RchiOBHm_Chr5g0055681

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0018150
Physical Location & Seq
Reverse (-)
58987521 .. 58990970
3450 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ33264

Sequence Viewer

Length: 1467 bp
ATGCAACTCGAGACAAATCTACATACATTACAGAAAAATGATGATTCTATAGACAAGTATCTTCAACGTGTCAAACATGCTAGAGACGAGTTGGCTTTTGTAGGTGTGCACTTTGCTGATGAAGACATTATGATCATAGCTCTCAACGGCTTGCCTCCCGAGTATAATAACATCAGAGTGGTCATTAAAGCCATGGACAGATCTGTCTCTATGGAAGAGTTTCGTTCTCAATTGTTGACTGTTGAGAGAGATTTTGAGAAAATGGTGCTTCAAACAACTCAAAATACCATTTCTGCTATGGTTGCTCATACTGAACAGTCTGCTCGAAGGTTCAATGAGAGCTCTTCCAATGCTGGCAATTACAGCAACAGTTTCTCTCAAAATGTGCAATATGGAATGTCACATACTGGAATGTCATCTCGGTATACTGGTGATTGTTCTACGGCACCTGTTTTACACAATGCTACATCAAATGTTGGTTTCTTGCCTAATGTTACCAATACTAGTGTGCTATCTGGTATATCTGCTTATAATCGTTTCACCACATCATCTTCTGGTTCCAATGTTCATCATCATTATTCTCCATCACCTATTTCCACTACACATTTTGGGATGCCACAGAACAAAATAATATCAAGCTCAATTCATAATGTTCCTACTGCTGCCCCAAACTGTCAAGAAATTGTTCCACTCACTCAAAGTATTGGTATTTCACAATCTGCACCTACTTCTGGATATTTGTTGAGCAACAATGTTGGAAATGGAACTTTATATTCAGCATCCCCTCCACCTTGTGTTTATGCAACAGAGAATGGTAATTCTATGATTCAAAATGGTGGTCAAATGGTTCAAAATGGTGGCTATGTTTCTTTTCCTCAGCACAATTATTCTCAGAAGCAAGGATTCTCTAATAACAGTGGCACATACAGTAATGCACCAATGCAACAAGGTTCTTTCTCACAGGGACCAAATATTTCATCCTCTCAAGGCAAGTGTAACATTCAAAAGGAGAATTTGAGCAACAATGGGAATTATCACAGTGAGACTTTCAATGGTAAATTCACCTGTAGGAGCTTTGGTAACAAAGGAAACAGAAGCTTTGGTGATAATAAGAGGAGAGATGATAGAGGAAGGAACAATGGTAACAATGTTTCTAGTGGTTACAGCAGTGGAAACAATGTTATACCAGAGTGCCAGATTTGTCGCAAGAGAGGACATACAACAGTCATTTGCTACTGGAGGTCTGACAATAATGCTTCACCCTCTATTGTTGATTGTCAAATTTGTGGGAAAAGAGGGCACGTTTCTTCTGTTTGTCATCAGCGATCCAACAGCTCTTTTCTCTGTGCTGCTCCTCCACCTACATTCACTGCCATGAATGTTCTGGCAACTATTGAGCATTGCTGCAATCTCAGTGTGCTTACCCCCACTGAGATTGAGGGGAGGTGTTACCAGAACCAAGCCTAG
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
RVT_2 Retrotran_gag_2

Protein Analysis

488

Amino Acids

53.28

Weight (kDa)

8.3

Isoelectric Point (pI)

51.55

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 5 - 84 5.7e-09 gag-polypeptide of LTR copia-type
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

