RchiOBHm_Chr6g0266711

gag-polypeptide of LTR copia-type

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_chinensis
6
OG0001471
Physical Location & Seq
Reverse (-)
23201183 .. 23203643
2461 bp
Loading structure...
UTR
Exon/CDS
Intron
PRQ23920

Sequence Viewer

Length: 1404 bp
ATGGTTCAATCTCAACACTCAAGGGTACAGCCTTACTTTACTCATACTCAGTCCACTCCTCCACATGTTTTGCCCACACCTGTCCCAAATTCTACAGTAGCTGCTCCCACAGGTTCACTTTCAAACTCTGACACTATTTTTTCTTCACACAATGACTCTGTCAACAATATTGTCTCTACTGGTGCTACACCTAATCTGATCTCTTTGCCATTGAGTAATACAGTATGTGATCTTGGTTCTCTTCCCAATATCACACCTCATGCTTCTTTATCAGAGACTGATACTACTGACTATTCATTGTCACCTTTTAGTCCCAATGTTCACACATCAATACAGTTTGAAGAGCAAAATGGTAATATCAGTGTCAACACTCAGCCTGGTATTGGTATTGAGGTGATTTTGGATCGTGCCAATAAGAACGTGCTTTCCAATAGTAATTTGTCAGAATCAAATATCTTGCATCCTGTAGATGGATTGACTAATGCTATAGTCAATGATCATAGTATGCTTACAAGAGGCAAAAGAGGAATTGTGCAGAAGAAAAGCTTTTTATCTGTCCTCACTGAACCTAGTTGTGATCCTACTGATTTTGAACCTTCTCACTATAAGGCAGCCTTAAAAATCCCTGCTTGGAAACAGGCTATGCAAGAGGAATATGATGCTCTTATGAATCAAAACACTTGGACTCTTGTCCCATTACCACCTGACAAAAATTTAGTCCCCTGCAAATGGATTTTCAAAATAAAGAGAAACTCAGATGGTTCAATTGCTAGACATAAGGCAAGATTGGTTGCTCGGGGCTTCAGTCAAGAGTATGGGGTAGATTTTGAGGAAACTTTTTCACCTGTTGTCCGGCATACCACAGTTCGATTAATTCTTGGTTTAGCTGCAAGTTCAGGTTGGAAACTTCATCAAATGGATGTCAAAAATGCTTTTCTTCATGGAATCCTAAACGAAGAGGTGTACATGACTCAGCCAAGTGGTTTTGAGAATCCTTCATATCCTTCATTTGTATGTAAGCTACAAAAATCGCTTTATGGACTGAAGCAAGCACCTAGGGCATGGAATGAACGATTTACCAGTTTTTTGCCTTCTATTGGTTTTAAATTTTCTTATGCAAATCCCTCTCTATTTGTCAAAGTTTCTGGCTCTTCTAGGGTCTATCTTTTGTTGTATGTTGATGACATTATCATCACTGGGGATAGTGAAGATCTTATCTCAGAAGTCAAGGCTGCTCTCCAAGCTGAATTTGATATGAAAGACTTGGGGGATCTTCATTTCTTTCTTGGCCTAGAAATTAAGTATATCAAGGATGGCATTTTCCTATCCCAACACAAATATACCAAGGATCTCATTCATAAAGCTGGTATGGATGCTTGTCACACTCATATCACTCCATGTTAA
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
No domains found.

Protein Analysis

467

Amino Acids

51.75

Weight (kDa)

6.31

Isoelectric Point (pI)

