Rmu_sc0002012.1_g000001

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0002012.1
OG0003630
Physical Location & Seq
Forward (+)
1 .. 3227
3227 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 1436 bp
acagctcagacagatacccttgggccttttcttcactatcatccagagtatctgcatcagtacgtagtctccgtctcacctccgccatgatgccttggcccgtcaacttgtgtagtgttaacgagtcaatgttgtgcctctggtcaaagtttgctggagaatgcctcggagggacaggacccttcggttatattgatggtaatactctttgtcctacaaagtatgtgatcactgatagtgagggagtaacaggtgagatcactgcagcctacaaaatatggaagaaaacagataaggctttgcttagtcttcttgttgcaacttcttgttactccctcactataacaggtgagatcactgcagcttacaaaatatggaagaaaacagataaggctttgcttagtcttcttgttgcaactttggacgatgaaataatggacattgtgctcaagattgaccttcaaacaatcaagaaaggaaatgattctattcagaggtacttgattcgtgtgaagcgtgcaagatatcagttagcttttgttggggttactatttcagatgaagacatagttgttgtgactctaaatgggctacctgcagaatatgcaatgattaaaactgtcatttattcccgagatactctcatccctctagaaaatctcaggtctcaattgttagctgctgagagagacattgaaggcattttcctaactcattctcacatgtcagcaatggtaacaagaagcaactctcaaagaactcatttttatgcttctgatgaagtagataacagagagaaatataagaacttgtctggaagtgacaaatgcaatggaagtagcttcaacagttggccttacaattccacattcaattccacatttcaaaacaattgtagcaacaaaggcaattcatttgcaggagaacagaatgtgataaataatggtcaaagtgatgtgcacttgcagttgcctccctatttttcacaagcttcaaataagaatggtctaatagctatggttgctcataataccttttcatctcatcttggttatgttgcaccaattgatgaaagtggaaaggatcttgtacattatgttggtagccaaattgccatcgtcccttccaaagatgatatcctttatacacaagtagactcaaatcataaagaccatatggtgttgtctcgagttggtcatctgcctattcactccaccatgattgaatcatctttgcaacctaagaccaatgctgcaacaagaaatggattctctgaaactgaaaatgacaaagacagaaaactagaggtgctttcaagggatgatgtttctccaaacacaactggtaaaggtggctccaagaagcgaaagtttgattcccctggagtagctgaaaacatctttaatagcgtggctactagcattgagcaggtctag
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 gag_pre-integrs rve

Protein Analysis

477

Amino Acids

52.65

Weight (kDa)

6.82

Isoelectric Point (pI)

