Rmu_sc0000968.1_g000018

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_multiflora
Rmu_sc0000968.1
OG0016252
Physical Location & Seq
Forward (+)
117618 .. 121555
3938 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 1785 bp
atggaggtatggatcactctcaaacgacattatgcagcaaattctgaatttcacattatgcgattaaagtctgctttgcaaaatatcagaaaaggtgcagattcgatagacaagtatttgttgcgcttcaaaactgttagagatcatttagctgttgttggtattagaatatcagatcaagaggttaaaagtttgattcttgctggtctcccttgtgagtatggtcacactagacaaattataagagaaaaaaatcctataatcatggaggaattaaggtctttacttctttctgctgaatttgaacttgaattgaagcataaaactcatccaatgacacccttaactactgtggttgcaaataatagctctatgtcattccctgactctcattttggaagttcatttgttataccctctactactgtgccccaacgtggcaaaaatcatattgattataataacacttctacatgtcatgtacctgttgtggccaagtccagtatcagtgctcttactagtactcctacaagtccagttactcaaattgcttgtacaccacagtcggctattttgtcaaataatgtcaacattgctactgcatacatgagtaatactatggcatcgaatgggaactttgctatgcaatctatgccaaataacggatgcatgatggattttgtttctacacctagtggtctcctgattcccaactctggctcaaattttgttactccatacacatctactggtgcaacacaacagcttggtgactttcatcattcccatgcaacttatgcacagccacaagtcaattctaatggaagaatccagtataattggggattttctcaacccaacagtaacttcattctacaaagtggtaggcttcagcaaagcaatggatttcaatctggtatgggtacttctaatggttatcaagcttcatttaatactaatgcaatgatgaatggtggaaattgctttcctcgtactggtttggttaggaatagcgttgcatctccttcattagctcaatacaatggtgtgatgaagatggataactcagttttggaggaagctggcaatggtcaggatataaaggagaataccttgagtacagagaatcaggttgatgagactctggatgtggatcatgtggtagatacttctgttgttgttaccttgaagcctgaagatgacgagggtgtggacttgcaagagagaaatatggatccagaggatactgaatgtgagagtaccaactcaaaagatgctatgtctatcactgaagcaaggcaagtggttaataaaagttctgcaaatgaggacacgaagaagattcaggttggtgtatcacctaaagcgttgtctgcttccatctgcactcaaccaaagccaccctccactgctactgagccaaataacaactcttttcaatcacaagttgtcaagcctctaacaattacatctgcatacccattatcagttcctcctcaccctcatttgcagcaactccactcaagaaaattgaacgactatgctaaaaaaatccctaatttcttggaagagactacgctcaggaatttaatagtttttcgtggcagcctttttcgctccgaaactaaccctaatcttatgttgtttttcaagatgagttacctacacaagttgaactttgttccaccagagacaactggtgcaggataccataggtgggtcagagatgtgcgccaacatcttaaggctgatagacttctggaagccatccaagagcctagttag
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

594

Amino Acids

65.63

Weight (kDa)

6.68

Isoelectric Point (pI)