46.74

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
RVT_2 PF07727 226 - 466 2.3e-78 Reverse transcriptase (RNA-dependent DNA polymerase)
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)
AclWI GGATC 4 cut(s) 411, 572, 1278, 1356
AcsI RAATTY 4 cut(s) 88, 712, 1106, 1247
AcuI CTGAAG 2 cut(s) 787, 1064
AfaI GTAC 2 cut(s) 27, 965
AfiI CCNNNNNNNGG 4 cut(s) 383, 470, 729, 1097
AflIII ACRYGT 1 cut(s) 64
AgsI TTSAA 6 cut(s) 8, 123, 341, 593, 739, 765
AjnI CCWGG 1 cut(s) 376
AloI GAACNNNNNNTCC 2 cut(s) 410, 442
AluBI AGCT 6 cut(s) 101, 546, 887, 1021, 1244, 1364
AluI AGCT 6 cut(s) 101, 546, 887, 1021, 1244, 1364
Alw26I GTCTC 2 cut(s) 178, 269
AlwI GGATC 4 cut(s) 411, 572, 1278, 1356
AlwNI CAGNNNCTG 2 cut(s) 101, 278
Ama87I CYCGRG 1 cut(s) 795
AoxI GGCC 1 cut(s) 1288
ApeKI GCWGC 4 cut(s) 101, 611, 887, 1232
ApoI RAATTY 4 cut(s) 88, 712, 1106, 1247
ArsI GACNNNNNNTTYG 2 cut(s) 702, 734
AseI ATTAAT 1 cut(s) 872
AspA2I CCTAGG 1 cut(s) 1055
AsuHPI GGTGA 3 cut(s) 294, 406, 834
AvaI CYCGRG 1 cut(s) 795
AvrII CCTAGG 1 cut(s) 1055
BbvI GCAGC 4 cut(s) 88, 623, 874, 1219
BccI CCATC 3 cut(s) 464, 752, 1307
BciT130I CCWGG 1 cut(s) 378
BclI TGATCA 1 cut(s) 496
BcoDI GTCTC 2 cut(s) 178, 269
BfaI CTAG 5 cut(s) 570, 771, 1056, 1155, 1292
BfmI CTRYAG 3 cut(s) 93, 465, 486
BglII AGATCT 1 cut(s) 1210
BisI GCNGC 4 cut(s) 102, 612, 888, 1233
BlnI CCTAGG 1 cut(s) 1055
BlsI GCNGC 4 cut(s) 103, 613, 889, 1234
Bme1390I CCNGG 1 cut(s) 378
BmeT110I CYCGRG 1 cut(s) 795
BmrFI CCNGG 1 cut(s) 378
BmrI ACTGGG 1 cut(s) 1206
BmsI GCATC 3 cut(s) 469, 649, 1363
BmuI ACTGGG 1 cut(s) 1206
BoxI GACNNNNGTC 1 cut(s) 689
BpuEI CTTGAG 1 cut(s) 4
BsaJI CCNNGG 2 cut(s) 1055, 1344
Bsc4I CCNNNNNNNGG 4 cut(s) 383, 470, 729, 1097
Bse1I ACTGG 3 cut(s) 184, 1080, 1201
BseBI CCWGG 1 cut(s) 378
BseDI CCNNGG 2 cut(s) 1055, 1344
BseGI GGATG 4 cut(s) 460, 925, 1318, 1378
BseLI CCNNNNNNNGG 4 cut(s) 383, 470, 729, 1097
BseMII CTCAG 5 cut(s) 62, 386, 768, 986, 1233
BseNI ACTGG 3 cut(s) 184, 1080, 1201
BseRI GAGGAG 1 cut(s) 48
BseXI GCAGC 4 cut(s) 88, 623, 874, 1219
BsgI GTGCAG 1 cut(s) 554
BshFI GGCC 1 cut(s) 1290
BsiHKCI CYCGRG 1 cut(s) 795
BsiSI CCGG 1 cut(s) 853
BslFI GGGAC 4 cut(s) 68, 297, 677, 704
BslI CCNNNNNNNGG 4 cut(s) 383, 470, 729, 1097
BsmAI GTCTC 2 cut(s) 178, 269
BsmFI GGGAC 4 cut(s) 68, 297, 677, 704
BsnI GGCC 1 cut(s) 1290
BsoBI CYCGRG 1 cut(s) 795
Bsp1407I TGTACA 1 cut(s) 963
Bsp143I GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
BspANI GGCC 1 cut(s) 1290
BspCNI CTCAG 5 cut(s) 61, 385, 767, 985, 1232
BspPI GGATC 4 cut(s) 411, 572, 1278, 1356
BspQI GCTCTTC 2 cut(s) 336, 1156
BsrGI TGTACA 1 cut(s) 963
BsrI ACTGG 3 cut(s) 184, 1080, 1201
BssECI CCNNGG 2 cut(s) 1055, 1344
BssMI GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
BssT1I CCWWGG 2 cut(s) 1055, 1344
Bst2UI CCWGG 1 cut(s) 378
