Rw5G029960

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000258
Physical Location & Seq
Forward (+)
46906548 .. 46907968
1421 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G029960.1

Sequence Viewer

Length: 1365 bp
ATGGATCAATCGGTATCTACTATGAAGAATCATGTGGAGAAACCTGAGAAATTCAAGGGTTCGGATTTCAAACGTTGGCAACAGAAGATGTTGTTCTATTTGACAACTCTTCATAATGTTCCAACTTATGCTCAAAAGGCCGAAAATCAGAAGGCCATTGTTGCCTGGGCGAGCAATGAGTTTCTGTGCAGGAATTATATCCTCAATGCCTTAGACGATTCCTTGTATGATATTTACTCATCATTCAAAACAGCAAAGGAATTATGGGAGTCGTTGGACAACAAATACAAGACTGAAGTTGCTTGTTCAAAGAAGTTTGTCATTGGCAAGTTTCTGAATTACAAGATGGTCGATGCCAAGTCTGTTGTCAAGCAAGTGAAGGAACTTCAAGTCATTGTTCATGAGTTAGATGAAGAAGGTATGGGACTGAACTCGAATTTTCTTGTTGGTTCTGTTATTGAAAAGTTACCTCCTTCATGGAAAGATTTCAAAGTATATCTAAAACATCTAACTGAGGACATGAATTTTGAGCAATTGGTTCTGAAACTTCGTGTTGAAGAGGATCACCGGAAGAATGAAAGGGCTGATGCTACTTCTATGGAGCCAAACGCAAACATGATTGGAGGAAGTCCATCAAAGGCCAAGTTTCAGAAAAACAAAGGCAAGAATGTTGCTGCCAAACCAAGTCTTGTTGCTGCCAAGAAGTCACTCACCCCACAAAAGACCAAAGTTTTCAAAAAACCACAAACTGGTGGATGTTGGGTTTGTGGCAAATCAGGGCATAGAGCAAAAGAATGTCACTTCAAGAAAGATCAAGGAGGTAGTGGTTCTGGAAATTCCAACAACCAAGCAAACCTTGCTGGAAATGAAAATCAATTCATTGGAGTGGTTTCTGCAGCAAATCTGGTAACTAATACAACTGATTGGTGGATTGATACTGGTGCTTCAATGCACGTATGCTCTGCAAGGGAGATATTCACTTCATACCAGCCAATCAAGGAAGGAGAACCTTTGTTCATGGGGAATGCCAAAACTGCCAAAGTTGAAGGAAAAGGGAAGGTGATTCTGAAATTCACTTCTGGAAAAGAACTTGTACTTACTAATGTACTTCATGTACCTGAAATATGTAAGAACCTAGTGTTTGGTCCTGTTCTAAGTAACAAGGGATTCAAACTAGTGTTCGAATCTGACAAATTTGTACTCACCAAGGGTGGGGTGTATGTAGGAAATGGTTACCTTAGTGAAGGGCTCTTTAAACTAAATGTGTACCTACTATGGCTGCAGCTATTAATAATAATAATGCAGGCACTAGCGCTGCTTCTATGTACATGGTTGAGTCCTCTTCCTTATGGCATTCTAGATTAG
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

454

Amino Acids

50.86

Weight (kDa)

9.24

Isoelectric Point (pI)