44.76

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
Retrotran_gag_2 PF14223 2 - 100 6.1e-12 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)
AanI TTATAA 2 cut(s) 242, 459
AclWI GGATC 4 cut(s) 20, 1161, 1229, 1242
AcoI YGGCCR 1 cut(s) 492
AcsI RAATTY 5 cut(s) 40, 47, 299, 724, 1585
AcuI CTGAAG 3 cut(s) 875, 1215, 1311
AdeI CACNNNGTG 1 cut(s) 695
AfaI GTAC 7 cut(s) 483, 523, 556, 925, 994, 1120, 1261
AfiI CCNNNNNNNGG 5 cut(s) 437, 662, 716, 995, 1717
AflII CTTAAG 1 cut(s) 1742
AflIII ACRYGT 1 cut(s) 473
AhlI ACTAGT 1 cut(s) 518
AjuI GAANNNNNNNTTGG 2 cut(s) 851, 883
AluBI AGCT 6 cut(s) 152, 369, 766, 944, 1034, 1082
AluI AGCT 6 cut(s) 152, 369, 766, 944, 1034, 1082
Alw21I GWGCWC 1 cut(s) 514
Alw26I GTCTC 5 cut(s) 212, 704, 1133, 1565, 1685
AlwI GGATC 4 cut(s) 20, 1161, 1229, 1242
AoxI GGCC 1 cut(s) 492
ApeKI GCWGC 3 cut(s) 35, 1510, 1605
ApoI RAATTY 5 cut(s) 40, 47, 299, 724, 1585
ArsI GACNNNNNNTTYG 2 cut(s) 377, 409
AspLEI GCGC 2 cut(s) 126, 1734
AsuHPI GGTGA 3 cut(s) 782, 1350, 1490
BaeGI GKGCMC 1 cut(s) 432
BaeI ACNNNNGTAYC 2 cut(s) 1158, 1191
BalI TGGCCA 1 cut(s) 494
BamHI GGATCC 1 cut(s) 1234
BarI GAAGNNNNNNTAC 2 cut(s) 910, 942
Bbv12I GWGCWC 1 cut(s) 514
BbvI GCAGC 3 cut(s) 47, 1522, 1617
BccI CCATC 4 cut(s) 667, 1051, 1388, 1775
BciVI GTATCC 2 cut(s) 1237, 1700
BcoDI GTCTC 5 cut(s) 212, 704, 1133, 1565, 1685
BcuI ACTAGT 1 cut(s) 518
BfaI CTAG 4 cut(s) 231, 519, 693, 1779
BfrI CTTAAG 1 cut(s) 1742
BfuI GTATCC 2 cut(s) 1237, 1700
BisI GCNGC 3 cut(s) 36, 1511, 1606
BlsI GCNGC 3 cut(s) 37, 1512, 1607
BmcAI AGTACT 1 cut(s) 523
BmiI GGNNCC 1 cut(s) 1236
BmsI GCATC 4 cut(s) 632, 656, 1028, 1264
Bpu10I CCTNAGC 1 cut(s) 1580
BpuEI CTTGAG 2 cut(s) 1135, 1507
BsaBI GATNNNNATC 2 cut(s) 910, 1152
BsaI GGTCTC 2 cut(s) 212, 704
BsaXI ACNNNNNCTCC 2 cut(s) 508, 538
Bsc4I CCNNNNNNNGG 5 cut(s) 437, 662, 716, 995, 1717
Bse1I ACTGG 6 cut(s) 501, 536, 754, 832, 1000, 1702
Bse3DI GCAATG 4 cut(s) 591, 907, 969, 1093
Bse8I GATNNNNATC 2 cut(s) 910, 1152
BseGI GGATG 4 cut(s) 328, 671, 1153, 1767
BseJI GATNNNNATC 2 cut(s) 910, 1152
BseLI CCNNNNNNNGG 5 cut(s) 437, 662, 716, 995, 1717
BseMI GCAATG 4 cut(s) 591, 907, 969, 1093
BseMII CTCAG 3 cut(s) 1080, 1407, 1594
BseNI ACTGG 6 cut(s) 501, 536, 754, 832, 1000, 1702
BseRI GAGGAG 1 cut(s) 1485
BseSI GKGCMC 1 cut(s) 432
BseXI GCAGC 3 cut(s) 47, 1522, 1617
BsgI GTGCAG 3 cut(s) 117, 1369, 1722
BshFI GGCC 1 cut(s) 494
BsiHKAI GWGCWC 1 cut(s) 514
BslI CCNNNNNNNGG 5 cut(s) 437, 662, 716, 995, 1717
BsmAI GTCTC 5 cut(s) 212, 704, 1133, 1565, 1685
BsnI GGCC 1 cut(s) 494
Bso31I GGTCTC 2 cut(s) 212, 704
Bsp1286I GDGCHC 2 cut(s) 432, 514
Bsp1407I TGTACA 1 cut(s) 554
Bsp143I GATC 5 cut(s) 12, 142, 175, 1153, 1234
BspANI GGCC 1 cut(s) 494
BspCNI CTCAG 3 cut(s) 1079, 1408, 1593
BspLI GGNNCC 1 cut(s) 1236