Bst4CI ACNGT 4 cut(s) 97, 223, 336, 865
Bst6I CTCTTC 4 cut(s) 246, 336, 951, 1156
BstAUI TGTACA 1 cut(s) 963
BstC8I GCNNGC 1 cut(s) 1050
BstDEI CTNAG 5 cut(s) 48, 372, 754, 972, 1219
BstF5I GGATG 4 cut(s) 460, 925, 1318, 1378
BstKTI GATC 8 cut(s) 201, 232, 406, 499, 580, 1213, 1273, 1351
BstMAI GTCTC 2 cut(s) 178, 269
BstMBI GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
BstMWI GCNNNNNNNGC 2 cut(s) 1058, 1241
BstNI CCWGG 1 cut(s) 378
BstNSI RCATGY 1 cut(s) 68
BstPAI GACNNNNGTC 1 cut(s) 689
BstSCI CCNGG 1 cut(s) 376
BstSFI CTRYAG 3 cut(s) 93, 465, 486
BstV1I GCAGC 4 cut(s) 88, 623, 874, 1219
BstX2I RGATCY 3 cut(s) 1210, 1270, 1348
BstYI RGATCY 3 cut(s) 1210, 1270, 1348
BsuRI GGCC 1 cut(s) 1290
BtsCI GGATG 4 cut(s) 460, 925, 1318, 1378
BtsIMutI CAGTG 3 cut(s) 367, 561, 1194
Cac8I GCNNGC 1 cut(s) 1050
CaiI CAGNNNCTG 2 cut(s) 101, 278
Csp6I GTAC 2 cut(s) 26, 964
CspCI CAANNNNNGTGG 2 cut(s) 51, 86
CviAII CATG 6 cut(s) 65, 260, 941, 967, 1062, 1398
CviQI GTAC 2 cut(s) 26, 964
DdeI CTNAG 5 cut(s) 48, 372, 754, 972, 1219
DpnI GATC 8 cut(s) 200, 231, 405, 498, 579, 1212, 1272, 1350
DpnII GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
DraI TTTAAA 1 cut(s) 1105
Eam1104I CTCTTC 4 cut(s) 246, 336, 951, 1156
EarI CTCTTC 4 cut(s) 246, 336, 951, 1156
Eco130I CCWWGG 2 cut(s) 1055, 1344
Eco57I CTGAAG 2 cut(s) 787, 1064
Eco88I CYCGRG 1 cut(s) 795
EcoRII CCWGG 1 cut(s) 376
EcoT14I CCWWGG 2 cut(s) 1055, 1344
ErhI CCWWGG 2 cut(s) 1055, 1344
FaeI CATG 6 cut(s) 68, 263, 944, 970, 1065, 1401
FalI AAGNNNNNCTT 4 cut(s) 530, 562, 599, 631
FaqI GGGAC 4 cut(s) 68, 297, 677, 704
FatI CATG 6 cut(s) 64, 259, 940, 966, 1061, 1397
FbaI TGATCA 1 cut(s) 496
Fnu4HI GCNGC 4 cut(s) 102, 612, 888, 1233
FokI GGATG 4 cut(s) 447, 932, 1325, 1385
Fsp4HI GCNGC 4 cut(s) 102, 612, 888, 1233
FspBI CTAG 5 cut(s) 570, 771, 1056, 1155, 1292
GluI GCNGC 4 cut(s) 102, 612, 888, 1233
HaeIII GGCC 1 cut(s) 1290
HapII CCGG 1 cut(s) 853
Hin1II CATG 6 cut(s) 68, 263, 944, 970, 1065, 1401
HincII GTYRAC 2 cut(s) 163, 367
HindII GTYRAC 2 cut(s) 163, 367
HindIII AAGCTT 1 cut(s) 544
HinfI GANTC 7 cut(s) 155, 446, 670, 685, 945, 970, 991
HpaII CCGG 1 cut(s) 853
HphI GGTGA 3 cut(s) 294, 406, 834
Hpy166II GTNNAC 6 cut(s) 54, 116, 163, 322, 367, 964
Hpy188I TCNGA 6 cut(s) 130, 198, 274, 445, 757, 1222
Hpy188III TCNNGA 1 cut(s) 809
Hpy8I GTNNAC 6 cut(s) 54, 116, 163, 322, 367, 964
HpyAV CCTTC 4 cut(s) 606, 1005, 1014, 1101
HpyCH4III ACNGT 4 cut(s) 97, 223, 336, 865
HpyCH4IV ACGT 1 cut(s) 420
HpyCH4V TGCA 6 cut(s) 460, 535, 646, 726, 890, 1118
HpyF10VI GCNNNNNNNGC 2 cut(s) 1058, 1241
HpyF3I CTNAG 5 cut(s) 48, 372, 754, 972, 1219
HpySE526I ACGT 1 cut(s) 420
Hsp92II CATG 6 cut(s) 68, 263, 944, 970, 1065, 1401
Ksp22I TGATCA 1 cut(s) 496
Kzo9I GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
LguI GCTCTTC 2 cut(s) 336, 1156
