Rw5G002350

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr5
OG0000258
Physical Location & Seq
Reverse (-)
2024903 .. 2026243
1341 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw5G002350.1

Sequence Viewer

Length: 1341 bp
ATGGCTGGTGACGATGCTGACGTTACTGGAAATGATAAGGGAAAAGGAATGGCTATTGCTGCACCTGTGTTGATTCCTCCTTCCTCCACTCATGGGGAGAAACCCGAGAAATTTAGTGGGACAAACTTCAAATGCTGGCAGCAAAAGATGTTGTTCTACCTCACTACTCTGAACTTGGCCAAATTTCTGAAAGAAAGTGCTCCTGCATCAGGAAGCACTGCAGAAGAGGTTGCTGCTGCAGACGCATGGTATCATTCAGATTTTCTATGCAAGAATTACATTCTTAATGGATTGGACATTGTACTTTACAAAGTGTACAGTCCAATAAAGAATGCTAAAAGCTTGTGGGAGTCTTTAGAAAAGAAATACAAGACCGAAGATGCTGGAGCAAAGAAATATATAATCGGTCGTTTCCTTGACTACAAGATGGTAGATACTAAAACTGTACTCAGTCAAGTTGAGGAGTTTCAATTGATTCTACATGAGATGGCTGCAGAAAATCTGTCAATTAATGAAACTTTGCAAGTGGGATGTATTATTGAGAAACTTCCTCCATCTTGGAAGGATTTCAAGAATTATCTCAAGCATAAGCGCAAGGAGATGGATCTTGAGGGTCTAATTGTGAGGCTACGGGTTGAGGAAGGCAATCGCATATCTGACAAGAGAAGTGATGCTAGTTCTATGATGGCCAAGGTACTTGTCATGGAAGATGAACCACAAAACAAAAATAAGAAGAGAAAGTTCTCTGGGAAAAATTATAAGCCAGGAAACTCAAAGAAGTTCAAAGGCAAGTGTTTCAATTGTAATAAGACAGGTCATCGTGCTATGGAATGTCATAGCAAGAAAAACAAAGGCTACAAGAAAGCCACTGAAGCAAACATGACTGAGGGAGATAGATTGTCTGTTGACATTGCTGATATGAACCTTTCAGCCATGGTGACTGAAGTCAATATGATAACAAGCGCCGAAGAATGGTGGATAGACACAGGGGCTACTTGCCATATATGTTTTGATAAGAAGATGTTCTCTACCTATGCGGAAGTAAATCAAGGAGAGCAATTATTCATGGGCAATGCTTCCACATCAATGGTTCAAGGCACTGGTAATATTGTTTTAAAGTTGATATCTGGCAAAGAAATTACTTTAAACAATGTACTTCATGTGCCTGATATTCGAAAGAATTTAATCTCTGGTTCGATGTTGATCAAAAATGGATTTCGTGTGATCTTTGAAGTTGATAAAGTCATACTTACCAAGAACGGGATATATGTAGGAAAAGGTTATCTCAGTAATGGCCTTTTCAAGATATGCTCCCAAGAAGTCCAAGGAAAGAGTATCTAA
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

446

Amino Acids

49.99

Weight (kDa)

9.02

Isoelectric Point (pI)

