Rw7G032600

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_wichuraiana
Chr7
OG0000258
Physical Location & Seq
Forward (+)
47419384 .. 47420715
1332 bp
Loading structure...
UTR
Exon/CDS
Intron
Rw7G032600.1

Sequence Viewer

Length: 1332 bp
ATGGCTGGTGACGATGTTGATGTTACTGGAAATGATAAGGGAAAAGGAATGGCTATTGCTGCACCTGTGTTGATTCCTCCTTCCTCCACTCATGGGGAGAAACCCGAGAAATTTAGTGGGACAAACTTCAAATGCTGGCAGCAAAAGATGTTGTTCTTCCTCACTACTCTGAACTTGGCCAAATTTCTGAAAGAAAGTGCTCCTGCATCAGGAAGCACTGCAGAAGAGGCTGCTACTGTAGACGCATGGCATCATTCAGATTTTCTATGCAAGAATTACATTCTTAATGGATTGGACATTGTACTTTACAAAGTGTACAGTCCAATAAAGAATGCTAAAAGCTTGTGGGAGTCTTTAGAAAAGAAATACAAGACCGAAGATGCTGGAGCAAAGAAATATATAATCGGTCGTTTCCTTGACTACAAGATGGTAGATACTAAAACTGTACTCAGTCAAGTTGAGGAGTTTCAATTGATTCTACATGAGATGGCTACAGAAAATCTGTCAATTAATGAAACTTTGCAAGTGGGATGTATTATTGAGAAACTTCCTCCATCTTGGAAGAATTTCAAGAATTATCTCAAGCATAAGCGCAAGGAGATGGATCTTGAGGGTCTAATTGTGAGGCTACGGGTTGAGGAAGGCAATCGCATATCTGACAAGAGAAGTGATGCTAGTTCTATGATGGCCAAGTTACTTGTCATGGAAGATGAACCACAAAACAAAAATAAGAAGAGAAAGTTCTCTGGGAAAAATTATAAGCCAGGAAACTCAAAAAAGTTCAAAGGCAAGTGTTTCAATTGTAATAAGACAGGTCATCGTGCTATGGAATGTCATAGCAAGAAAAACAAAGGCTACAAGAAAGCCACTGAAGCAAACATGACTGAGGGAGATAGATTGTCTGTTGACATTGCTGATATGAACCTTTTAGCCATGGTGACTGAAGTCAATATGATAACAAGCGCCGAAGAATGGTGGATAGACACAGGGGCTACTTGCCATATATGTTTTGATAAGAAGATGTTCTCTACCTATGCGGAAGTAAATCAAGGAGAGCAATTATTCATGGGCAATGCTTCCACATCAATGGTTCAAGGCACTGGTAATATTGTTTTAAAGTTGATATCTGGGAAAGAAATTACTTTAAACAATGTACTTCATGTGCCTGATATTCGAAAGAATTTAATCTCTGGTTCGATGTTGATCAAAAATGGATTTCGTGTGATCTTTGAAGTTGATAAAGTCATACTTACCAAGAACGGGATATATGTAGGAAAAGGTTATCTCAGTAATGGCCTTTTCAAGATATGCTCCCAAGAAGTCCACTACTAG
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

443

Amino Acids

49.86

Weight (kDa)

9.03

Isoelectric Point (pI)

