RchiOBHm_Chr3g0448951

GAG-pre-integrase domain

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
3
OG0018861
Physical Location & Seq
Forward (+)
957246 .. 959734
2489 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ41637

Sequence Viewer

Length: 1620 bp
ATGGCAACCTCATGTCAACATTGCAATGCGGTCTCTGTGCGGCTAGATGAGACAAATTACCCAACTTGGGTATTTCAGATGCAACATCATCTAAGGGGGCATGGTCTACTGAAATTAGTGAATGGAACTCATCCATGTCCTCCAGAATTCATTGCTGGCACTGATGGTTCTCTCACAGAAAATACCGAAGCTTATGAAAAATGGTTGCAACAAGATAGTTTTGTTATCTCTAAGATTACCAACACTCTCTCTGCTGAGGCTCTTATATTGGTAATTGGCTGTGAAACTTCAATGGAGGTATGGACCACTCTCAAACAGCAATTTGCACCAAATTCTGAATTTCACATTATGCGATTGAAGTATACTTTGCAAAATATCCGAAAAGGATCAGATTCTATTGACAAATATTTGTTGCGATTTATAAATGTCAGAAATCATTTAGCTGTTGTTGGTGTTAGTATGTCAGATCAGGATATCAAAATGCTGATTTTAGCTGGCCTTCCTAATGAATATGCTCACACTAGGCAAATTATCAGAGGGAAAGATCATATTACTATGGCAGAAGTGAGGTCATTGCTTTTATCTGCTGAGTTTGAATTGGAATTAGAGCAAAAAGGTCCTCCTTTCTCACCAATGAATGCAATGGTAGCAAATAATGTCGGCTATGTTGGAACTTCCCCTAGATTTAGTTCAAATGAAGTTGCATGTTCTGTACCTAATGCACCTTCTGGGTTCATTGTTGCCACTCCTGGACCAATTATTGCCTCATCTACATCATACATGCCTACTGGTGTCACTCCACAAGTTGGTGTGTTTTCAAACAATGCTTATGTTCAATCACAAGCCAATACAGTTCCGAACAATTACCCTCAGTTTCCAAACAACAACAATTCAAGGAATGGAGGCAATAACAATATAAACAGCAACTCAGGGAGCTACTTCAAACCAAGGTTTAACTCAAATCAAGGTCCACTGAAATGCCAAATTTGTGAGAAGCCTGGACATAGTGCTTATAAATGCTTTCAGAGAAACCCACATAAACAAGGTGAAGCCTCTAGCTCTACTGTTGAATGTCATATTTGCAAGAAATCAGGCCATACTACAAAAACTTGCAGGTACAGAGTCAATAATCAAAATGGGAATACTGTAATGGATGCCTGCACTGATAATGCATCTGTTCATGAAGTTTGGCTAGTTGGCATGCAGAAGCAACGTGATGAATGTGCACCAACTATTTTTGAAAGAAGAATCGCTGATAATGATGATAAAATGGTGGAAGTAGGAGCAGCTGTAAATGCAGCAGATTTCCATAGGCACTACTATGGTATTCAACCACCAACTTGTGCAGCACCTAAAGCTTTGTCTGCTGCCATCTGCACTCAACCAAAGCCACCGTCCATTGCTACTCAACCAAATACCAATGCTTCTCAATCACAAGTTGTCAAGCCTCTGCCATTTGCATTTTCTCTATTATCAGTTCCTACTTGCCCTCGTTTGCAGCAAACTCTCCTTAAGAAAATTGAAGCTTTTCCGTCACCAGGCACTTGGCTACTTCCTTCTAATCCGGACAGACATCTAATGAATTGTAGGCAAACTTGTGAGTCTACTAATTTGTGGTAA
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

539

Amino Acids

59.55

Weight (kDa)

8.46

Isoelectric Point (pI)