30.03

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 46 - 194 1.2e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 309 - 390 3e-23 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)
AccB7I CCANNNNNTGG 1 cut(s) 749
AclI AACGTT 1 cut(s) 73
AclWI GGATC 2 cut(s) 12, 570
AcsI RAATTY 6 cut(s) 50, 436, 523, 835, 1070, 1193
AcuI CTGAAG 1 cut(s) 315
AfaI GTAC 6 cut(s) 1095, 1107, 1116, 1200, 1268, 1327
AfeI AGCGCT 1 cut(s) 1314
AfiI CCNNNNNNNGG 2 cut(s) 749, 1212
AhlI ACTAGT 1 cut(s) 1174
AjnI CCWGG 1 cut(s) 164
AluBI AGCT 1 cut(s) 1285
AluI AGCT 1 cut(s) 1285
AlwI GGATC 2 cut(s) 12, 570
Aor51HI AGCGCT 1 cut(s) 1314
AoxI GGCC 3 cut(s) 138, 153, 639
ApeKI GCWGC 6 cut(s) 674, 695, 896, 1279, 1282, 1315
ApoI RAATTY 6 cut(s) 50, 436, 523, 835, 1070, 1193
ArsI GACNNNNNNTTYG 2 cut(s) 509, 541
AseI ATTAAT 1 cut(s) 1289
Asp700I GAANNNNTTC 1 cut(s) 485
AspLEI GCGC 1 cut(s) 1315
AspS9I GGNCC 1 cut(s) 1145
AsuHPI GGTGA 4 cut(s) 557, 703, 1072, 1195
AsuII TTCGAA 1 cut(s) 1182
AvaII GGWCC 1 cut(s) 1145
BanII GRGCYC 1 cut(s) 1251
BbvI GCAGC 6 cut(s) 661, 682, 908, 1266, 1294, 1302
BccI CCATC 2 cut(s) 340, 640
BciT130I CCWGG 1 cut(s) 166
BcuI ACTAGT 1 cut(s) 1174
BfaI CTAG 4 cut(s) 1136, 1175, 1310, 1358
BfmI CTRYAG 2 cut(s) 894, 1280
BfoI RGCGCY 1 cut(s) 1316
BisI GCNGC 6 cut(s) 675, 696, 897, 1280, 1283, 1316
BlsI GCNGC 6 cut(s) 676, 697, 898, 1281, 1284, 1317
Bme1390I CCNGG 1 cut(s) 166
Bme18I GGWCC 1 cut(s) 1145
BmgT120I GGNCC 1 cut(s) 1145
BmiI GGNNCC 1 cut(s) 603
BmrFI CCNGG 1 cut(s) 166
BmsI GCATC 2 cut(s) 343, 577
Bpu14I TTCGAA 1 cut(s) 1182
BsaAI YACGTR 1 cut(s) 955
BsaJI CCNNGG 2 cut(s) 165, 1206
BsaWI WCCGGW 1 cut(s) 567
Bsc4I CCNNNNNNNGG 2 cut(s) 749, 1212
Bse1I ACTGG 2 cut(s) 754, 943
Bse3DI GCAATG 1 cut(s) 181
BseBI CCWGG 1 cut(s) 166
BseDI CCNNGG 2 cut(s) 165, 1206
BseGI GGATG 1 cut(s) 761
BseLI CCNNNNNNNGG 2 cut(s) 749, 1212
BseMI GCAATG 1 cut(s) 181
BseMII CTCAG 2 cut(s) 36, 504
BseNI ACTGG 2 cut(s) 754, 943
BseXI GCAGC 6 cut(s) 661, 682, 908, 1266, 1294, 1302
BsgI GTGCAG 1 cut(s) 208
BshFI GGCC 3 cut(s) 140, 155, 641
BsiSI CCGG 1 cut(s) 568
BslFI GGGAC 1 cut(s) 438