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AanI TTATAA 1 cut(s) 531
AasI GACNNNNNNGTC 1 cut(s) 203
AccB1I GGYRCC 1 cut(s) 445
AccI GTMKAC 1 cut(s) 425
AclWI GGATC 1 cut(s) 1320
AcsI RAATTY 3 cut(s) 1012, 1058, 1281
AdeI CACNNNGTG 1 cut(s) 794
AfiI CCNNNNNNNGG 1 cut(s) 731
AflIII ACRYGT 1 cut(s) 67
AgsI TTSAA 7 cut(s) 65, 272, 334, 830, 851, 1004, 1051
AhlI ACTAGT 1 cut(s) 503
AluBI AGCT 6 cut(s) 140, 342, 639, 1074, 1098, 1335
AluI AGCT 6 cut(s) 140, 342, 639, 1074, 1098, 1335
Alw21I GWGCWC 2 cut(s) 111, 344
Alw26I GTCTC 4 cut(s) 5, 78, 211, 1037
Alw44I GTGCAC 1 cut(s) 107
AlwI GGATC 1 cut(s) 1320
Ama87I CYCGRG 2 cut(s) 8, 158
ApaLI GTGCAC 1 cut(s) 107
ApeKI GCWGC 3 cut(s) 662, 1349, 1404
ApoI RAATTY 3 cut(s) 1012, 1058, 1281
ArsI GACNNNNNNTTYG 2 cut(s) 823, 855
Asp700I GAANNNNTTC 2 cut(s) 219, 684
AspS9I GGNCC 1 cut(s) 965
AsuHPI GGTGA 6 cut(s) 443, 532, 579, 1054, 1115, 1251
AvaI CYCGRG 2 cut(s) 8, 158
AvaII GGWCC 1 cut(s) 965
BaeGI GKGCMC 2 cut(s) 111, 1302
BanI GGYRCC 1 cut(s) 445
BanII GRGCYC 1 cut(s) 344
BbsI GAAGAC 1 cut(s) 129
Bbv12I GWGCWC 2 cut(s) 111, 344
BbvCI CCTCAGC 1 cut(s) 876
BbvI GCAGC 3 cut(s) 649, 1336, 1391
BccI CCATC 1 cut(s) 592
BceAI ACGGC 2 cut(s) 163, 459
BclI TGATCA 1 cut(s) 132
BcoDI GTCTC 4 cut(s) 5, 78, 211, 1037
BcuI ACTAGT 1 cut(s) 503
BfaI CTAG 4 cut(s) 81, 504, 1155, 1465
BfmI CTRYAG 2 cut(s) 48, 1066
BglII AGATCT 1 cut(s) 200
BisI GCNGC 3 cut(s) 663, 1350, 1405
BlsI GCNGC 3 cut(s) 664, 1351, 1406
Bme18I GGWCC 1 cut(s) 965
BmeT110I CYCGRG 2 cut(s) 8, 158
BmgT120I GGNCC 1 cut(s) 965
BmiI GGNNCC 3 cut(s) 447, 559, 966
BmsI GCATC 2 cut(s) 603, 788
BpiI GAAGAC 1 cut(s) 129
BpmI CTGGAG 1 cut(s) 1258
Bpu10I CCTNAGC 1 cut(s) 876
BpuEI CTTGAG 1 cut(s) 969
BsaJI CCNNGG 1 cut(s) 192
BsaXI ACNNNNNCTCC 2 cut(s) 1063, 1093
Bsc4I CCNNNNNNNGG 1 cut(s) 731
Bse1I ACTGG 3 cut(s) 412, 433, 1241
Bse3DI GCAATG 1 cut(s) 1399
BseDI CCNNGG 1 cut(s) 192
BseGI GGATG 3 cut(s) 618, 779, 977
BseLI CCNNNNNNNGG 1 cut(s) 731
BseMI GCAATG 1 cut(s) 1399
BseMII CTCAG 4 cut(s) 890, 905, 1422, 1426
BseNI ACTGG 3 cut(s) 412, 433, 1241
BseRI GAGGAG 2 cut(s) 1129, 1344
BseSI GKGCMC 2 cut(s) 111, 1302
BseXI GCAGC 3 cut(s) 649, 1336, 1391
BsgI GTGCAG 1 cut(s) 705
BshNI GGYRCC 1 cut(s) 445
BsiHKAI GWGCWC 2 cut(s) 111, 344
BsiHKCI CYCGRG 2 cut(s) 8, 158
BslFI GGGAC 1 cut(s) 978
BslI CCNNNNNNNGG 1 cut(s) 731
BsmAI GTCTC 4 cut(s) 5, 78, 211, 1037
BsmBI CGTCTC 1 cut(s) 78
BsmFI GGGAC 1 cut(s) 978
BsoBI CYCGRG 2 cut(s) 8, 158
Bsp1286I GDGCHC 3 cut(s) 111, 344, 1302
Bsp143I GATC 3 cut(s) 132, 200, 1325
Bsp19I CCATGG 1 cut(s) 192
BspCNI CTCAG 4 cut(s) 889, 904, 1423, 1425
BspLI GGNNCC 3 cut(s) 447, 559, 966
BspPI GGATC 1 cut(s) 1320
