsCI GGATG 2 cut(s) 204, 979
BtsIMutI CAGTG 1 cut(s) 877
Cac8I GCNNGC 3 cut(s) 470, 939, 1054
CciI TCATGA 3 cut(s) 541, 700, 930
Cfr13I GGNCC 2 cut(s) 44, 137
Csp6I GTAC 4 cut(s) 211, 315, 865, 874
CviQI GTAC 4 cut(s) 211, 315, 865, 874
DdeI CTNAG 6 cut(s) 34, 177, 407, 554, 725, 1074
DpnI GATC 6 cut(s) 189, 426, 635, 653, 705, 1014
DpnII GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
DriI GACNNNNNGTC 1 cut(s) 484
Eam1104I CTCTTC 2 cut(s) 574, 831
Eam1105I GACNNNNNGTC 1 cut(s) 484
EarI CTCTTC 2 cut(s) 574, 831
Ecl136II GAGCTC 2 cut(s) 343, 539
Eco24I GRGCYC 2 cut(s) 345, 541
Eco47I GGWCC 2 cut(s) 44, 137
Eco53kI GAGCTC 2 cut(s) 343, 539
Eco57I CTGAAG 1 cut(s) 295
Eco88I CYCGRG 1 cut(s) 534
EcoICRI GAGCTC 2 cut(s) 343, 539
EcoRI GAATTC 1 cut(s) 383
EcoT22I ATGCAT 2 cut(s) 474, 846
EcoT38I GRGCYC 2 cut(s) 345, 541
FalI AAGNNNNNCTT 4 cut(s) 736, 768, 777, 809
FaqI GGGAC 2 cut(s) 123, 491
FbaI TGATCA 2 cut(s) 703, 1012
Fnu4HI GCNGC 1 cut(s) 999
FokI GGATG 2 cut(s) 211, 986
FriOI GRGCYC 2 cut(s) 345, 541
Fsp4HI GCNGC 1 cut(s) 999
FspBI CTAG 4 cut(s) 11, 207, 564, 734
GluI GCNGC 1 cut(s) 999
GsaI CCCAGC 1 cut(s) 277
HphI GGTGA 3 cut(s) 337, 596, 884
Hpy166II GTNNAC 4 cut(s) 317, 404, 720, 1035
Hpy188I TCNGA 4 cut(s) 37, 259, 609, 766
Hpy188III TCNNGA 8 cut(s) 98, 146, 542, 649, 701, 758, 833, 931
Hpy8I GTNNAC 4 cut(s) 317, 404, 720, 1035
Hpy99I CGWCG 2 cut(s) 324, 901
HpyAV CCTTC 1 cut(s) 503
HpyCH4III ACNGT 5 cut(s) 234, 395, 438, 486, 881
HpyCH4IV ACGT 3 cut(s) 319, 613, 829
HpyCH4V TGCA 9 cut(s) 404, 420, 459, 472, 720, 825, 844, 870, 1045
HpyF10VI GCNNNNNNNGC 4 cut(s) 330, 417, 465, 536
HpyF3I CTNAG 6 cut(s) 34, 177, 407, 554, 725, 1074
HpySE526I ACGT 3 cut(s) 319, 613, 829
KpnI GGTACC 1 cut(s) 214
Ksp22I TGATCA 2 cut(s) 703, 1012
Kzo9I GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
LmnI GCTCC 2 cut(s) 277, 691
LpnPI CCDG 5 cut(s) 259, 657, 771, 846, 1031
Lsp1109I GCAGC 1 cut(s) 985
LweI GCATC 5 cut(s) 189, 567, 831, 853, 858
MaeI CTAG 4 cut(s) 11, 207, 564, 734
MaeII ACGT 3 cut(s) 319, 613, 829
MaeIII GTNAC 2 cut(s) 746, 890
MalI GATC 6 cut(s) 189, 426, 635, 653, 705, 1014
MboI GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
MboII GAAGA 5 cut(s) 301, 533, 591, 797, 848
MhlI GDGCHC 4 cut(s) 345, 406, 541, 722
MluCI AATT 8 cut(s) 15, 84, 248, 383, 588, 807, 812, 1067
MlyI GAGTC 8 cut(s) 26, 59, 263, 380, 423, 632, 672, 691
MmeI TCCRAC 3 cut(s) 377, 669, 762
MnlI CCTC 9 cut(s) 151, 189, 228, 422, 519, 569, 575, 935, 964
Mph1103I ATGCAT 2 cut(s) 474, 846
MroXI GAANNNNTTC 1 cut(s) 305
MseI TTAA 1 cut(s) 810