BslI CCNNNNNNNGG 2 cut(s) 749, 1212
BsmFI GGGAC 1 cut(s) 438
BsmI GAATGC 2 cut(s) 1030, 1353
BsnI GGCC 3 cut(s) 140, 155, 641
Bsp119I TTCGAA 1 cut(s) 1182
Bsp1286I GDGCHC 1 cut(s) 1251
Bsp1407I TGTACA 1 cut(s) 1325
Bsp143I GATC 3 cut(s) 4, 562, 811
BspANI GGCC 3 cut(s) 140, 155, 641
BspCNI CTCAG 2 cut(s) 37, 505
BspHI TCATGA 1 cut(s) 400
BspLI GGNNCC 1 cut(s) 603
BspMAI CTGCAG 2 cut(s) 898, 1284
BspPI GGATC 2 cut(s) 12, 570
BspT104I TTCGAA 1 cut(s) 1182
BsrDI GCAATG 1 cut(s) 181
BsrGI TGTACA 1 cut(s) 1325
BsrI ACTGG 2 cut(s) 754, 943
BssECI CCNNGG 2 cut(s) 165, 1206
BssMI GATC 3 cut(s) 4, 562, 811
BssT1I CCWWGG 1 cut(s) 1206
Bst2UI CCWGG 1 cut(s) 166
Bst6I CTCTTC 3 cut(s) 114, 552, 1347
BstAPI GCANNNNNTGC 1 cut(s) 857
BstAUI TGTACA 1 cut(s) 1325
BstBAI YACGTR 1 cut(s) 955
BstBI TTCGAA 1 cut(s) 1182
BstC8I GCNNGC 2 cut(s) 172, 1305
BstDEI CTNAG 5 cut(s) 45, 211, 513, 1154, 1238
BstEII GGTNACC 1 cut(s) 1232
BstF5I GGATG 1 cut(s) 761
BstH2I RGCGCY 1 cut(s) 1316
BstHHI GCGC 1 cut(s) 1315
BstKTI GATC 3 cut(s) 7, 565, 814
BstMBI GATC 3 cut(s) 4, 562, 811
BstMWI GCNNNNNNNGC 4 cut(s) 137, 161, 857, 1034
BstNI CCWGG 1 cut(s) 166
BstPI GGTNACC 1 cut(s) 1232
BstSCI CCNGG 1 cut(s) 164
BstSFI CTRYAG 2 cut(s) 894, 1280
BstV1I GCAGC 6 cut(s) 661, 682, 908, 1266, 1294, 1302
BsuRI GGCC 3 cut(s) 140, 155, 641
BtsCI GGATG 1 cut(s) 761
Cac8I GCNNGC 2 cut(s) 172, 1305
CciI TCATGA 1 cut(s) 400
CfoI GCGC 1 cut(s) 1315
Cfr13I GGNCC 1 cut(s) 1145
Csp6I GTAC 6 cut(s) 1094, 1106, 1115, 1199, 1267, 1326
CviAII CATG 8 cut(s) 32, 401, 477, 520, 616, 1018, 1112, 1329
CviJI RGCY 9 cut(s) 140, 155, 584, 604, 641, 991, 1249, 1279, 1285
CviKI_1 RGCY 9 cut(s) 140, 155, 584, 604, 641, 991, 1249, 1279, 1285
CviQI GTAC 6 cut(s) 1094, 1106, 1115, 1199, 1267, 1326
DdeI CTNAG 5 cut(s) 45, 211, 513, 1154, 1238
DpnI GATC 3 cut(s) 6, 564, 813
DpnII GATC 3 cut(s) 4, 562, 811
DraI TTTAAA 1 cut(s) 1255
Eam1104I CTCTTC 3 cut(s) 114, 552, 1347
EarI CTCTTC 3 cut(s) 114, 552, 1347
Eco130I CCWWGG 1 cut(s) 1206
Eco24I GRGCYC 1 cut(s) 1251
Eco47I GGWCC 1 cut(s) 1145
Eco47III AGCGCT 1 cut(s) 1314
Eco57I CTGAAG 1 cut(s) 315
Eco91I GGTNACC 1 cut(s) 1232