BspQI GCTCTTC 1 cut(s) 349
BspT107I GGYRCC 1 cut(s) 445
BsrDI GCAATG 1 cut(s) 1399
BsrI ACTGG 3 cut(s) 412, 433, 1241
BssECI CCNNGG 1 cut(s) 192
BssMI GATC 3 cut(s) 132, 200, 1325
BssNAI GTATAC 1 cut(s) 426
BssT1I CCWWGG 1 cut(s) 192
Bst1107I GTATAC 1 cut(s) 426
Bst4CI ACNGT 8 cut(s) 241, 318, 371, 674, 917, 929, 1040, 1225
Bst6I CTCTTC 2 cut(s) 210, 349
BstC8I GCNNGC 2 cut(s) 152, 355
BstDEI CTNAG 4 cut(s) 876, 891, 1412, 1431
BstDSI CCRYGG 1 cut(s) 192
BstF5I GGATG 3 cut(s) 618, 779, 977
BstKTI GATC 3 cut(s) 135, 203, 1328
BstMAI GTCTC 4 cut(s) 5, 78, 211, 1037
BstMBI GATC 3 cut(s) 132, 200, 1325
BstMWI GCNNNNNNNGC 2 cut(s) 302, 363
BstNSI RCATGY 1 cut(s) 80
BstSFI CTRYAG 2 cut(s) 48, 1066
BstSLI GKGCMC 2 cut(s) 111, 1302
BstV1I GCAGC 3 cut(s) 649, 1336, 1391
BstV2I GAAGAC 1 cut(s) 129
BstX2I RGATCY 1 cut(s) 200
BstYI RGATCY 1 cut(s) 200
BstZ17I GTATAC 1 cut(s) 426
BtgI CCRYGG 1 cut(s) 192
BtsCI GGATG 3 cut(s) 618, 779, 977
BtsI GCAGTG 2 cut(s) 1174, 1368
BtsIMutI CAGTG 6 cut(s) 922, 1045, 1174, 1368, 1420, 1428
Cac8I GCNNGC 2 cut(s) 152, 355
Cfr13I GGNCC 1 cut(s) 965
CspCI CAANNNNNGTGG 2 cut(s) 1417, 1452
CviAII CATG 3 cut(s) 77, 193, 1375
DdeI CTNAG 4 cut(s) 876, 891, 1412, 1431
DpnI GATC 3 cut(s) 134, 202, 1327
DpnII GATC 3 cut(s) 132, 200, 1325
DraIII CACNNNGTG 1 cut(s) 794
DrdI GACNNNNNNGTC 1 cut(s) 203
DseDI GACNNNNNNGTC 1 cut(s) 203
Eam1104I CTCTTC 2 cut(s) 210, 349
EarI CTCTTC 2 cut(s) 210, 349
Ecl136II GAGCTC 1 cut(s) 342
Eco130I CCWWGG 1 cut(s) 192
Eco24I GRGCYC 1 cut(s) 344
Eco47I GGWCC 1 cut(s) 965
Eco53kI GAGCTC 1 cut(s) 342
Eco88I CYCGRG 2 cut(s) 8, 158
EcoICRI GAGCTC 1 cut(s) 342
EcoT14I CCWWGG 1 cut(s) 192
EcoT38I GRGCYC 1 cut(s) 344
ErhI CCWWGG 1 cut(s) 192
Esp3I CGTCTC 1 cut(s) 78
FaeI CATG 3 cut(s) 80, 196, 1378
FaqI GGGAC 1 cut(s) 978
FatI CATG 3 cut(s) 76, 192, 1374
FbaI TGATCA 1 cut(s) 132
FblI GTMKAC 1 cut(s) 425
Fnu4HI GCNGC 3 cut(s) 663, 1350, 1405
FokI GGATG 3 cut(s) 625, 766, 964
FriOI GRGCYC 1 cut(s) 344
Fsp4HI GCNGC 3 cut(s) 663, 1350, 1405
FspBI CTAG 4 cut(s) 81, 504, 1155, 1465
GluI GCNGC 3 cut(s) 663, 1350, 1405
GsuI CTGGAG 1 cut(s) 1258
Hin1II CATG 3 cut(s) 80, 196, 1378
HincII GTYRAC 1 cut(s) 237
HindII GTYRAC 1 cut(s) 237
HindIII AAGCTT 1 cut(s) 1096
HinfI GANTC 3 cut(s) 44, 826, 903
HphI GGTGA 6 cut(s) 443, 532, 579, 1054, 1115, 1251
Hpy166II GTNNAC 3 cut(s) 109, 237, 426
Hpy188I TCNGA 3 cut(s) 176, 894, 1246
Hpy188III TCNNGA 4 cut(s) 10, 158, 677, 732
Hpy8I GTNNAC 3 cut(s) 109, 237, 426
HpyAV CCTTC 2 cut(s) 321, 1125
HpyCH4III ACNGT 8 cut(s) 241, 318, 371, 674, 917, 929, 1040, 1225
HpyCH4IV ACGT 2 cut(s) 67, 1302
HpyCH4V TGCA 8 cut(s) 4, 109, 388, 722, 803, 935, 943, 1407
HpyF10VI GCNNNNNNNGC 2 cut(s) 302, 363