28.43

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 50 - 220 6.3e-25 gag-polypeptide of LTR copia-type
Pol_BBD PF22936 325 - 406 3.2e-25 Pol polyprotein, beta-barrel domain
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: 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)
AanI TTATAA 1 cut(s) 759
AciI CCGC 1 cut(s) 1037
AclWI GGATC 1 cut(s) 612
AcoI YGGCCR 2 cut(s) 177, 687
AcsI RAATTY 3 cut(s) 110, 182, 1180
AcuI CTGAAG 2 cut(s) 891, 963
AfaI GTAC 5 cut(s) 303, 317, 447, 696, 1155
AfiI CCNNNNNNNGG 4 cut(s) 93, 209, 972, 1260
AgsI TTSAA 8 cut(s) 130, 470, 571, 784, 799, 1094, 1232, 1303
AjnI CCWGG 1 cut(s) 763
AluBI AGCT 1 cut(s) 342
AluI AGCT 1 cut(s) 342
Alw21I GWGCWC 1 cut(s) 202
AlwI GGATC 1 cut(s) 612
Ama87I CYCGRG 1 cut(s) 104
AoxI GGCC 3 cut(s) 177, 687, 1294
ApeKI GCWGC 5 cut(s) 59, 139, 233, 236, 491
ApoI RAATTY 3 cut(s) 110, 182, 1180
AseI ATTAAT 1 cut(s) 510
Asp700I GAANNNNTTC 2 cut(s) 566, 1022
AspLEI GCGC 2 cut(s) 594, 965
AsuHPI GGTGA 2 cut(s) 20, 949
AsuII TTCGAA 1 cut(s) 1174
AvaI CYCGRG 1 cut(s) 104
BalI TGGCCA 2 cut(s) 179, 689
Bbv12I GWGCWC 1 cut(s) 202
BbvI GCAGC 5 cut(s) 46, 151, 220, 223, 478
BccI CCATC 5 cut(s) 421, 481, 562, 595, 679
BciT130I CCWGG 1 cut(s) 765
BclI TGATCA 1 cut(s) 1203
BfaI CTAG 1 cut(s) 675
BfmI CTRYAG 3 cut(s) 219, 237, 492
BfoI RGCGCY 1 cut(s) 966
BisI GCNGC 5 cut(s) 60, 140, 234, 237, 492
BlsI GCNGC 5 cut(s) 61, 141, 235, 238, 493
Bme1390I CCNGG 1 cut(s) 765
BmeT110I CYCGRG 1 cut(s) 104
BmrFI CCNGG 1 cut(s) 765
BmsI GCATC 4 cut(s) 4, 215, 370, 661
BoxI GACNNNNGTC 1 cut(s) 944
BpmI CTGGAG 1 cut(s) 405
Bpu14I TTCGAA 1 cut(s) 1174
BpuEI CTTGAG 2 cut(s) 566, 629
BsaBI GATNNNNATC 1 cut(s) 1202
BsaJI CCNNGG 3 cut(s) 690, 933, 1324
Bsc4I CCNNNNNNNGG 4 cut(s) 93, 209, 972, 1260
Bse1I ACTGG 2 cut(s) 31, 1105
Bse3DI GCAATG 2 cut(s) 909, 1078
Bse8I GATNNNNATC 1 cut(s) 1202
BseBI CCWGG 1 cut(s) 765
BseDI CCNNGG 3 cut(s) 690, 933, 1324
BseGI GGATG 1 cut(s) 536
BseJI GATNNNNATC 1 cut(s) 1202
BseLI CCNNNNNNNGG 4 cut(s) 93, 209, 972, 1260
BseMI GCAATG 2 cut(s) 909, 1078
BseMII CTCAG 3 cut(s) 463, 876, 1300
BseNI ACTGG 2 cut(s) 31, 1105
BseRI GAGGAG 1 cut(s) 476
BseXI GCAGC 5 cut(s) 46, 151, 220, 223, 478
BsgI GTGCAG 1 cut(s) 45
