RchiOBHm_Chr5g0022021

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
5
OG0001340
Physical Location & Seq
Reverse (-)
16097100 .. 16099965
2866 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ30203

Sequence Viewer

Length: 1758 bp
ATGTGGCTAAAAGATAGTAGTCTCTGTTACTTAACATTGTTAAAAGGCTGTGGCCTAATGAGATATGTCGATGGATCAGTCCCTTGTCCTTCAGAACGCGTGATTATGGAAGAAAATGGGGTTGCATCTGATATAGAAAAGGAGTACATGAATTGGGTGCAAATTGATTCTGCCATTATGTCGATACTTGCTTCTACTCTATCCAGTGATGCTCTCTGCTTCATTATTGGAAGTAAGTCTTCTAAGGAAATTTGGTGTCGACTTAAGGAGAAATATGTTGATGATTCACGATATAACATCATGAATCTCAAAAACTCCTTATACAACATCCAAAAAGGCTCAGACTCTATTGATAGGTACTTACTTCGAGTCAAGTCAATCTGTGATCAGCTTGCTACAATGGGAGTTTATATGGATGATGAGGACATGGTAGTCTCGGTTCTCCATGGTTTGCCCTCAGAGTTTGCTACCATAAAAGCTGTAATAAGAATCAAAACACTAAGCTCCCCTGTTTCAATGAGAGAATTAAGATCTCTTTTGCTCATTGCTGAAGATGAGATTGAACAAACTATGAAGTCTATCTATGCTCCTGCAAGTCTTCCTTTGTCACCATTGAATGCAAGTATTCCTTTGTCACCTCTGGCTGCTATGGCTGCACAAAATAATCCTGTCAACTCATCTCAGAAAATGCAATATGGGATATCAAATGCAGGAACACCACCCAATGCATTCTTTCCATCTCCATATGTTGGTAATTGTTTTGTGTCATCTACTTCACATACTACTGCACCTATTATTGGTTTGATGCCCTCATTGTCTATCAGTAATGGTGCACTTAATGGGGCATTCAATGGTACTCGACAACTACAATCACAAGTACACAATGCTGCATATGGTGATGGTTATTTTCAGCACAATGGAGGTTTTTCACAACAGCAAAGTAGTGGTGGTTTTCAACAAAACAATGCCCTTCAATCTATTGGTAACCTATCATATAGTGGATCTAAATCTCAAGGTCAAGCTCAACATGATGTCAAGTTTAGTAAAGGCTGCTCAAAATCAAAAGGTGGTGTGTCTCAACACAATGTGAGTTCTTATCATAAGTCAAGAAACTCTAACTCAGGTGATGGATTTTATATGCATATTCTACCAATTCTTGTTCCCCCTGAAAAACCTGTTGCACATGTGAGTATTCCACAACAAAATGATAAAAGTGAGCCAAGTAGTTCTATTATGGGTGCTACTGCTACTACACCAGGAGAGATTTTGGTAGGAACAGATTTTGAGAAGACAGGAAATGAAGGTACAATGAAACAATCTGAAGAACTTGAAGCTTCCTCTATTCTTAACACTACAAATGGTCATGCTACTATCGATAGTGTGATTAATTCGAGGAAGGGAAATATCAGCAAAGGTGATGATTTTGGAAATGAAGGTACAATGAAACAATCTGAAGAACTTGAAGCTTCCTCTATTCTTAACACTACAAATGGTCATGCTACTATCGATAGTGTGATTAATTCGAGGAAGGGAAATATCAGCAAAGTTTGTGGAGATGGTTCTATCCGGTTGCAGTTTGTCTCCACTCATGATCGACTTGCTGATTTGTTTACCAAAGGCCTATGCTCCCCTCAGCATGTCTACCTCTGCCATCACCTCATGTTGGGTCCTCTCCATCTGTCACCTCTCTGTTCTTCATCAGTTCAACTAGTCCAGCTTGATGACCCGCCTCCCCATCAAGCTGAGGAGGGGTGTTAG
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 gag_pre-integrs

Protein Analysis

585

Amino Acids

63.18

Weight (kDa)

5.94

Isoelectric Point (pI)