43.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 27 - 197 4.1e-22 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 2 cut(s) 422, 1014
Acc36I ACCTGC 1 cut(s) 1104
AccB7I CCANNNNNTGG 1 cut(s) 806
AccI GTMKAC 3 cut(s) 106, 362, 1604
AccIII TCCGGA 1 cut(s) 1564
AciI CCGC 2 cut(s) 29, 40
AclWI GGATC 1 cut(s) 394
AcsI RAATTY 4 cut(s) 146, 331, 338, 984
AfaI GTAC 2 cut(s) 714, 1118
AfiI CCNNNNNNNGG 3 cut(s) 67, 806, 1538
AflII CTTAAG 1 cut(s) 1511
AjnI CCWGG 3 cut(s) 748, 997, 1537
AluBI AGCT 8 cut(s) 191, 443, 494, 936, 1059, 1289, 1358, 1526
AluI AGCT 8 cut(s) 191, 443, 494, 936, 1059, 1289, 1358, 1526
Alw21I GWGCWC 1 cut(s) 1228
Alw26I GTCTC 2 cut(s) 37, 44
Alw44I GTGCAC 1 cut(s) 1224
AlwI GGATC 1 cut(s) 394
Aor13HI TCCGGA 1 cut(s) 1564
AoxI GGCC 2 cut(s) 496, 1093
ApaLI GTGCAC 1 cut(s) 1224
ApeKI GCWGC 5 cut(s) 1286, 1298, 1346, 1367, 1498
ApoI RAATTY 4 cut(s) 146, 331, 338, 984
ArsI GACNNNNNNTTYG 2 cut(s) 1379, 1411
Asp700I GAANNNNTTC 1 cut(s) 1527
AspS9I GGNCC 4 cut(s) 303, 617, 752, 968
AsuHPI GGTGA 3 cut(s) 621, 1058, 1527
AvaII GGWCC 4 cut(s) 303, 617, 752, 968
BaeGI GKGCMC 1 cut(s) 1228
Bbv12I GWGCWC 1 cut(s) 1228
BbvCI CCTCAGC 1 cut(s) 255
BbvI GCAGC 5 cut(s) 1298, 1310, 1354, 1358, 1510
BccI CCATC 2 cut(s) 158, 1379
BciT130I CCWGG 3 cut(s) 750, 999, 1539
BcoDI GTCTC 2 cut(s) 37, 44
BfaI CTAG 5 cut(s) 44, 522, 681, 1056, 1193
BfrI CTTAAG 1 cut(s) 1511
BfuAI ACCTGC 1 cut(s) 1104
BisI GCNGC 6 cut(s) 41, 1287, 1299, 1347, 1368, 1499
BlsI GCNGC 6 cut(s) 42, 1288, 1300, 1348, 1369, 1500
Bme1390I CCNGG 3 cut(s) 750, 999, 1539
Bme18I GGWCC 4 cut(s) 303, 617, 752, 968
BmgT120I GGNCC 4 cut(s) 303, 617, 752, 968
BmrFI CCNGG 3 cut(s) 750, 999, 1539
BmsI GCATC 3 cut(s) 69, 1144, 1181
BpmI CTGGAG 1 cut(s) 126
Bpu10I CCTNAGC 1 cut(s) 255
BsaI GGTCTC 1 cut(s) 37
BsaJI CCNNGG 1 cut(s) 947
BsaWI WCCGGW 1 cut(s) 1564
BsaXI ACNNNNNCTCC 2 cut(s) 1275, 1305
Bsc4I CCNNNNNNNGG 3 cut(s) 67, 806, 1538
Bse1I ACTGG 1 cut(s) 793
Bse3DI GCAATG 6 cut(s) 19, 31, 150, 572, 648, 1398
BseAI TCCGGA 1 cut(s) 1564
BseBI CCWGG 3 cut(s) 750, 999, 1539
BseDI CCNNGG 1 cut(s) 947
BseGI GGATG 2 cut(s) 130, 1159
BseLI CCNNNNNNNGG 3 cut(s) 67, 806, 1538
BseMI GCAATG 6 cut(s) 19, 31, 150, 572, 648, 1398