LmnI GCTCC 1 cut(s) 109
Lsp1109I GCAGC 4 cut(s) 88, 623, 874, 1219
LweI GCATC 3 cut(s) 469, 649, 1363
MaeI CTAG 5 cut(s) 570, 771, 1056, 1155, 1292
MaeII ACGT 1 cut(s) 420
MaeIII GTNAC 2 cut(s) 300, 1379
MalI GATC 8 cut(s) 200, 231, 405, 498, 579, 1212, 1272, 1350
MboI GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
MboII GAAGA 9 cut(s) 135, 233, 353, 550, 929, 968, 1143, 1220, 1265
MfeI CAATTG 1 cut(s) 765
MflI RGATCY 3 cut(s) 1210, 1270, 1348
MluCI AATT 9 cut(s) 88, 436, 528, 712, 765, 873, 1106, 1247, 1296
MlyI GAGTC 3 cut(s) 149, 679, 964
MmeI TCCRAC 1 cut(s) 881
MseI TTAA 5 cut(s) 617, 872, 1104, 1299, 1402
MslI CAYNNNNRTG 1 cut(s) 1012
MspI CCGG 1 cut(s) 853
MspR9I CCNGG 1 cut(s) 378
MunI CAATTG 1 cut(s) 765
MvaI CCWGG 1 cut(s) 378
MwoI GCNNNNNNNGC 2 cut(s) 1058, 1241
NdeII GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
NlaIII CATG 6 cut(s) 68, 263, 944, 970, 1065, 1401
NmuCI GTSAC 2 cut(s) 300, 1379
NspI RCATGY 1 cut(s) 68
PciI ACATGT 1 cut(s) 64
PciSI GCTCTTC 2 cut(s) 336, 1156
PfeI GAWTC 4 cut(s) 446, 670, 945, 991
PflFI GACNNNGTC 1 cut(s) 158
PkrI GCNGC 4 cut(s) 103, 613, 889, 1234
PleI GAGTC 3 cut(s) 149, 679, 964
PpsI GAGTC 3 cut(s) 149, 679, 964
PscI ACATGT 1 cut(s) 64
PshAI GACNNNNGTC 1 cut(s) 689
PshBI ATTAAT 1 cut(s) 872
Psp6I CCWGG 1 cut(s) 376
PspGI CCWGG 1 cut(s) 376
PstNI CAGNNNCTG 2 cut(s) 101, 278
PsuI RGATCY 3 cut(s) 1210, 1270, 1348
PsyI GACNNNGTC 1 cut(s) 158
RsaI GTAC 2 cut(s) 27, 965
RsaNI GTAC 2 cut(s) 26, 964
RseI CAYNNNNRTG 1 cut(s) 1012
SapI GCTCTTC 2 cut(s) 336, 1156
SaqAI TTAA 5 cut(s) 617, 872, 1104, 1299, 1402
SatI GCNGC 4 cut(s) 102, 612, 888, 1233
Sau3AI GATC 8 cut(s) 198, 229, 403, 496, 577, 1210, 1270, 1348
SchI GAGTC 3 cut(s) 149, 679, 964
ScrFI CCNGG 1 cut(s) 378
SfaNI GCATC 3 cut(s) 469, 649, 1363
SfcI CTRYAG 3 cut(s) 93, 465, 486
SmiMI CAYNNNNRTG 1 cut(s) 1012
SmlI CTYRAG 1 cut(s) 19
SmoI CTYRAG 1 cut(s) 19
Sse9I AATT 9 cut(s) 88, 436, 528, 712, 765, 873, 1106, 1247, 1296
SspI AATATT 1 cut(s) 169
SspMI CTAG 5 cut(s) 570, 771, 1056, 1155, 1292
StyD4I CCNGG 1 cut(s) 376
StyI CCWWGG 2 cut(s) 1055, 1344
TaaI ACNGT 4 cut(s) 97, 223, 336, 865
TaiI ACGT 1 cut(s) 423
TaqI TCGA 1 cut(s) 868
TasI AATT 9 cut(s) 88, 436, 528, 712, 765, 873, 1106, 1247, 1296
TatI WGTACW 1 cut(s) 963
TfiI GAWTC 4 cut(s) 446, 670, 945, 991
Tru1I TTAA 5 cut(s) 617, 872, 1104, 1299, 1402
Tru9I TTAA 5 cut(s) 617, 872, 1104, 1299, 1402
TscAI CASTG 3 cut(s) 367, 568, 1201
TseFI GTSAC 2 cut(s) 300, 1379
TseI GCWGC 4 cut(s) 101, 611, 887, 1232
Tsp45I GTSAC 2 cut(s) 300, 1379
TspRI CASTG 3 cut(s) 367, 568, 1201
Tth111I GACNNNGTC 1 cut(s) 158
VspI ATTAAT 1 cut(s) 872
XapI RAATTY 4 cut(s) 88, 712, 1106, 1247
XceI RCATGY 1 cut(s) 68
XmaJI CCTAGG 1 cut(s) 1055
XspI CTAG 5 cut(s) 570, 771, 1056, 1155, 1292
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.