EcoO65I GGTNACC 1 cut(s) 1232
EcoRII CCWGG 1 cut(s) 164
EcoT14I CCWWGG 1 cut(s) 1206
EcoT38I GRGCYC 1 cut(s) 1251
ErhI CCWWGG 1 cut(s) 1206
FaeI CATG 8 cut(s) 35, 404, 480, 523, 619, 1021, 1115, 1332
FalI AAGNNNNNCTT 2 cut(s) 840, 872
FaqI GGGAC 1 cut(s) 438
FatI CATG 8 cut(s) 31, 400, 476, 519, 615, 1017, 1111, 1328
Fnu4HI GCNGC 6 cut(s) 675, 696, 897, 1280, 1283, 1316
FokI GGATG 1 cut(s) 768
FriOI GRGCYC 1 cut(s) 1251
Fsp4HI GCNGC 6 cut(s) 675, 696, 897, 1280, 1283, 1316
FspBI CTAG 4 cut(s) 1136, 1175, 1310, 1358
GlaI GCGC 1 cut(s) 1314
GluI GCNGC 6 cut(s) 675, 696, 897, 1280, 1283, 1316
HaeII RGCGCY 1 cut(s) 1316
HaeIII GGCC 3 cut(s) 140, 155, 641
HapII CCGG 1 cut(s) 568
HhaI GCGC 1 cut(s) 1315
Hin1II CATG 8 cut(s) 35, 404, 480, 523, 619, 1021, 1115, 1332
Hin6I GCGC 1 cut(s) 1313
HinP1I GCGC 1 cut(s) 1313
HinfI GANTC 7 cut(s) 28, 218, 269, 1063, 1167, 1184, 1336
HpaII CCGG 1 cut(s) 568
HphI GGTGA 4 cut(s) 557, 703, 1072, 1195
Hpy166II GTNNAC 1 cut(s) 1267
Hpy188I TCNGA 7 cut(s) 64, 150, 336, 543, 651, 1068, 1189
Hpy188III TCNNGA 5 cut(s) 401, 805, 831, 1080, 1358
Hpy8I GTNNAC 1 cut(s) 1267
HpyAV CCTTC 8 cut(s) 145, 373, 410, 483, 995, 1040, 1051, 1238
HpyCH4IV ACGT 2 cut(s) 73, 954
HpyCH4V TGCA 6 cut(s) 189, 896, 952, 965, 1282, 1303
HpyF10VI GCNNNNNNNGC 4 cut(s) 137, 161, 857, 1034
HpyF3I CTNAG 5 cut(s) 45, 211, 513, 1154, 1238
HpySE526I ACGT 2 cut(s) 73, 954
Hsp92II CATG 8 cut(s) 35, 404, 480, 523, 619, 1021, 1115, 1332
HspAI GCGC 1 cut(s) 1313
Kzo9I GATC 3 cut(s) 4, 562, 811
LmnI GCTCC 1 cut(s) 601
Lsp1109I GCAGC 6 cut(s) 661, 682, 908, 1266, 1294, 1302
LweI GCATC 2 cut(s) 343, 577
MaeI CTAG 4 cut(s) 1136, 1175, 1310, 1358
MaeII ACGT 2 cut(s) 73, 954
MaeIII GTNAC 6 cut(s) 465, 705, 797, 907, 1157, 1232
MalI GATC 3 cut(s) 6, 564, 813
MboI GATC 3 cut(s) 4, 562, 811
MboII GAAGA 7 cut(s) 37, 97, 101, 425, 569, 583, 1334
MfeI CAATTG 1 cut(s) 533
MhlI GDGCHC 1 cut(s) 1251
MlyI GAGTC 2 cut(s) 278, 1345
MmeI TCCRAC 3 cut(s) 146, 255, 864
MnlI CCTC 7 cut(s) 212, 480, 508, 553, 617, 812, 1350
MroXI GAANNNNTTC 1 cut(s) 485
MseI TTAA 2 cut(s) 1254, 1289
MslI CAYNNNNRTG 1 cut(s) 884