BseMII CTCAG 4 cut(s) 246, 579, 884, 942
BseNI ACTGG 1 cut(s) 793
BseSI GKGCMC 1 cut(s) 1228
BseXI GCAGC 5 cut(s) 1298, 1310, 1354, 1358, 1510
BsgI GTGCAG 3 cut(s) 1144, 1360, 1365
BshFI GGCC 2 cut(s) 498, 1095
BsiHKAI GWGCWC 1 cut(s) 1228
BsiSI CCGG 1 cut(s) 1565
BslI CCNNNNNNNGG 3 cut(s) 67, 806, 1538
BsmAI GTCTC 2 cut(s) 37, 44
BsmI GAATGC 1 cut(s) 643
BsnI GGCC 2 cut(s) 498, 1095
Bso31I GGTCTC 1 cut(s) 37
Bsp1286I GDGCHC 1 cut(s) 1228
Bsp13I TCCGGA 1 cut(s) 1564
Bsp143I GATC 3 cut(s) 386, 466, 544
BspACI CCGC 2 cut(s) 29, 40
BspANI GGCC 2 cut(s) 498, 1095
BspCNI CTCAG 4 cut(s) 247, 580, 883, 941
BspEI TCCGGA 1 cut(s) 1564
BspHI TCATGA 1 cut(s) 1180
BspMI ACCTGC 1 cut(s) 1104
BspPI GGATC 1 cut(s) 394
BspTI CTTAAG 1 cut(s) 1511
BspTNI GGTCTC 1 cut(s) 37
BsrDI GCAATG 6 cut(s) 19, 31, 150, 572, 648, 1398
BsrI ACTGG 1 cut(s) 793
BssECI CCNNGG 1 cut(s) 947
BssMI GATC 3 cut(s) 386, 466, 544
BssNAI GTATAC 1 cut(s) 363
BssT1I CCWWGG 1 cut(s) 947
Bst1107I GTATAC 1 cut(s) 363
Bst2UI CCWGG 3 cut(s) 750, 999, 1539
Bst4CI ACNGT 4 cut(s) 853, 1066, 1147, 1395
BstAFI CTTAAG 1 cut(s) 1511
BstC8I GCNNGC 4 cut(s) 157, 496, 1159, 1202
BstDEI CTNAG 6 cut(s) 92, 231, 255, 588, 870, 928
BstF5I GGATG 2 cut(s) 130, 1159
BstKTI GATC 3 cut(s) 389, 469, 547
BstMAI GTCTC 2 cut(s) 37, 44
BstMBI GATC 3 cut(s) 386, 466, 544
BstMWI GCNNNNNNNGC 4 cut(s) 647, 1295, 1355, 1364
BstNI CCWGG 3 cut(s) 750, 999, 1539
BstNSI RCATGY 3 cut(s) 708, 784, 1204
BstSCI CCNGG 3 cut(s) 748, 997, 1537
BstSLI GKGCMC 1 cut(s) 1228
BstV1I GCAGC 5 cut(s) 1298, 1310, 1354, 1358, 1510
BstXI CCANNNNNNTGG 1 cut(s) 1545
BstZ17I GTATAC 1 cut(s) 363
BsuRI GGCC 2 cut(s) 498, 1095
BtsCI GGATG 2 cut(s) 130, 1159
BtsIMutI CAGTG 3 cut(s) 159, 971, 1161
BveI ACCTGC 1 cut(s) 1104
Cac8I GCNNGC 4 cut(s) 157, 496, 1159, 1202
CciI TCATGA 1 cut(s) 1180
Cfr13I GGNCC 4 cut(s) 303, 617, 752, 968
Csp6I GTAC 2 cut(s) 713, 1117
CviAII CATG 7 cut(s) 12, 101, 135, 705, 781, 1181, 1201
CviQI GTAC 2 cut(s) 713, 1117
DdeI CTNAG 6 cut(s) 92, 231, 255, 588, 870, 928
DpnI GATC 3 cut(s) 388, 468, 546
DpnII GATC 3 cut(s) 386, 466, 544
Eco130I CCWWGG 1 cut(s) 947
Eco31I GGTCTC 1 cut(s) 37
Eco32I GATATC 1 cut(s) 475
Eco47I GGWCC 4 cut(s) 303, 617, 752, 968
EcoO109I RGGNCCY 1 cut(s) 617