Bsh1285I CGRYCG 1 cut(s) 409
BshFI GGCC 3 cut(s) 179, 689, 1296
BsiEI CGRYCG 1 cut(s) 409
BsiHKAI GWGCWC 1 cut(s) 202
BsiHKCI CYCGRG 1 cut(s) 104
BslFI GGGAC 1 cut(s) 133
BslI CCNNNNNNNGG 4 cut(s) 93, 209, 972, 1260
BsmFI GGGAC 1 cut(s) 133
BsmI GAATGC 1 cut(s) 337
BsnI GGCC 3 cut(s) 179, 689, 1296
BsoBI CYCGRG 1 cut(s) 104
Bsp119I TTCGAA 1 cut(s) 1174
Bsp1286I GDGCHC 1 cut(s) 202
Bsp1407I TGTACA 1 cut(s) 315
Bsp143I GATC 3 cut(s) 604, 1203, 1224
Bsp19I CCATGG 1 cut(s) 933
BspACI CCGC 1 cut(s) 1037
BspANI GGCC 3 cut(s) 179, 689, 1296
BspCNI CTCAG 3 cut(s) 462, 877, 1299
BspMAI CTGCAG 3 cut(s) 223, 241, 496
BspPI GGATC 1 cut(s) 612
BspT104I TTCGAA 1 cut(s) 1174
BsrDI GCAATG 2 cut(s) 909, 1078
BsrGI TGTACA 1 cut(s) 315
BsrI ACTGG 2 cut(s) 31, 1105
BssECI CCNNGG 3 cut(s) 690, 933, 1324
BssMI GATC 3 cut(s) 604, 1203, 1224
BssT1I CCWWGG 3 cut(s) 690, 933, 1324
Bst2UI CCWGG 1 cut(s) 765
Bst4CI ACNGT 2 cut(s) 320, 445
Bst6I CTCTTC 2 cut(s) 219, 728
BstAUI TGTACA 1 cut(s) 315
BstBI TTCGAA 1 cut(s) 1174
BstC8I GCNNGC 1 cut(s) 137
BstDEI CTNAG 3 cut(s) 449, 885, 1286
BstDSI CCRYGG 1 cut(s) 933
BstENI CCTNNNNNAGG 1 cut(s) 207
BstF5I GGATG 1 cut(s) 536
BstH2I RGCGCY 1 cut(s) 966
BstHHI GCGC 2 cut(s) 594, 965
BstKTI GATC 3 cut(s) 607, 1206, 1227
BstMBI GATC 3 cut(s) 604, 1203, 1224
BstMCI CGRYCG 1 cut(s) 409
BstMWI GCNNNNNNNGC 3 cut(s) 59, 242, 872
BstNI CCWGG 1 cut(s) 765
BstPAI GACNNNNGTC 1 cut(s) 944
BstSCI CCNGG 1 cut(s) 763
BstSFI CTRYAG 3 cut(s) 219, 237, 492
BstV1I GCAGC 5 cut(s) 46, 151, 220, 223, 478
BstX2I RGATCY 1 cut(s) 604
BstXI CCANNNNNNTGG 1 cut(s) 1087
BstYI RGATCY 1 cut(s) 604
BsuRI GGCC 3 cut(s) 179, 689, 1296
BtgI CCRYGG 1 cut(s) 933
BtsCI GGATG 1 cut(s) 536
BtsI GCAGTG 1 cut(s) 216
BtsIMutI CAGTG 3 cut(s) 216, 867, 1098
Cac8I GCNNGC 1 cut(s) 137
CfoI GCGC 2 cut(s) 594, 965
CseI GACGC 1 cut(s) 251
Csp6I GTAC 5 cut(s) 302, 316, 446, 695, 1154
CviAII CATG 8 cut(s) 92, 246, 482, 703, 880, 934, 1066, 1160
CviQI GTAC 5 cut(s) 302, 316, 446, 695, 1154
DdeI CTNAG 3 cut(s) 449, 885, 1286
DpnI GATC 3 cut(s) 606, 1205, 1226
DpnII GATC 3 cut(s) 604, 1203, 1224
DraI TTTAAA 2 cut(s) 1116, 1146
EaeI YGGCCR 2 cut(s) 177, 687
Eam1104I CTCTTC 2 cut(s) 219, 728
EarI CTCTTC 2 cut(s) 219, 728