39.34

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 88 - 229 5.9e-11 gag-polypeptide of LTR copia-type
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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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 2 cut(s) 603, 1419
AccI GTMKAC 1 cut(s) 1154
AciI CCGC 1 cut(s) 83
AclWI GGATC 1 cut(s) 1091
AfaI GTAC 3 cut(s) 62, 499, 1091
AflIII ACRYGT 1 cut(s) 722
AgsI TTSAA 8 cut(s) 463, 697, 846, 873, 886, 995, 1225, 1316
AjnI CCWGG 1 cut(s) 1380
AluBI AGCT 8 cut(s) 5, 364, 535, 679, 842, 991, 1015, 1390
AluI AGCT 8 cut(s) 5, 364, 535, 679, 842, 991, 1015, 1390
Alw21I GWGCWC 2 cut(s) 449, 962
Alw26I GTCTC 5 cut(s) 73, 79, 671, 683, 1190
Alw44I GTGCAC 1 cut(s) 958
AlwI GGATC 1 cut(s) 1091
Ama87I CYCGRG 2 cut(s) 632, 1187
AoxI GGCC 3 cut(s) 23, 97, 853
ApaLI GTGCAC 1 cut(s) 958
ApeKI GCWGC 4 cut(s) 265, 361, 679, 1252
Asp700I GAANNNNTTC 1 cut(s) 483
AspS9I GGNCC 3 cut(s) 23, 98, 178
AsuHPI GGTGA 3 cut(s) 69, 265, 361
AvaI CYCGRG 2 cut(s) 632, 1187
AvaII GGWCC 1 cut(s) 178
BaeGI GKGCMC 1 cut(s) 962
BbsI GAAGAC 3 cut(s) 301, 397, 569
Bbv12I GWGCWC 2 cut(s) 449, 962
BbvI GCAGC 4 cut(s) 277, 373, 666, 1239
BccI CCATC 2 cut(s) 190, 1123
BciT130I CCWGG 1 cut(s) 1382
BclI TGATCA 1 cut(s) 227
BcoDI GTCTC 5 cut(s) 73, 79, 671, 683, 1190
BfaI CTAG 4 cut(s) 652, 1303, 1418, 1434
BfmI CTRYAG 3 cut(s) 263, 359, 596
BfuAI ACCTGC 2 cut(s) 603, 1419
BisI GCNGC 4 cut(s) 266, 362, 680, 1253
BlsI GCNGC 4 cut(s) 267, 363, 681, 1254
Bme1390I CCNGG 1 cut(s) 1382
Bme18I GGWCC 1 cut(s) 178
BmeT110I CYCGRG 2 cut(s) 632, 1187
BmgT120I GGNCC 3 cut(s) 23, 98, 178
BmiI GGNNCC 2 cut(s) 180, 1356
BmrFI CCNGG 1 cut(s) 1382
BmsI GCATC 2 cut(s) 64, 80
BpiI GAAGAC 3 cut(s) 301, 397, 569
BplI GAGNNNNNCTC 4 cut(s) 149, 181, 626, 658
BpmI CTGGAG 2 cut(s) 176, 1403
BpuEI CTTGAG 1 cut(s) 433
BsaAI YACGTR 1 cut(s) 64
BsaI GGTCTC 1 cut(s) 671
BsaJI CCNNGG 4 cut(s) 19, 94, 165, 1380
BsaXI ACNNNNNCTCC 2 cut(s) 53, 83
Bse1I ACTGG 1 cut(s) 1347
Bse3DI GCAATG 3 cut(s) 614, 737, 837
BseBI CCWGG 1 cut(s) 1382
BseDI CCNNGG 4 cut(s) 19, 94, 165, 1380
BseGI GGATG 3 cut(s) 40, 644, 1326
BseMI GCAATG 3 cut(s) 614, 737, 837
BseMII CTCAG 3 cut(s) 20, 674, 675
BseNI ACTGG 1 cut(s) 1347
BseSI GKGCMC 1 cut(s) 962
BseXI GCAGC 4 cut(s) 277, 373, 666, 1239