53.16

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 20 - 186 4.7e-20 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)
AasI GACNNNNNNGTC 1 cut(s) 431
AccB7I CCANNNNNTGG 1 cut(s) 749
AccI GTMKAC 2 cut(s) 259, 1641
AccII CGCG 1 cut(s) 99
AciI CCGC 1 cut(s) 1727
AclWI GGATC 2 cut(s) 82, 1009
AcsI RAATTY 1 cut(s) 249
AcuI CTGAAG 4 cut(s) 75, 570, 1341, 1473
AdeI CACNNNGTG 1 cut(s) 1087
AfaI GTAC 6 cut(s) 146, 359, 856, 879, 1306, 1438
AfiI CCNNNNNNNGG 3 cut(s) 749, 797, 1663
AflII CTTAAG 1 cut(s) 263
AflIII ACRYGT 2 cut(s) 97, 1183
AgsI TTSAA 9 cut(s) 516, 563, 616, 850, 956, 974, 1331, 1463, 1706
AhlI ACTAGT 1 cut(s) 1708
AjnI CCWGG 1 cut(s) 1255
AluBI AGCT 8 cut(s) 391, 479, 504, 1022, 1334, 1466, 1717, 1742
AluI AGCT 8 cut(s) 391, 479, 504, 1022, 1334, 1466, 1717, 1742
Alw21I GWGCWC 1 cut(s) 835
Alw26I GTCTC 4 cut(s) 26, 439, 1080, 1585
Alw44I GTGCAC 1 cut(s) 831
AlwI GGATC 2 cut(s) 82, 1009
AoxI GGCC 2 cut(s) 52, 1618
ApaLI GTGCAC 1 cut(s) 831
ApeKI GCWGC 4 cut(s) 644, 653, 887, 1050
ApoI RAATTY 1 cut(s) 249
AseI ATTAAT 2 cut(s) 1386, 1518
AspS9I GGNCC 1 cut(s) 1667
AsuHPI GGTGA 7 cut(s) 600, 627, 908, 1136, 1427, 1646, 1674
AvaII GGWCC 1 cut(s) 1667
BaeGI GKGCMC 1 cut(s) 835
BbsI GAAGAC 3 cut(s) 231, 590, 1295
Bbv12I GWGCWC 1 cut(s) 835
BbvCI CCTCAGC 2 cut(s) 1632, 1743
BbvI GCAGC 4 cut(s) 631, 640, 874, 1037
BccI CCATC 8 cut(s) 65, 745, 893, 1121, 1550, 1659, 1683, 1743
BciT130I CCWGG 1 cut(s) 1257
BclI TGATCA 1 cut(s) 385
BcoDI GTCTC 4 cut(s) 26, 439, 1080, 1585
BcuI ACTAGT 1 cut(s) 1708
BfaI CTAG 1 cut(s) 1709
BfrI CTTAAG 1 cut(s) 263
BglII AGATCT 1 cut(s) 530
BisI GCNGC 4 cut(s) 645, 654, 888, 1051
BlsI GCNGC 4 cut(s) 646, 655, 889, 1052
Bme1390I CCNGG 1 cut(s) 1257
Bme18I GGWCC 1 cut(s) 1667
BmgT120I GGNCC 1 cut(s) 1667
BmiI GGNNCC 1 cut(s) 1668
BmrFI CCNGG 1 cut(s) 1257
BmsI GCATC 3 cut(s) 134, 199, 795
BpiI GAAGAC 3 cut(s) 231, 590, 1295
Bpu10I CCTNAGC 2 cut(s) 1632, 1743
BpuEI CTTGAG 1 cut(s) 996
Bsa29I ATCGAT 2 cut(s) 1374, 1506
BsaBI GATNNNNATC 1 cut(s) 1006
BsaJI CCNNGG 1 cut(s) 445
BsaWI WCCGGW 1 cut(s) 1566
Bsc4I CCNNNNNNNGG 3 cut(s) 749, 797, 1663
Bse1I ACTGG 1 cut(s) 204
Bse3DI GCAATG 1 cut(s) 543
Bse8I GATNNNNATC 1 cut(s) 1006
BseBI CCWGG 1 cut(s) 1257
BseCI ATCGAT 2 cut(s) 1374, 1506
BseDI CCNNGG 1 cut(s) 445
BseGI GGATG 2 cut(s) 327, 421
BseJI GATNNNNATC 1 cut(s) 1006
BseLI CCNNNNNNNGG 3 cut(s) 749, 797, 1663
BseMI GCAATG 1 cut(s) 543