EcoRI GAATTC 1 cut(s) 146
EcoRII CCWGG 3 cut(s) 748, 997, 1537
EcoRV GATATC 1 cut(s) 475
EcoT14I CCWWGG 1 cut(s) 947
EcoT22I ATGCAT 1 cut(s) 1174
ErhI CCWWGG 1 cut(s) 947
FaeI CATG 7 cut(s) 15, 104, 138, 708, 784, 1184, 1204
FatI CATG 7 cut(s) 11, 100, 134, 704, 780, 1180, 1200
FblI GTMKAC 3 cut(s) 106, 362, 1604
Fnu4HI GCNGC 6 cut(s) 41, 1287, 1299, 1347, 1368, 1499
FokI GGATG 2 cut(s) 117, 1166
Fsp4HI GCNGC 6 cut(s) 41, 1287, 1299, 1347, 1368, 1499
FspBI CTAG 5 cut(s) 44, 522, 681, 1056, 1193
GluI GCNGC 6 cut(s) 41, 1287, 1299, 1347, 1368, 1499
GsuI CTGGAG 1 cut(s) 126
HaeIII GGCC 2 cut(s) 498, 1095
HapII CCGG 1 cut(s) 1565
Hin1II CATG 7 cut(s) 15, 104, 138, 708, 784, 1184, 1204
HincII GTYRAC 1 cut(s) 17
HindII GTYRAC 1 cut(s) 17
HindIII AAGCTT 3 cut(s) 189, 1356, 1524
HinfI GANTC 4 cut(s) 392, 1122, 1248, 1601
HpaII CCGG 1 cut(s) 1565
HphI GGTGA 3 cut(s) 621, 1058, 1527
Hpy166II GTNNAC 6 cut(s) 17, 107, 363, 971, 1226, 1605
Hpy188I TCNGA 9 cut(s) 78, 337, 380, 391, 431, 466, 536, 858, 1026
Hpy188III TCNNGA 4 cut(s) 143, 470, 1181, 1565
Hpy8I GTNNAC 6 cut(s) 17, 107, 363, 971, 1226, 1605
HpyAV CCTTC 3 cut(s) 509, 735, 1566
HpyCH4III ACNGT 4 cut(s) 853, 1066, 1147, 1395
HpyCH4IV ACGT 1 cut(s) 1213
HpyF10VI GCNNNNNNNGC 4 cut(s) 647, 1295, 1355, 1364
HpyF3I CTNAG 6 cut(s) 92, 231, 255, 588, 870, 928
HpySE526I ACGT 1 cut(s) 1213
Hsp92II CATG 7 cut(s) 15, 104, 138, 708, 784, 1184, 1204
Kpn2I TCCGGA 1 cut(s) 1564
Kzo9I GATC 3 cut(s) 386, 466, 544
LmnI GCTCC 2 cut(s) 933, 1283
Lsp1109I GCAGC 5 cut(s) 1298, 1310, 1354, 1358, 1510
LweI GCATC 3 cut(s) 69, 1144, 1181
MaeI CTAG 5 cut(s) 44, 522, 681, 1056, 1193
MaeII ACGT 1 cut(s) 1213
MaeIII GTNAC 2 cut(s) 793, 1533
MalI GATC 3 cut(s) 388, 468, 546
MboI GATC 3 cut(s) 386, 466, 544
MboII GAAGA 1 cut(s) 1257
MhlI GDGCHC 1 cut(s) 1228
MlyI GAGTC 2 cut(s) 1131, 1610
MmeI TCCRAC 1 cut(s) 649
Mph1103I ATGCAT 1 cut(s) 1174
MroI TCCGGA 1 cut(s) 1564
MroXI GAANNNNTTC 1 cut(s) 1527
MseI TTAA 2 cut(s) 954, 1512
MslI CAYNNNNRTG 3 cut(s) 24, 976, 1320
MspA1I CMGCKG 1 cut(s) 1289
MspCI CTTAAG 1 cut(s) 1511
MspI CCGG 1 cut(s) 1565
MspR9I CCNGG 3 cut(s) 750, 999, 1539
Mva1269I GAATGC 1 cut(s) 643
MvaI CCWGG 3 cut(s) 750, 999, 1539
MwoI GCNNNNNNNGC 4 cut(s) 647, 1295, 1355, 1364