BshFI GGCC 3 cut(s) 25, 99, 855
BsiHKAI GWGCWC 2 cut(s) 449, 962
BsiHKCI CYCGRG 2 cut(s) 632, 1187
BslFI GGGAC 2 cut(s) 186, 1105
BsmAI GTCTC 5 cut(s) 73, 79, 671, 683, 1190
BsmBI CGTCTC 1 cut(s) 79
BsmFI GGGAC 2 cut(s) 186, 1105
BsmI GAATGC 1 cut(s) 166
BsnI GGCC 3 cut(s) 25, 99, 855
Bso31I GGTCTC 1 cut(s) 671
BsoBI CYCGRG 2 cut(s) 632, 1187
Bsp1286I GDGCHC 2 cut(s) 449, 962
Bsp1407I TGTACA 1 cut(s) 1089
Bsp143I GATC 4 cut(s) 227, 257, 353, 1083
BspACI CCGC 1 cut(s) 83
BspANI GGCC 3 cut(s) 25, 99, 855
BspCNI CTCAG 3 cut(s) 19, 674, 675
BspLI GGNNCC 2 cut(s) 180, 1356
BspMAI CTGCAG 3 cut(s) 267, 363, 600
BspMI ACCTGC 2 cut(s) 603, 1419
BspPI GGATC 1 cut(s) 1091
BspTNI GGTCTC 1 cut(s) 671
BsrDI GCAATG 3 cut(s) 614, 737, 837
BsrGI TGTACA 1 cut(s) 1089
BsrI ACTGG 1 cut(s) 1347
BssECI CCNNGG 4 cut(s) 19, 94, 165, 1380
BssMI GATC 4 cut(s) 227, 257, 353, 1083
BssT1I CCWWGG 2 cut(s) 19, 94
Bst2UI CCWGG 1 cut(s) 1382
Bst4CI ACNGT 2 cut(s) 621, 850
BstAPI GCANNNNNTGC 1 cut(s) 604
BstAUI TGTACA 1 cut(s) 1089
BstBAI YACGTR 1 cut(s) 64
BstC8I GCNNGC 1 cut(s) 518
BstDEI CTNAG 6 cut(s) 6, 304, 400, 661, 683, 1241
BstF5I GGATG 3 cut(s) 40, 644, 1326
BstKTI GATC 4 cut(s) 230, 260, 356, 1086
BstMAI GTCTC 5 cut(s) 73, 79, 671, 683, 1190
BstMBI GATC 4 cut(s) 227, 257, 353, 1083
BstMWI GCNNNNNNNGC 3 cut(s) 604, 905, 1021
BstNI CCWGG 1 cut(s) 1382
BstNSI RCATGY 1 cut(s) 726
BstSCI CCNGG 1 cut(s) 1380
BstSFI CTRYAG 3 cut(s) 263, 359, 596
BstSLI GKGCMC 1 cut(s) 962
BstSNI TACGTA 1 cut(s) 64
BstV1I GCAGC 4 cut(s) 277, 373, 666, 1239
BstV2I GAAGAC 3 cut(s) 301, 397, 569
BstX2I RGATCY 1 cut(s) 1083
BstYI RGATCY 1 cut(s) 1083
BsuRI GGCC 3 cut(s) 25, 99, 855
BtsCI GGATG 3 cut(s) 40, 644, 1326
BtsI GCAGTG 2 cut(s) 260, 356
BtsIMutI CAGTG 3 cut(s) 230, 260, 356
BveI ACCTGC 2 cut(s) 603, 1419
Cac8I GCNNGC 1 cut(s) 518
Cfr13I GGNCC 3 cut(s) 23, 98, 178
Csp6I GTAC 3 cut(s) 61, 498, 1090
CspCI CAANNNNNGTGG 2 cut(s) 1203, 1238
CviAII CATG 3 cut(s) 87, 723, 1218
CviQI GTAC 3 cut(s) 61, 498, 1090
DdeI CTNAG 6 cut(s) 6, 304, 400, 661, 683, 1241
DpnI GATC 4 cut(s) 229, 259, 355, 1085
DpnII GATC 4 cut(s) 227, 257, 353, 1083
EciI GGCGGA 1 cut(s) 72
Eco105I TACGTA 1 cut(s) 64
Eco130I CCWWGG 2 cut(s) 19, 94
Eco31I GGTCTC 1 cut(s) 671
Eco32I GATATC 2 cut(s) 526, 1137
Eco47I GGWCC 1 cut(s) 178