BseMII CTCAG 6 cut(s) 354, 471, 695, 1134, 1646, 1734
BseNI ACTGG 1 cut(s) 204
BseSI GKGCMC 1 cut(s) 835
BseXI GCAGC 4 cut(s) 631, 640, 874, 1037
BsgI GTGCAG 2 cut(s) 639, 771
Bsh1236I CGCG 1 cut(s) 99
BshFI GGCC 2 cut(s) 54, 1620
BshVI ATCGAT 2 cut(s) 1374, 1506
BsiHKAI GWGCWC 1 cut(s) 835
BsiSI CCGG 1 cut(s) 1567
BslFI GGGAC 1 cut(s) 65
BslI CCNNNNNNNGG 3 cut(s) 749, 797, 1663
BsmAI GTCTC 4 cut(s) 26, 439, 1080, 1585
BsmFI GGGAC 1 cut(s) 65
BsmI GAATGC 3 cut(s) 622, 728, 845
BsnI GGCC 2 cut(s) 54, 1620
Bsp1286I GDGCHC 1 cut(s) 835
Bsp143I GATC 5 cut(s) 74, 385, 530, 1001, 1591
Bsp19I CCATGG 1 cut(s) 445
BspACI CCGC 1 cut(s) 1727
BspANI GGCC 2 cut(s) 54, 1620
BspCNI CTCAG 6 cut(s) 353, 470, 694, 1133, 1645, 1735
BspDI ATCGAT 2 cut(s) 1374, 1506
BspFNI CGCG 1 cut(s) 99
BspHI TCATGA 2 cut(s) 300, 1588
BspLI GGNNCC 1 cut(s) 1668
BspPI GGATC 2 cut(s) 82, 1009
BspTI CTTAAG 1 cut(s) 263
BsrDI GCAATG 1 cut(s) 543
BsrI ACTGG 1 cut(s) 204
BssECI CCNNGG 1 cut(s) 445
BssMI GATC 5 cut(s) 74, 385, 530, 1001, 1591
BssT1I CCWWGG 1 cut(s) 445
Bst2UI CCWGG 1 cut(s) 1257
BstAFI CTTAAG 1 cut(s) 263
BstC8I GCNNGC 1 cut(s) 393
BstDEI CTNAG 8 cut(s) 243, 340, 457, 500, 681, 1120, 1632, 1743
BstDSI CCRYGG 1 cut(s) 445
BstEII GGTNACC 1 cut(s) 983
BstF5I GGATG 2 cut(s) 327, 421
BstFNI CGCG 1 cut(s) 99
BstKTI GATC 5 cut(s) 77, 388, 533, 1004, 1594
BstMAI GTCTC 4 cut(s) 26, 439, 1080, 1585
BstMBI GATC 5 cut(s) 74, 385, 530, 1001, 1591
BstMWI GCNNNNNNNGC 2 cut(s) 650, 653
BstNI CCWGG 1 cut(s) 1257
BstNSI RCATGY 2 cut(s) 1187, 1640
BstPI GGTNACC 1 cut(s) 983
BstSCI CCNGG 1 cut(s) 1255
BstSLI GKGCMC 1 cut(s) 835
BstUI CGCG 1 cut(s) 99
BstV1I GCAGC 4 cut(s) 631, 640, 874, 1037
BstV2I GAAGAC 3 cut(s) 231, 590, 1295
BstX2I RGATCY 2 cut(s) 530, 1001
BstYI RGATCY 2 cut(s) 530, 1001
Bsu15I ATCGAT 2 cut(s) 1374, 1506
BsuRI GGCC 2 cut(s) 54, 1620
BsuTUI ATCGAT 2 cut(s) 1374, 1506
BtgI CCRYGG 1 cut(s) 445
BtsCI GGATG 2 cut(s) 327, 421
BtsIMutI CAGTG 1 cut(s) 211
Cac8I GCNNGC 1 cut(s) 393
CciI TCATGA 2 cut(s) 300, 1588
Cfr13I GGNCC 1 cut(s) 1667
ClaI ATCGAT 2 cut(s) 1374, 1506
Csp6I GTAC 6 cut(s) 145, 358, 855, 878, 1305, 1437
CspCI CAANNNNNGTGG 2 cut(s) 1531, 1566
CviQI GTAC 6 cut(s) 145, 358, 855, 878, 1305, 1437
DdeI CTNAG 8 cut(s) 243, 340, 457, 500, 681, 1120, 1632, 1743
DpnI GATC 5 cut(s) 76, 387, 532, 1003, 1593
DpnII GATC 5 cut(s) 74, 385, 530, 1001, 1591
DraIII CACNNNGTG 1 cut(s) 1087