NdeII GATC 3 cut(s) 386, 466, 544
NlaIII CATG 7 cut(s) 15, 104, 138, 708, 784, 1184, 1204
NmuCI GTSAC 2 cut(s) 793, 1533
NsiI ATGCAT 1 cut(s) 1174
NspI RCATGY 3 cut(s) 708, 784, 1204
PaeI GCATGC 1 cut(s) 1204
PagI TCATGA 1 cut(s) 1180
PctI GAATGC 1 cut(s) 643
PdmI GAANNNNTTC 1 cut(s) 1527
PfeI GAWTC 2 cut(s) 392, 1248
PflMI CCANNNNNTGG 1 cut(s) 806
PfoI TCCNGGA 1 cut(s) 748
PkrI GCNGC 6 cut(s) 42, 1288, 1300, 1348, 1369, 1500
PleI GAGTC 2 cut(s) 1130, 1609
PpsI GAGTC 2 cut(s) 1130, 1609
PpuMI RGGWCCY 1 cut(s) 617
PsiI TTATAA 2 cut(s) 422, 1014
Psp5II RGGWCCY 1 cut(s) 617
Psp6I CCWGG 3 cut(s) 748, 997, 1537
PspGI CCWGG 3 cut(s) 748, 997, 1537
PspPI GGNCC 4 cut(s) 303, 617, 752, 968
PspPPI RGGWCCY 1 cut(s) 617
PvuII CAGCTG 1 cut(s) 1289
RsaI GTAC 2 cut(s) 714, 1118
RsaNI GTAC 2 cut(s) 713, 1117
RseI CAYNNNNRTG 3 cut(s) 24, 976, 1320
SaqAI TTAA 2 cut(s) 954, 1512
SatI GCNGC 6 cut(s) 41, 1287, 1299, 1347, 1368, 1499
Sau3AI GATC 3 cut(s) 386, 466, 544
Sau96I GGNCC 4 cut(s) 303, 617, 752, 968
SchI GAGTC 2 cut(s) 1131, 1610
ScrFI CCNGG 3 cut(s) 750, 999, 1539
SduI GDGCHC 1 cut(s) 1228
SfaNI GCATC 3 cut(s) 69, 1144, 1181
SinI GGWCC 4 cut(s) 303, 617, 752, 968
SmiMI CAYNNNNRTG 3 cut(s) 24, 976, 1320
SmlI CTYRAG 1 cut(s) 1511
SmoI CTYRAG 1 cut(s) 1511
SphI GCATGC 1 cut(s) 1204
SsiI CCGC 2 cut(s) 29, 40
SspI AATATT 1 cut(s) 407
SspMI CTAG 5 cut(s) 44, 522, 681, 1056, 1193
StyD4I CCNGG 3 cut(s) 748, 997, 1537
StyI CCWWGG 1 cut(s) 947
TaaI ACNGT 4 cut(s) 853, 1066, 1147, 1395
TaiI ACGT 1 cut(s) 1216
TauI GCSGC 1 cut(s) 43
TfiI GAWTC 2 cut(s) 392, 1248
Tru1I TTAA 2 cut(s) 954, 1512
Tru9I TTAA 2 cut(s) 954, 1512
TscAI CASTG 3 cut(s) 166, 978, 1168
TseFI GTSAC 2 cut(s) 793, 1533
TseI GCWGC 5 cut(s) 1286, 1298, 1346, 1367, 1498
Tsp45I GTSAC 2 cut(s) 793, 1533
TspGWI ACGGA 1 cut(s) 1521
TspRI CASTG 3 cut(s) 166, 978, 1168
Van91I CCANNNNNTGG 1 cut(s) 806
Vha464I CTTAAG 1 cut(s) 1511
VneI GTGCAC 1 cut(s) 1224
VpaK11BI GGWCC 4 cut(s) 303, 617, 752, 968
XapI RAATTY 4 cut(s) 146, 331, 338, 984
XceI RCATGY 3 cut(s) 708, 784, 1204
XmiI GTMKAC 3 cut(s) 106, 362, 1604
XmnI GAANNNNTTC 1 cut(s) 1527
XspI CTAG 5 cut(s) 44, 522, 681, 1056, 1193
Zsp2I ATGCAT 1 cut(s) 1174
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.