Eco88I CYCGRG 2 cut(s) 632, 1187
EcoO109I RGGNCCY 1 cut(s) 178
EcoRII CCWGG 1 cut(s) 1380
EcoRV GATATC 2 cut(s) 526, 1137
EcoT14I CCWWGG 2 cut(s) 19, 94
ErhI CCWWGG 2 cut(s) 19, 94
Esp3I CGTCTC 1 cut(s) 79
FaeI CATG 3 cut(s) 90, 726, 1221
FaqI GGGAC 2 cut(s) 186, 1105
FatI CATG 3 cut(s) 86, 722, 1217
FauNDI CATATG 1 cut(s) 1175
FbaI TGATCA 1 cut(s) 227
FblI GTMKAC 1 cut(s) 1154
Fnu4HI GCNGC 4 cut(s) 266, 362, 680, 1253
FokI GGATG 3 cut(s) 27, 631, 1333
Fsp4HI GCNGC 4 cut(s) 266, 362, 680, 1253
FspBI CTAG 4 cut(s) 652, 1303, 1418, 1434
GluI GCNGC 4 cut(s) 266, 362, 680, 1253
GsuI CTGGAG 2 cut(s) 176, 1403
HaeIII GGCC 3 cut(s) 25, 99, 855
Hin1II CATG 3 cut(s) 90, 726, 1221
HincII GTYRAC 2 cut(s) 105, 120
HindII GTYRAC 2 cut(s) 105, 120
HindIII AAGCTT 1 cut(s) 989
HinfI GANTC 8 cut(s) 124, 484, 504, 579, 1156, 1225, 1268, 1375
HpaI GTTAAC 1 cut(s) 120
HphI GGTGA 3 cut(s) 69, 265, 361
Hpy166II GTNNAC 4 cut(s) 105, 120, 960, 1155
Hpy188I TCNGA 6 cut(s) 9, 169, 494, 558, 777, 1275
Hpy188III TCNNGA 7 cut(s) 44, 450, 471, 632, 652, 815, 1187
Hpy8I GTNNAC 4 cut(s) 105, 120, 960, 1155
HpyAV CCTTC 4 cut(s) 192, 469, 691, 1133
HpyCH4III ACNGT 2 cut(s) 621, 850
HpyCH4IV ACGT 1 cut(s) 63
HpyF10VI GCNNNNNNNGC 3 cut(s) 604, 905, 1021
HpyF3I CTNAG 6 cut(s) 6, 304, 400, 661, 683, 1241
HpySE526I ACGT 1 cut(s) 63
Hsp92II CATG 3 cut(s) 90, 726, 1221
Ksp22I TGATCA 1 cut(s) 227
KspAI GTTAAC 1 cut(s) 120
Kzo9I GATC 4 cut(s) 227, 257, 353, 1083
LmnI GCTCC 1 cut(s) 1360
Lsp1109I GCAGC 4 cut(s) 277, 373, 666, 1239
LweI GCATC 2 cut(s) 64, 80
MaeI CTAG 4 cut(s) 652, 1303, 1418, 1434
MaeII ACGT 1 cut(s) 63
MaeIII GTNAC 6 cut(s) 246, 328, 546, 576, 735, 820
MalI GATC 4 cut(s) 229, 259, 355, 1085
MboI GATC 4 cut(s) 227, 257, 353, 1083
MboII GAAGA 6 cut(s) 23, 294, 301, 390, 397, 574
MfeI CAATTG 3 cut(s) 670, 891, 1064
MflI RGATCY 1 cut(s) 1083
MhlI GDGCHC 2 cut(s) 449, 962
MluCI AATT 7 cut(s) 670, 861, 873, 891, 909, 1064, 1109
MlyI GAGTC 3 cut(s) 133, 573, 1150
MroXI GAANNNNTTC 1 cut(s) 483
MseI TTAA 3 cut(s) 119, 614, 1403
MslI CAYNNNNRTG 1 cut(s) 767
MspR9I CCNGG 1 cut(s) 1382
MunI CAATTG 3 cut(s) 670, 891, 1064
Mva1269I GAATGC 1 cut(s) 166
MvaI CCWGG 1 cut(s) 1382
MwoI GCNNNNNNNGC 3 cut(s) 604, 905, 1021
NdeI CATATG 1 cut(s) 1175
NdeII GATC 4 cut(s) 227, 257, 353, 1083