BspPI GGATC 4 cut(s) 20, 1161, 1229, 1242
BspTI CTTAAG 1 cut(s) 1742
BspTNI GGTCTC 2 cut(s) 212, 704
BsrDI GCAATG 4 cut(s) 591, 907, 969, 1093
BsrGI TGTACA 1 cut(s) 554
BsrI ACTGG 6 cut(s) 501, 536, 754, 832, 1000, 1702
BssMI GATC 5 cut(s) 12, 142, 175, 1153, 1234
Bst4CI ACNGT 5 cut(s) 136, 352, 427, 564, 863
Bst6I CTCTTC 1 cut(s) 1563
BstAFI CTTAAG 1 cut(s) 1742
BstAPI GCANNNNNTGC 2 cut(s) 652, 797
BstAUI TGTACA 1 cut(s) 554
BstC8I GCNNGC 1 cut(s) 1084
BstDEI CTNAG 3 cut(s) 1066, 1416, 1580
BstF5I GGATG 4 cut(s) 328, 671, 1153, 1767
BstHHI GCGC 2 cut(s) 126, 1734
BstKTI GATC 5 cut(s) 15, 145, 178, 1156, 1237
BstMAI GTCTC 5 cut(s) 212, 704, 1133, 1565, 1685
BstMBI GATC 5 cut(s) 12, 142, 175, 1153, 1234
BstMWI GCNNNNNNNGC 4 cut(s) 652, 797, 1373, 1614
BstNSI RCATGY 1 cut(s) 477
BstSLI GKGCMC 1 cut(s) 432
BstV1I GCAGC 3 cut(s) 47, 1522, 1617
BstX2I RGATCY 1 cut(s) 1234
BstYI RGATCY 1 cut(s) 1234
BsuI GTATCC 2 cut(s) 1237, 1700
BsuRI GGCC 1 cut(s) 494
BtsCI GGATG 4 cut(s) 328, 671, 1153, 1767
BtsI GCAGTG 1 cut(s) 1407
BtsIMutI CAGTG 3 cut(s) 514, 1287, 1407
Cac8I GCNNGC 1 cut(s) 1084
CfoI GCGC 2 cut(s) 126, 1734
Csp6I GTAC 7 cut(s) 482, 522, 555, 924, 993, 1119, 1260
CspCI CAANNNNNGTGG 2 cut(s) 1284, 1319
CviAII CATG 7 cut(s) 265, 474, 479, 607, 670, 788, 1157
CviQI GTAC 7 cut(s) 482, 522, 555, 924, 993, 1119, 1260
DdeI CTNAG 3 cut(s) 1066, 1416, 1580
DpnI GATC 5 cut(s) 14, 144, 177, 1155, 1236
DpnII GATC 5 cut(s) 12, 142, 175, 1153, 1234
DraIII CACNNNGTG 1 cut(s) 695
EaeI YGGCCR 1 cut(s) 492
Eam1104I CTCTTC 1 cut(s) 1563
EarI CTCTTC 1 cut(s) 1563
Eco31I GGTCTC 2 cut(s) 212, 704
Eco57I CTGAAG 3 cut(s) 875, 1215, 1311
EcoT22I ATGCAT 1 cut(s) 671
FaeI CATG 7 cut(s) 268, 477, 482, 610, 673, 791, 1160
FalI AAGNNNNNCTT 2 cut(s) 1661, 1693
FatI CATG 7 cut(s) 264, 473, 478, 606, 669, 787, 1156
Fnu4HI GCNGC 3 cut(s) 36, 1511, 1606
FokI GGATG 4 cut(s) 315, 678, 1160, 1754
Fsp4HI GCNGC 3 cut(s) 36, 1511, 1606
FspBI CTAG 4 cut(s) 231, 519, 693, 1779
GlaI GCGC 2 cut(s) 125, 1733
GluI GCNGC 3 cut(s) 36, 1511, 1606
HaeIII GGCC 1 cut(s) 494
HhaI GCGC 2 cut(s) 126, 1734
Hin1II CATG 7 cut(s) 268, 477, 482, 610, 673, 791, 1160
Hin6I GCGC 2 cut(s) 124, 1732
HinP1I GCGC 2 cut(s) 124, 1732
HincII GTYRAC 1 cut(s) 589
HindII GTYRAC 1 cut(s) 589
HindIII AAGCTT 1 cut(s) 942
HinfI GANTC 8 cut(s) 101, 196, 386, 706, 828, 1126, 1141, 1342
HphI GGTGA 3 cut(s) 782, 1350, 1490
Hpy166II GTNNAC 3 cut(s) 557, 589, 1213
Hpy188I TCNGA 5 cut(s) 46, 89, 175, 1621, 1724
Hpy188III TCNNGA 9 cut(s) 179, 703, 1094, 1145, 1238, 1524, 1582, 1651, 1760
Hpy8I GTNNAC 3 cut(s) 557, 589, 1213
HpyAV CCTTC 1 cut(s) 1035
HpyCH4III ACNGT 5 cut(s) 136, 352, 427, 564, 863
HpyCH4IV ACGT 1 cut(s) 436
HpyF10VI GCNNNNNNNGC 4 cut(s) 652, 797, 1373, 1614
HpyF3I CTNAG 3 cut(s) 1066, 1416, 1580
HpySE526I ACGT 1 cut(s) 436