MslI CAYNNNNRTG 1 cut(s) 27
MspA1I CMGCKG 3 cut(s) 273, 377, 446
Mva1269I GAATGC 1 cut(s) 459
MvnI CGCG 1 cut(s) 49
MwoI GCNNNNNNNGC 4 cut(s) 330, 417, 465, 536
NdeII GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
NlaIV GGNNCC 3 cut(s) 139, 212, 693
NmuCI GTSAC 1 cut(s) 890
NsiI ATGCAT 2 cut(s) 474, 846
NspI RCATGY 4 cut(s) 337, 472, 781, 1056
PaeI GCATGC 2 cut(s) 472, 1056
PaeR7I CTCGAG 1 cut(s) 534
PagI TCATGA 3 cut(s) 541, 700, 930
PciI ACATGT 1 cut(s) 777
PctI GAATGC 1 cut(s) 459
PdmI GAANNNNTTC 1 cut(s) 305
PfeI GAWTC 3 cut(s) 260, 301, 761
PkrI GCNGC 1 cut(s) 1000
PleI GAGTC 8 cut(s) 26, 59, 262, 379, 423, 631, 671, 691
PpsI GAGTC 8 cut(s) 26, 59, 262, 379, 423, 631, 671, 691
PscI ACATGT 1 cut(s) 777
Psp124BI GAGCTC 2 cut(s) 345, 541
PspFI CCCAGC 1 cut(s) 273
PspN4I GGNNCC 3 cut(s) 139, 212, 693
PspPI GGNCC 2 cut(s) 44, 137
PspXI VCTCGAGB 1 cut(s) 534
PvuII CAGCTG 2 cut(s) 273, 377
RsaI GTAC 4 cut(s) 212, 316, 866, 875
RsaNI GTAC 4 cut(s) 211, 315, 865, 874
RseI CAYNNNNRTG 1 cut(s) 27
SacI GAGCTC 2 cut(s) 345, 541
SaqAI TTAA 1 cut(s) 810
SatI GCNGC 1 cut(s) 999
Sau3AI GATC 6 cut(s) 187, 424, 633, 651, 703, 1012
Sau96I GGNCC 2 cut(s) 44, 137
ScaI AGTACT 1 cut(s) 866
SchI GAGTC 8 cut(s) 26, 59, 263, 380, 423, 632, 672, 691
SduI GDGCHC 4 cut(s) 345, 406, 541, 722
SfaNI GCATC 5 cut(s) 189, 567, 831, 853, 858
SfcI CTRYAG 1 cut(s) 378
Sfr274I CTCGAG 1 cut(s) 534
SinI GGWCC 2 cut(s) 44, 137
SlaI CTCGAG 1 cut(s) 534
SmiMI CAYNNNNRTG 1 cut(s) 27
SmlI CTYRAG 2 cut(s) 144, 534
SmoI CTYRAG 2 cut(s) 144, 534
SphI GCATGC 2 cut(s) 472, 1056
Sse9I AATT 8 cut(s) 15, 84, 248, 383, 588, 807, 812, 1067
SsiI CCGC 4 cut(s) 47, 181, 446, 715
SspMI CTAG 4 cut(s) 11, 207, 564, 734
SstI GAGCTC 2 cut(s) 345, 541
TaaI ACNGT 5 cut(s) 234, 395, 438, 486, 881
TaiI ACGT 3 cut(s) 322, 616, 832
TaqI TCGA 6 cut(s) 237, 414, 427, 535, 574, 1020
TasI AATT 8 cut(s) 15, 84, 248, 383, 588, 807, 812, 1067
TatI WGTACW 2 cut(s) 314, 864
TfiI GAWTC 3 cut(s) 260, 301, 761
Tru1I TTAA 1 cut(s) 810
Tru9I TTAA 1 cut(s) 810
TscAI CASTG 1 cut(s) 884
TseFI GTSAC 1 cut(s) 890
TseI GCWGC 1 cut(s) 998
Tsp45I GTSAC 1 cut(s) 890
TspDTI ATGAA 3 cut(s) 66, 376, 947
TspGWI ACGGA 1 cut(s) 914
TspRI CASTG 1 cut(s) 884
VneI GTGCAC 2 cut(s) 402, 718
VpaK11BI GGWCC 2 cut(s) 44, 137
XapI RAATTY 3 cut(s) 15, 383, 1067
XceI RCATGY 4 cut(s) 337, 472, 781, 1056
XhoI CTCGAG 1 cut(s) 534
XmnI GAANNNNTTC 1 cut(s) 305
XspI CTAG 4 cut(s) 11, 207, 564, 734
ZrmI AGTACT 1 cut(s) 866
Zsp2I ATGCAT 2 cut(s) 474, 846
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.