NlaIII CATG 3 cut(s) 90, 726, 1221
NlaIV GGNNCC 2 cut(s) 180, 1356
NmuCI GTSAC 2 cut(s) 576, 820
NspI RCATGY 1 cut(s) 726
PaeR7I CTCGAG 1 cut(s) 1187
PciI ACATGT 1 cut(s) 722
PcsI WCGNNNNNNNCGW 2 cut(s) 69, 513
PctI GAATGC 1 cut(s) 166
PdmI GAANNNNTTC 1 cut(s) 483
PfeI GAWTC 5 cut(s) 484, 504, 1225, 1268, 1375
PkrI GCNGC 4 cut(s) 267, 363, 681, 1254
PleI GAGTC 3 cut(s) 132, 573, 1150
PpsI GAGTC 3 cut(s) 132, 573, 1150
Ppu21I YACGTR 1 cut(s) 64
PpuMI RGGWCCY 1 cut(s) 178
PscI ACATGT 1 cut(s) 722
Psp5II RGGWCCY 1 cut(s) 178
Psp6I CCWGG 1 cut(s) 1380
PspGI CCWGG 1 cut(s) 1380
PspN4I GGNNCC 2 cut(s) 180, 1356
PspPI GGNCC 3 cut(s) 23, 98, 178
PspPPI RGGWCCY 1 cut(s) 178
PstI CTGCAG 3 cut(s) 267, 363, 600
PsuI RGATCY 1 cut(s) 1083
RsaI GTAC 3 cut(s) 62, 499, 1091
RsaNI GTAC 3 cut(s) 61, 498, 1090
RseI CAYNNNNRTG 1 cut(s) 767
SaqAI TTAA 3 cut(s) 119, 614, 1403
SatI GCNGC 4 cut(s) 266, 362, 680, 1253
Sau3AI GATC 4 cut(s) 227, 257, 353, 1083
Sau96I GGNCC 3 cut(s) 23, 98, 178
SchI GAGTC 3 cut(s) 133, 573, 1150
ScrFI CCNGG 1 cut(s) 1382
SduI GDGCHC 2 cut(s) 449, 962
SfaNI GCATC 2 cut(s) 64, 80
SfcI CTRYAG 3 cut(s) 263, 359, 596
Sfr274I CTCGAG 1 cut(s) 1187
SinI GGWCC 1 cut(s) 178
SlaI CTCGAG 1 cut(s) 1187
SmiMI CAYNNNNRTG 1 cut(s) 767
SmlI CTYRAG 2 cut(s) 448, 1187
SmoI CTYRAG 2 cut(s) 448, 1187
SnaBI TACGTA 1 cut(s) 64
Sse9I AATT 7 cut(s) 670, 861, 873, 891, 909, 1064, 1109
SsiI CCGC 1 cut(s) 83
SspMI CTAG 4 cut(s) 652, 1303, 1418, 1434
StyD4I CCNGG 1 cut(s) 1380
StyI CCWWGG 2 cut(s) 19, 94
TaaI ACNGT 2 cut(s) 621, 850
TaiI ACGT 1 cut(s) 66
TaqI TCGA 1 cut(s) 1188
TasI AATT 7 cut(s) 670, 861, 873, 891, 909, 1064, 1109
TatI WGTACW 1 cut(s) 1089
TfiI GAWTC 5 cut(s) 484, 504, 1225, 1268, 1375
Tru1I TTAA 3 cut(s) 119, 614, 1403
Tru9I TTAA 3 cut(s) 119, 614, 1403
TscAI CASTG 3 cut(s) 237, 267, 363
TseFI GTSAC 2 cut(s) 576, 820
TseI GCWGC 4 cut(s) 265, 361, 679, 1252
Tsp45I GTSAC 2 cut(s) 576, 820
TspDTI ATGAA 6 cut(s) 443, 575, 794, 902, 1028, 1085
TspGWI ACGGA 1 cut(s) 61
TspRI CASTG 3 cut(s) 237, 267, 363
VneI GTGCAC 1 cut(s) 958
VpaK11BI GGWCC 1 cut(s) 178
XbaI TCTAGA 1 cut(s) 651
XceI RCATGY 1 cut(s) 726
XhoI CTCGAG 1 cut(s) 1187
XmiI GTMKAC 1 cut(s) 1154
XmnI GAANNNNTTC 1 cut(s) 483
XspI CTAG 4 cut(s) 652, 1303, 1418, 1434
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.