Hsp92II CATG 7 cut(s) 268, 477, 482, 610, 673, 791, 1160
HspAI GCGC 2 cut(s) 124, 1732
Kzo9I GATC 5 cut(s) 12, 142, 175, 1153, 1234
LmnI GCTCC 1 cut(s) 1622
Lsp1109I GCAGC 3 cut(s) 47, 1522, 1617
LweI GCATC 4 cut(s) 632, 656, 1028, 1264
MaeI CTAG 4 cut(s) 231, 519, 693, 1779
MaeII ACGT 1 cut(s) 436
MaeIII GTNAC 7 cut(s) 224, 538, 730, 770, 863, 1180, 1658
MalI GATC 5 cut(s) 14, 144, 177, 1155, 1236
MboI GATC 5 cut(s) 12, 142, 175, 1153, 1234
MboII GAAGA 6 cut(s) 837, 1066, 1208, 1348, 1351, 1580
MflI RGATCY 1 cut(s) 1234
MhlI GDGCHC 2 cut(s) 432, 514
MlsI TGGCCA 1 cut(s) 494
MluNI TGGCCA 1 cut(s) 494
MlyI GAGTC 2 cut(s) 380, 1135
Mox20I TGGCCA 1 cut(s) 494
Mph1103I ATGCAT 1 cut(s) 671
MscI TGGCCA 1 cut(s) 494
MseI TTAA 8 cut(s) 65, 186, 275, 344, 951, 1308, 1589, 1743
MslI CAYNNNNRTG 1 cut(s) 786
Msp20I TGGCCA 1 cut(s) 494
MspCI CTTAAG 1 cut(s) 1742
MwoI GCNNNNNNNGC 4 cut(s) 652, 797, 1373, 1614
NdeII GATC 5 cut(s) 12, 142, 175, 1153, 1234
NlaIII CATG 7 cut(s) 268, 477, 482, 610, 673, 791, 1160
NlaIV GGNNCC 1 cut(s) 1236
NmuCI GTSAC 2 cut(s) 224, 770
NsiI ATGCAT 1 cut(s) 671
NspI RCATGY 1 cut(s) 477
PciI ACATGT 1 cut(s) 473
PfeI GAWTC 6 cut(s) 101, 196, 706, 828, 1126, 1342
PkrI GCNGC 3 cut(s) 37, 1512, 1607
PleI GAGTC 2 cut(s) 380, 1135
PpsI GAGTC 2 cut(s) 380, 1135
PscI ACATGT 1 cut(s) 473
PsiI TTATAA 2 cut(s) 242, 459
PspN4I GGNNCC 1 cut(s) 1236
PsuI RGATCY 1 cut(s) 1234
RsaI GTAC 7 cut(s) 483, 523, 556, 925, 994, 1120, 1261
RsaNI GTAC 7 cut(s) 482, 522, 555, 924, 993, 1119, 1260
RseI CAYNNNNRTG 1 cut(s) 786
SaqAI TTAA 8 cut(s) 65, 186, 275, 344, 951, 1308, 1589, 1743
SatI GCNGC 3 cut(s) 36, 1511, 1606
Sau3AI GATC 5 cut(s) 12, 142, 175, 1153, 1234
ScaI AGTACT 1 cut(s) 523
SchI GAGTC 2 cut(s) 380, 1135
SduI GDGCHC 2 cut(s) 432, 514
SfaNI GCATC 4 cut(s) 632, 656, 1028, 1264
SmiMI CAYNNNNRTG 1 cut(s) 786
SmlI CTYRAG 3 cut(s) 1114, 1522, 1742
SmoI CTYRAG 3 cut(s) 1114, 1522, 1742
SpeI ACTAGT 1 cut(s) 518
SspMI CTAG 4 cut(s) 231, 519, 693, 1779
TaaI ACNGT 5 cut(s) 136, 352, 427, 564, 863
TaiI ACGT 1 cut(s) 439
TaqI TCGA 2 cut(s) 104, 626
TatI WGTACW 3 cut(s) 521, 554, 1118
TfiI GAWTC 6 cut(s) 101, 196, 706, 828, 1126, 1342
Tru1I TTAA 8 cut(s) 65, 186, 275, 344, 951, 1308, 1589, 1743
Tru9I TTAA 8 cut(s) 65, 186, 275, 344, 951, 1308, 1589, 1743
TscAI CASTG 3 cut(s) 514, 1294, 1414
TseFI GTSAC 2 cut(s) 224, 770
TseI GCWGC 3 cut(s) 35, 1510, 1605
Tsp45I GTSAC 2 cut(s) 224, 770
TspDTI ATGAA 7 cut(s) 393, 767, 859, 936, 983, 1017, 1067
TspGWI ACGGA 1 cut(s) 678
TspRI CASTG 3 cut(s) 514, 1294, 1414
Vha464I CTTAAG 1 cut(s) 1742
XapI RAATTY 5 cut(s) 40, 47, 299, 724, 1585
XceI RCATGY 1 cut(s) 477
XspI CTAG 4 cut(s) 231, 519, 693, 1779
ZrmI AGTACT 1 cut(s) 523
Zsp2I ATGCAT 1 cut(s) 671
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.