Eco130I CCWWGG 3 cut(s) 690, 933, 1324
Eco32I GATATC 1 cut(s) 1125
Eco57I CTGAAG 2 cut(s) 891, 963
Eco88I CYCGRG 1 cut(s) 104
EcoNI CCTNNNNNAGG 1 cut(s) 207
EcoRII CCWGG 1 cut(s) 763
EcoRV GATATC 1 cut(s) 1125
EcoT14I CCWWGG 3 cut(s) 690, 933, 1324
ErhI CCWWGG 3 cut(s) 690, 933, 1324
FaeI CATG 8 cut(s) 95, 249, 485, 706, 883, 937, 1069, 1163
FalI AAGNNNNNCTT 2 cut(s) 1233, 1265
FaqI GGGAC 1 cut(s) 133
FatI CATG 8 cut(s) 91, 245, 481, 702, 879, 933, 1065, 1159
FbaI TGATCA 1 cut(s) 1203
Fnu4HI GCNGC 5 cut(s) 60, 140, 234, 237, 492
FokI GGATG 1 cut(s) 543
Fsp4HI GCNGC 5 cut(s) 60, 140, 234, 237, 492
FspBI CTAG 1 cut(s) 675
GlaI GCGC 2 cut(s) 593, 964
GluI GCNGC 5 cut(s) 60, 140, 234, 237, 492
GsuI CTGGAG 1 cut(s) 405
HaeII RGCGCY 1 cut(s) 966
HaeIII GGCC 3 cut(s) 179, 689, 1296
HgaI GACGC 1 cut(s) 251
HhaI GCGC 2 cut(s) 594, 965
Hin1II CATG 8 cut(s) 95, 249, 485, 706, 883, 937, 1069, 1163
Hin6I GCGC 2 cut(s) 592, 963
HinP1I GCGC 2 cut(s) 592, 963
HincII GTYRAC 1 cut(s) 907
HindII GTYRAC 1 cut(s) 907
HindIII AAGCTT 1 cut(s) 340
HinfI GANTC 3 cut(s) 73, 350, 475
HphI GGTGA 2 cut(s) 20, 949
Hpy166II GTNNAC 2 cut(s) 316, 907
Hpy188I TCNGA 4 cut(s) 171, 189, 259, 658
Hpy188III TCNNGA 4 cut(s) 210, 571, 608, 1303
Hpy8I GTNNAC 2 cut(s) 316, 907
HpyAV CCTTC 3 cut(s) 90, 556, 635
HpyCH4III ACNGT 2 cut(s) 320, 445
HpyCH4IV ACGT 1 cut(s) 21
HpyCH4V TGCA 7 cut(s) 62, 206, 221, 239, 270, 494, 523
HpyF10VI GCNNNNNNNGC 3 cut(s) 59, 242, 872
HpyF3I CTNAG 3 cut(s) 449, 885, 1286
HpySE526I ACGT 1 cut(s) 21
Hsp92II CATG 8 cut(s) 95, 249, 485, 706, 883, 937, 1069, 1163
HspAI GCGC 2 cut(s) 592, 963
Ksp22I TGATCA 1 cut(s) 1203
Kzo9I GATC 3 cut(s) 604, 1203, 1224
LmnI GCTCC 3 cut(s) 205, 386, 1316
Lsp1109I GCAGC 5 cut(s) 46, 151, 220, 223, 478
LweI GCATC 4 cut(s) 4, 215, 370, 661
MaeI CTAG 1 cut(s) 675
MaeII ACGT 1 cut(s) 21
MaeIII GTNAC 3 cut(s) 8, 22, 937
MalI GATC 3 cut(s) 606, 1205, 1226
MboI GATC 3 cut(s) 604, 1203, 1224
MboII GAAGA 6 cut(s) 236, 389, 719, 745, 980, 1030
MfeI CAATTG 2 cut(s) 470, 799
MflI RGATCY 1 cut(s) 604
MhlI GDGCHC 1 cut(s) 202
MlsI TGGCCA 2 cut(s) 179, 689
MluNI TGGCCA 2 cut(s) 179, 689
MlyI GAGTC 1 cut(s) 359
Mox20I TGGCCA 2 cut(s) 179, 689
MroXI GAANNNNTTC 2 cut(s) 566, 1022