DrdI GACNNNNNNGTC 1 cut(s) 431
DseDI GACNNNNNNGTC 1 cut(s) 431
Eco130I CCWWGG 1 cut(s) 445
Eco147I AGGCCT 1 cut(s) 1620
Eco32I GATATC 1 cut(s) 702
Eco47I GGWCC 1 cut(s) 1667
Eco57I CTGAAG 4 cut(s) 75, 570, 1341, 1473
Eco91I GGTNACC 1 cut(s) 983
EcoO109I RGGNCCY 1 cut(s) 1667
EcoO65I GGTNACC 1 cut(s) 983
EcoRII CCWGG 1 cut(s) 1255
EcoRV GATATC 1 cut(s) 702
EcoT14I CCWWGG 1 cut(s) 445
EcoT22I ATGCAT 2 cut(s) 730, 1143
ErhI CCWWGG 1 cut(s) 445
FalI AAGNNNNNCTT 6 cut(s) 223, 255, 586, 618, 613, 645
FaqI GGGAC 1 cut(s) 65
FauI CCCGC 1 cut(s) 1734
FauNDI CATATG 2 cut(s) 745, 892
FbaI TGATCA 1 cut(s) 385
FblI GTMKAC 2 cut(s) 259, 1641
Fnu4HI GCNGC 4 cut(s) 645, 654, 888, 1051
FokI GGATG 2 cut(s) 314, 428
Fsp4HI GCNGC 4 cut(s) 645, 654, 888, 1051
FspBI CTAG 1 cut(s) 1709
GluI GCNGC 4 cut(s) 645, 654, 888, 1051
HaeIII GGCC 2 cut(s) 54, 1620
HapII CCGG 1 cut(s) 1567
HincII GTYRAC 2 cut(s) 260, 673
HindII GTYRAC 2 cut(s) 260, 673
HindIII AAGCTT 2 cut(s) 1332, 1464
HinfI GANTC 6 cut(s) 167, 284, 304, 344, 369, 489
HpaII CCGG 1 cut(s) 1567
HphI GGTGA 7 cut(s) 600, 627, 908, 1136, 1427, 1646, 1674
Hpy166II GTNNAC 6 cut(s) 260, 673, 833, 880, 1611, 1642
Hpy188I TCNGA 7 cut(s) 94, 130, 343, 460, 684, 1321, 1453
Hpy188III TCNNGA 4 cut(s) 288, 301, 1107, 1589
Hpy8I GTNNAC 6 cut(s) 260, 673, 833, 880, 1611, 1642
HpyAV CCTTC 6 cut(s) 99, 980, 1295, 1390, 1427, 1522
HpyF10VI GCNNNNNNNGC 2 cut(s) 650, 653
HpyF3I CTNAG 8 cut(s) 243, 340, 457, 500, 681, 1120, 1632, 1743
Ksp22I TGATCA 1 cut(s) 385
Kzo9I GATC 5 cut(s) 74, 385, 530, 1001, 1591
LmnI GCTCC 3 cut(s) 509, 592, 1631
Lsp1109I GCAGC 4 cut(s) 631, 640, 874, 1037
LweI GCATC 3 cut(s) 134, 199, 795
MaeI CTAG 1 cut(s) 1709
MaeIII GTNAC 5 cut(s) 26, 606, 633, 983, 1680
MalI GATC 5 cut(s) 76, 387, 532, 1003, 1593
MboI GATC 5 cut(s) 74, 385, 530, 1001, 1591
MboII GAAGA 8 cut(s) 122, 231, 563, 590, 1300, 1334, 1466, 1686
MflI RGATCY 2 cut(s) 530, 1001
MhlI GDGCHC 1 cut(s) 835
MluCI AATT 8 cut(s) 151, 162, 249, 524, 754, 1152, 1387, 1519
MluI ACGCGT 1 cut(s) 97
MlyI GAGTC 2 cut(s) 338, 378
Mph1103I ATGCAT 2 cut(s) 730, 1143
MseI TTAA 9 cut(s) 32, 41, 264, 527, 837, 1347, 1386, 1479, 1518
MspCI CTTAAG 1 cut(s) 263
MspI CCGG 1 cut(s) 1567
MspR9I CCNGG 1 cut(s) 1257
Mva1269I GAATGC 3 cut(s) 622, 728, 845
MvaI CCWGG 1 cut(s) 1257
MvnI CGCG 1 cut(s) 99
MwoI GCNNNNNNNGC 2 cut(s) 650, 653
NcoI CCATGG 1 cut(s) 445
NdeI CATATG 2 cut(s) 745, 892