29.23

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 52 - 220 2.4e-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
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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)
AanI TTATAA 1 cut(s) 759
AccI GTMKAC 1 cut(s) 240
AciI CCGC 1 cut(s) 1037
AclWI GGATC 1 cut(s) 612
AcoI YGGCCR 2 cut(s) 177, 687
AcsI RAATTY 4 cut(s) 110, 182, 565, 1180
AcuI CTGAAG 2 cut(s) 891, 963
AfaI GTAC 4 cut(s) 303, 317, 447, 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 3 cut(s) 59, 139, 230
ApoI RAATTY 4 cut(s) 110, 182, 565, 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 3 cut(s) 46, 151, 217
BccI CCATC 5 cut(s) 421, 481, 562, 595, 679
BciT130I CCWGG 1 cut(s) 765
BclI TGATCA 1 cut(s) 1203
BfaI CTAG 2 cut(s) 675, 1330
BfmI CTRYAG 3 cut(s) 219, 237, 492
BfoI RGCGCY 1 cut(s) 966
BisI GCNGC 3 cut(s) 60, 140, 231
BlsI GCNGC 3 cut(s) 61, 141, 232
Bme1390I CCNGG 1 cut(s) 765
BmeT110I CYCGRG 1 cut(s) 104
BmrFI CCNGG 1 cut(s) 765
BmsI GCATC 4 cut(s) 215, 259, 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 1 cut(s) 933
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 1 cut(s) 933
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 3 cut(s) 46, 151, 217
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 1 cut(s) 223
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 1 cut(s) 933
BssMI GATC 3 cut(s) 604, 1203, 1224
BssT1I CCWWGG 1 cut(s) 933
Bst2UI CCWGG 1 cut(s) 765
Bst4CI ACNGT 3 cut(s) 238, 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, 227, 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 3 cut(s) 46, 151, 217
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 4 cut(s) 302, 316, 446, 1154
CviAII CATG 8 cut(s) 92, 246, 482, 703, 880, 934, 1066, 1160
CviQI GTAC 4 cut(s) 302, 316, 446, 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 1 cut(s) 933
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 1 cut(s) 933
ErhI CCWWGG 1 cut(s) 933
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
FblI GTMKAC 1 cut(s) 240
Fnu4HI GCNGC 3 cut(s) 60, 140, 231
FokI GGATG 1 cut(s) 543
Fsp4HI GCNGC 3 cut(s) 60, 140, 231
FspBI CTAG 2 cut(s) 675, 1330
GlaI GCGC 2 cut(s) 593, 964
GluI GCNGC 3 cut(s) 60, 140, 231
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 4 cut(s) 241, 316, 907, 1324
Hpy188I TCNGA 4 cut(s) 171, 189, 259, 658
Hpy188III TCNNGA 4 cut(s) 210, 571, 608, 1303
Hpy8I GTNNAC 4 cut(s) 241, 316, 907, 1324
HpyAV CCTTC 2 cut(s) 90, 635
HpyCH4III ACNGT 3 cut(s) 238, 320, 445
HpyCH4V TGCA 5 cut(s) 62, 206, 221, 270, 523
HpyF10VI GCNNNNNNNGC 3 cut(s) 59, 227, 872
HpyF3I CTNAG 3 cut(s) 449, 885, 1286
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 3 cut(s) 46, 151, 217
LweI GCATC 4 cut(s) 215, 259, 370, 661
MaeI CTAG 2 cut(s) 675, 1330
MaeIII GTNAC 4 cut(s) 8, 22, 693, 937
MalI GATC 3 cut(s) 606, 1205, 1226
MboI GATC 3 cut(s) 604, 1203, 1224
MboII GAAGA 8 cut(s) 148, 236, 389, 574, 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, 227, 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
PctI GAATGC 1 cut(s) 337
PdmI GAANNNNTTC 2 cut(s) 566, 1022
PfeI GAWTC 2 cut(s) 73, 475
PkrI GCNGC 3 cut(s) 61, 141, 232
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 1 cut(s) 223
PsuI RGATCY 1 cut(s) 604
RsaI GTAC 4 cut(s) 303, 317, 447, 1155
RsaNI GTAC 4 cut(s) 302, 316, 446, 1154
RseI CAYNNNNRTG 1 cut(s) 1085
SaqAI TTAA 5 cut(s) 285, 510, 1115, 1145, 1184
SatI GCNGC 3 cut(s) 60, 140, 231
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
SetI ASST 6 cut(s) 67, 344, 817, 927, 1034, 1282
SfaNI GCATC 4 cut(s) 215, 259, 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 2 cut(s) 675, 1330
StyD4I CCNGG 1 cut(s) 763
StyI CCWWGG 1 cut(s) 933
TaaI ACNGT 3 cut(s) 238, 320, 445
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 3 cut(s) 59, 139, 230
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 4 cut(s) 110, 182, 565, 1180
XmiI GTMKAC 1 cut(s) 240
XmnI GAANNNNTTC 2 cut(s) 566, 1022
XspI CTAG 2 cut(s) 675, 1330
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.