HpyF3I CTNAG 4 cut(s) 876, 891, 1412, 1431
HpySE526I ACGT 2 cut(s) 67, 1302
Hsp92II CATG 3 cut(s) 80, 196, 1378
Ksp22I TGATCA 1 cut(s) 132
Kzo9I GATC 3 cut(s) 132, 200, 1325
LguI GCTCTTC 1 cut(s) 349
LmnI GCTCC 2 cut(s) 1071, 1357
Lsp1109I GCAGC 3 cut(s) 649, 1336, 1391
LweI GCATC 2 cut(s) 603, 788
MaeI CTAG 4 cut(s) 81, 504, 1155, 1465
MaeII ACGT 2 cut(s) 67, 1302
MaeIII GTNAC 7 cut(s) 399, 493, 995, 1079, 1142, 1160, 1448
MalI GATC 3 cut(s) 134, 202, 1327
MboI GATC 3 cut(s) 132, 200, 1325
MboII GAAGA 6 cut(s) 53, 134, 227, 336, 543, 1299
MfeI CAATTG 1 cut(s) 230
MflI RGATCY 1 cut(s) 200
MhlI GDGCHC 3 cut(s) 111, 344, 1302
MmeI TCCRAC 2 cut(s) 736, 1353
MroXI GAANNNNTTC 2 cut(s) 219, 684
MseI TTAA 1 cut(s) 186
MslI CAYNNNNRTG 2 cut(s) 176, 1373
MunI CAATTG 1 cut(s) 230
MwoI GCNNNNNNNGC 2 cut(s) 302, 363
NcoI CCATGG 1 cut(s) 192
NdeII GATC 3 cut(s) 132, 200, 1325
NlaIII CATG 3 cut(s) 80, 196, 1378
NlaIV GGNNCC 3 cut(s) 447, 559, 966
NmuCI GTSAC 1 cut(s) 399
NspI RCATGY 1 cut(s) 80
PaeR7I CTCGAG 1 cut(s) 8
PciSI GCTCTTC 1 cut(s) 349
PdmI GAANNNNTTC 2 cut(s) 219, 684
PfeI GAWTC 3 cut(s) 44, 826, 903
PkrI GCNGC 3 cut(s) 664, 1351, 1406
PsiI TTATAA 1 cut(s) 531
Psp124BI GAGCTC 1 cut(s) 344
PspN4I GGNNCC 3 cut(s) 447, 559, 966
PspPI GGNCC 1 cut(s) 965
PsuI RGATCY 1 cut(s) 200
RseI CAYNNNNRTG 2 cut(s) 176, 1373
SacI GAGCTC 1 cut(s) 344
SapI GCTCTTC 1 cut(s) 349
SaqAI TTAA 1 cut(s) 186
SatI GCNGC 3 cut(s) 663, 1350, 1405
Sau3AI GATC 3 cut(s) 132, 200, 1325
Sau96I GGNCC 1 cut(s) 965
SduI GDGCHC 3 cut(s) 111, 344, 1302
SfaNI GCATC 2 cut(s) 603, 788
SfcI CTRYAG 2 cut(s) 48, 1066
Sfr274I CTCGAG 1 cut(s) 8
SinI GGWCC 1 cut(s) 965
SlaI CTCGAG 1 cut(s) 8
SmiMI CAYNNNNRTG 2 cut(s) 176, 1373
SmlI CTYRAG 2 cut(s) 8, 984
SmoI CTYRAG 2 cut(s) 8, 984
SpeI ACTAGT 1 cut(s) 503
SspI AATATT 1 cut(s) 973
SspMI CTAG 4 cut(s) 81, 504, 1155, 1465
SstI GAGCTC 1 cut(s) 344
StyI CCWWGG 1 cut(s) 192
TaaI ACNGT 8 cut(s) 241, 318, 371, 674, 917, 929, 1040, 1225
TaiI ACGT 2 cut(s) 70, 1305
TaqI TCGA 2 cut(s) 9, 325
TfiI GAWTC 3 cut(s) 44, 826, 903
Tru1I TTAA 1 cut(s) 186
Tru9I TTAA 1 cut(s) 186
TscAI CASTG 6 cut(s) 922, 1045, 1174, 1375, 1420, 1435
TseFI GTSAC 1 cut(s) 399
TseI GCWGC 3 cut(s) 662, 1349, 1404
Tsp45I GTSAC 1 cut(s) 399
TspDTI ATGAA 5 cut(s) 135, 557, 635, 966, 1391
TspRI CASTG 6 cut(s) 922, 1045, 1174, 1375, 1420, 1435
VneI GTGCAC 1 cut(s) 107
VpaK11BI GGWCC 1 cut(s) 965
XapI RAATTY 3 cut(s) 1012, 1058, 1281
XceI RCATGY 1 cut(s) 80
XcmI CCANNNNNNNNNTGG 2 cut(s) 295, 1381
XhoI CTCGAG 1 cut(s) 8
XmiI GTMKAC 1 cut(s) 425
XmnI GAANNNNTTC 2 cut(s) 219, 684
XspI CTAG 4 cut(s) 81, 504, 1155, 1465
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.