MspI CCGG 1 cut(s) 568
MspR9I CCNGG 1 cut(s) 166
MunI CAATTG 1 cut(s) 533
Mva1269I GAATGC 2 cut(s) 1030, 1353
MvaI CCWGG 1 cut(s) 166
MwoI GCNNNNNNNGC 4 cut(s) 137, 161, 857, 1034
NdeII GATC 3 cut(s) 4, 562, 811
NlaIII CATG 8 cut(s) 35, 404, 480, 523, 619, 1021, 1115, 1332
NlaIV GGNNCC 1 cut(s) 603
NmuCI GTSAC 2 cut(s) 705, 797
NspV TTCGAA 1 cut(s) 1182
PagI TCATGA 1 cut(s) 400
PctI GAATGC 2 cut(s) 1030, 1353
PdmI GAANNNNTTC 1 cut(s) 485
PfeI GAWTC 5 cut(s) 28, 218, 1063, 1167, 1184
PflMI CCANNNNNTGG 1 cut(s) 749
PkrI GCNGC 6 cut(s) 676, 697, 898, 1281, 1284, 1317
PleI GAGTC 2 cut(s) 277, 1344
PpsI GAGTC 2 cut(s) 277, 1344
Ppu21I YACGTR 1 cut(s) 955
PshBI ATTAAT 1 cut(s) 1289
Psp1406I AACGTT 1 cut(s) 73
Psp6I CCWGG 1 cut(s) 164
PspEI GGTNACC 1 cut(s) 1232
PspGI CCWGG 1 cut(s) 164
PspN4I GGNNCC 1 cut(s) 603
PspPI GGNCC 1 cut(s) 1145
PstI CTGCAG 2 cut(s) 898, 1284
RsaI GTAC 6 cut(s) 1095, 1107, 1116, 1200, 1268, 1327
RsaNI GTAC 6 cut(s) 1094, 1106, 1115, 1199, 1267, 1326
RseI CAYNNNNRTG 1 cut(s) 884
SaqAI TTAA 2 cut(s) 1254, 1289
SatI GCNGC 6 cut(s) 675, 696, 897, 1280, 1283, 1316
Sau3AI GATC 3 cut(s) 4, 562, 811
Sau96I GGNCC 1 cut(s) 1145
SchI GAGTC 2 cut(s) 278, 1345
ScrFI CCNGG 1 cut(s) 166
SduI GDGCHC 1 cut(s) 1251
SfaNI GCATC 2 cut(s) 343, 577
SfcI CTRYAG 2 cut(s) 894, 1280
SfuI TTCGAA 1 cut(s) 1182
SinI GGWCC 1 cut(s) 1145
SmiMI CAYNNNNRTG 1 cut(s) 884
SpeI ACTAGT 1 cut(s) 1174
SspMI CTAG 4 cut(s) 1136, 1175, 1310, 1358
StyD4I CCNGG 1 cut(s) 164
StyI CCWWGG 1 cut(s) 1206
TaiI ACGT 2 cut(s) 76, 957
TaqI TCGA 3 cut(s) 351, 434, 1182
TatI WGTACW 4 cut(s) 1093, 1105, 1198, 1325
TfiI GAWTC 5 cut(s) 28, 218, 1063, 1167, 1184
Tru1I TTAA 2 cut(s) 1254, 1289
Tru9I TTAA 2 cut(s) 1254, 1289
TseFI GTSAC 2 cut(s) 705, 797
TseI GCWGC 6 cut(s) 674, 695, 896, 1279, 1282, 1315
Tsp45I GTSAC 2 cut(s) 705, 797
Van91I CCANNNNNTGG 1 cut(s) 749
VpaK11BI GGWCC 1 cut(s) 1145
VspI ATTAAT 1 cut(s) 1289
XapI RAATTY 6 cut(s) 50, 436, 523, 835, 1070, 1193
XbaI TCTAGA 1 cut(s) 1357
XmnI GAANNNNTTC 1 cut(s) 485
XspI CTAG 4 cut(s) 1136, 1175, 1310, 1358
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.