MscI TGGCCA 2 cut(s) 179, 689
MseI TTAA 5 cut(s) 285, 510, 1115, 1145, 1184
MslI CAYNNNNRTG 1 cut(s) 1085
Msp20I TGGCCA 2 cut(s) 179, 689
MspR9I CCNGG 1 cut(s) 765
MunI CAATTG 2 cut(s) 470, 799
Mva1269I GAATGC 1 cut(s) 337
MvaI CCWGG 1 cut(s) 765
MwoI GCNNNNNNNGC 3 cut(s) 59, 242, 872
NcoI CCATGG 1 cut(s) 933
NdeII GATC 3 cut(s) 604, 1203, 1224
NlaIII CATG 8 cut(s) 95, 249, 485, 706, 883, 937, 1069, 1163
NmuCI GTSAC 2 cut(s) 8, 937
NspV TTCGAA 1 cut(s) 1174
PcsI WCGNNNNNNNCGW 1 cut(s) 18
PctI GAATGC 1 cut(s) 337
PdmI GAANNNNTTC 2 cut(s) 566, 1022
PfeI GAWTC 2 cut(s) 73, 475
PkrI GCNGC 5 cut(s) 61, 141, 235, 238, 493
PleI GAGTC 1 cut(s) 358
PpsI GAGTC 1 cut(s) 358
PshAI GACNNNNGTC 1 cut(s) 944
PshBI ATTAAT 1 cut(s) 510
PsiI TTATAA 1 cut(s) 759
Psp6I CCWGG 1 cut(s) 763
PspGI CCWGG 1 cut(s) 763
PstI CTGCAG 3 cut(s) 223, 241, 496
PsuI RGATCY 1 cut(s) 604
RsaI GTAC 5 cut(s) 303, 317, 447, 696, 1155
RsaNI GTAC 5 cut(s) 302, 316, 446, 695, 1154
RseI CAYNNNNRTG 1 cut(s) 1085
SaqAI TTAA 5 cut(s) 285, 510, 1115, 1145, 1184
SatI GCNGC 5 cut(s) 60, 140, 234, 237, 492
Sau3AI GATC 3 cut(s) 604, 1203, 1224
SchI GAGTC 1 cut(s) 359
ScrFI CCNGG 1 cut(s) 765
SduI GDGCHC 1 cut(s) 202
SfaNI GCATC 4 cut(s) 4, 215, 370, 661
SfcI CTRYAG 3 cut(s) 219, 237, 492
SfuI TTCGAA 1 cut(s) 1174
SmiMI CAYNNNNRTG 1 cut(s) 1085
SmlI CTYRAG 2 cut(s) 581, 608
SmoI CTYRAG 2 cut(s) 581, 608
SsiI CCGC 1 cut(s) 1037
SspI AATATT 1 cut(s) 1108
SspMI CTAG 1 cut(s) 675
StyD4I CCNGG 1 cut(s) 763
StyI CCWWGG 3 cut(s) 690, 933, 1324
TaaI ACNGT 2 cut(s) 320, 445
TaiI ACGT 1 cut(s) 24
TaqI TCGA 2 cut(s) 1174, 1196
TaqII GACCGA 2 cut(s) 389, 395
TatI WGTACW 4 cut(s) 301, 315, 445, 1153
TfiI GAWTC 2 cut(s) 73, 475
Tru1I TTAA 5 cut(s) 285, 510, 1115, 1145, 1184
Tru9I TTAA 5 cut(s) 285, 510, 1115, 1145, 1184
TscAI CASTG 3 cut(s) 223, 874, 1105
TseFI GTSAC 2 cut(s) 8, 937
TseI GCWGC 5 cut(s) 59, 139, 233, 236, 491
Tsp45I GTSAC 2 cut(s) 8, 937
TspDTI ATGAA 5 cut(s) 528, 726, 935, 1054, 1148
TspRI CASTG 3 cut(s) 223, 874, 1105
VspI ATTAAT 1 cut(s) 510
XagI CCTNNNNNAGG 1 cut(s) 207
XapI RAATTY 3 cut(s) 110, 182, 1180
XmnI GAANNNNTTC 2 cut(s) 566, 1022
XspI CTAG 1 cut(s) 675
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.