NdeII GATC 5 cut(s) 74, 385, 530, 1001, 1591
NlaIV GGNNCC 1 cut(s) 1668
NmuCI GTSAC 3 cut(s) 606, 633, 1680
NsiI ATGCAT 2 cut(s) 730, 1143
NspI RCATGY 2 cut(s) 1187, 1640
PagI TCATGA 2 cut(s) 300, 1588
PceI AGGCCT 1 cut(s) 1620
PciI ACATGT 1 cut(s) 1183
PctI GAATGC 3 cut(s) 622, 728, 845
PfeI GAWTC 4 cut(s) 167, 284, 304, 489
PflMI CCANNNNNTGG 1 cut(s) 749
PkrI GCNGC 4 cut(s) 646, 655, 889, 1052
PleI GAGTC 2 cut(s) 338, 377
PpsI GAGTC 2 cut(s) 338, 377
PpuMI RGGWCCY 1 cut(s) 1667
PscI ACATGT 1 cut(s) 1183
PshBI ATTAAT 2 cut(s) 1386, 1518
Psp5II RGGWCCY 1 cut(s) 1667
Psp6I CCWGG 1 cut(s) 1255
PspEI GGTNACC 1 cut(s) 983
PspGI CCWGG 1 cut(s) 1255
PspN4I GGNNCC 1 cut(s) 1668
PspPI GGNCC 1 cut(s) 1667
PspPPI RGGWCCY 1 cut(s) 1667
PsrI GAACNNNNNNTAC 2 cut(s) 423, 455
PsuI RGATCY 2 cut(s) 530, 1001
RsaI GTAC 6 cut(s) 146, 359, 856, 879, 1306, 1438
RsaNI GTAC 6 cut(s) 145, 358, 855, 878, 1305, 1437
SalI GTCGAC 1 cut(s) 258
SaqAI TTAA 9 cut(s) 32, 41, 264, 527, 837, 1347, 1386, 1479, 1518
SatI GCNGC 4 cut(s) 645, 654, 888, 1051
Sau3AI GATC 5 cut(s) 74, 385, 530, 1001, 1591
Sau96I GGNCC 1 cut(s) 1667
SchI GAGTC 2 cut(s) 338, 378
ScrFI CCNGG 1 cut(s) 1257
SduI GDGCHC 1 cut(s) 835
SfaNI GCATC 3 cut(s) 134, 199, 795
SinI GGWCC 1 cut(s) 1667
SmlI CTYRAG 2 cut(s) 263, 1011
SmoI CTYRAG 2 cut(s) 263, 1011
SpeI ACTAGT 1 cut(s) 1708
Sse9I AATT 8 cut(s) 151, 162, 249, 524, 754, 1152, 1387, 1519
SseBI AGGCCT 1 cut(s) 1620
SsiI CCGC 1 cut(s) 1727
SspMI CTAG 1 cut(s) 1709
StuI AGGCCT 1 cut(s) 1620
StyD4I CCNGG 1 cut(s) 1255
StyI CCWWGG 1 cut(s) 445
TasI AATT 8 cut(s) 151, 162, 249, 524, 754, 1152, 1387, 1519
TatI WGTACW 2 cut(s) 144, 877
TfiI GAWTC 4 cut(s) 167, 284, 304, 489
Tru1I TTAA 9 cut(s) 32, 41, 264, 527, 837, 1347, 1386, 1479, 1518
Tru9I TTAA 9 cut(s) 32, 41, 264, 527, 837, 1347, 1386, 1479, 1518
TscAI CASTG 1 cut(s) 211
TseFI GTSAC 3 cut(s) 606, 633, 1680
TseI GCWGC 4 cut(s) 644, 653, 887, 1050
Tsp45I GTSAC 3 cut(s) 606, 633, 1680
TspDTI ATGAA 9 cut(s) 164, 211, 317, 587, 1314, 1325, 1446, 1457, 1686
TspRI CASTG 1 cut(s) 211
Van91I CCANNNNNTGG 1 cut(s) 749
Vha464I CTTAAG 1 cut(s) 263
VneI GTGCAC 1 cut(s) 831
VpaK11BI GGWCC 1 cut(s) 1667
VspI ATTAAT 2 cut(s) 1386, 1518
XapI RAATTY 1 cut(s) 249
XceI RCATGY 2 cut(s) 1187, 1640
XmiI GTMKAC 2 cut(s) 259, 1641
XspI CTAG 1 cut(s) 1709
Zsp2I ATGCAT 2 cut(s) 730, 1143
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.