Rroxscaffold_5G00342420

tRNA pseudouridine synthase

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
rosa_roxburghii
GWHEROQ00000005
OG0006106
Physical Location & Seq
Forward (+)
11381451 .. 11386008
4558 bp
Loading structure...
UTR
Exon/CDS
Intron
Rroxscaffold_5G00342420.1

Sequence Viewer

Length: 1389 bp
ATGGAGAGCAAGGTCTTTGTCCAATACAACCACACCGATCCCTGTGCATTTGCGCGCTGGACTACCAAGGAAAGCTTCCAGTTCATGTCAGCCAGGCCTTGGCAACAAGTCATCGACTTTTATTCCGATGTGGTAAAGGGTCAGAAGCCCTTGTCTGCGTTGTTGGGTACTACTTGTTTGAGTAAAAACAAAATTTACAATAGTGTAGAATGTGTAAATTCTCAAAATAGGGGTGGGAGGTGGGCAAGATTGACGTTCAAGATTGTGGTTTCGTATCATGGTGGTTCCTTTGATGGGTGGCAAAAGCAACCGGACCTCTACACTGTCCAAAGTGTTGTTGAACAATCTCTTGGGAAATTTGTTGATGACAAGAAAGCCCAGATGCTGAAAGACAAAGGGTTGCCATTGGAAGGGGCTGCTACTGTCGCCGGACGGACCGATAAAGGAGTCACAGCCCTTAATCAAGAGAATCTTGTTTTAGGGTCAATTGATTTTGCCACTGAATGCATTTCGGAGTTTGGAGTTCTTCTAATGTTGCTCCTTTTTGACTTTTTAGATACTTGGAGAAAGGATGTGCAATCTCAAGATATTGCAGATGCTATAAATAGTGCAGCACCAGGAAAACTCAGGACAGTATCAGTTACTGAGGTATCACGTGTATTCCATCCAAATTTTTCTGCCAAATGGAGGCATTATTTGTATATATTTCCATTTAATGATGATGAGGAGGAGAGGGAACAAAGCAATGAGACTGGAGAGAATACTCAAAAATTTAAGATTAATGATAATCATTATGAGCATGAAGTTGTATCTGATAAATGCAATGGGGAAAATGTTGGAAACTTAATCATCACTGATGACGTAGAGGTTGAAACTGAGAAGAAGCCACGGATGTTCAGCATTATAGCTTTGAGTCTTCCCTTGCAACTCAAATTAGCATCATCGTTGCCTTGTTCTTTCTGTGCCTCCAATTTTTATCATTTACTAACCCTTGGGGTCCACCAACAGAGTGTTTTGTCTTCCATGCTCGAGCAAGAGAGTACAGATTACCGTGTTCAGTTCACATCTTTTCAGGTTGGAGTATTGAATTCCGTTGTTCAGTTTTTGCACCCATATAGCCCCCAGACTTTTCAGGAGCATGAAAAAGGGAGAAGGGTCATGTGTATCGAACTGGTTGCCAACCGATTCTTACGCAGGATGGTTCGGGTTCTTGTGGCAACCTCAATTAGGGAAGCCGCTGCAGGTGCAGATGAGGACGCATTGCTAAAACTGATGGATGCAACATGCAGACGTGCTACTGCCCCCCCAGCTCCACCCGATGGTTTATGCCTTGTTGATGTTGGTTATGAAGAATTCGATCCGCTAGATTGCCTCATCTCGAAGGAGTAA
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
PseudoU_synth_1

Protein Analysis

462

Amino Acids

52.08

Weight (kDa)

5.43

Isoelectric Point (pI)

37.57

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_1 PF01416 384 - 450 6.9e-08 tRNA pseudouridine synthase
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)
AarI CACCTGC 1 cut(s) 1232
Acc36I ACCTGC 1 cut(s) 1232
AccB7I CCANNNNNTGG 2 cut(s) 99, 1319
AccII CGCG 1 cut(s) 55
AciI CCGC 2 cut(s) 1236, 1361
AclWI GGATC 2 cut(s) 32, 1352
AcsI RAATTY 7 cut(s) 192, 217, 356, 670, 770, 1087, 1352
AcvI CACGTG 1 cut(s) 656
AfaI GTAC 2 cut(s) 169, 1042
AfiI CCNNNNNNNGG 6 cut(s) 99, 294, 410, 687, 1227, 1319
AflIII ACRYGT 1 cut(s) 655
AgsI TTSAA 4 cut(s) 259, 341, 872, 1087
AjiI CACGTC 1 cut(s) 1292
AjnI CCWGG 2 cut(s) 92, 616
AjuI GAANNNNNNNTTGG 4 cut(s) 59, 91, 333, 365
AluBI AGCT 3 cut(s) 75, 908, 1310
AluI AGCT 3 cut(s) 75, 908, 1310
Alw26I GTCTC 1 cut(s) 743
AlwI GGATC 2 cut(s) 32, 1352
AlwNI CAGNNNCTG 2 cut(s) 385, 644
Ama87I CYCGRG 1 cut(s) 1028
AoxI GGCC 1 cut(s) 95
ApeKI GCWGC 3 cut(s) 416, 611, 1238
ApoI RAATTY 7 cut(s) 192, 217, 356, 670, 770, 1087, 1352
AseI ATTAAT 1 cut(s) 780
AspLEI GCGC 2 cut(s) 55, 57
AspS9I GGNCC 3 cut(s) 313, 435, 997
AvaI CYCGRG 1 cut(s) 1028
AvaII GGWCC 3 cut(s) 313, 435, 997
BaeI ACNNNNGTAYC 2 cut(s) 633, 666
BbrPI CACGTG 1 cut(s) 656
BbsI GAAGAC 2 cut(s) 908, 1011
BbvI GCAGC 3 cut(s) 403, 623, 1225
BccI CCATC 5 cut(s) 287, 672, 1192, 1267, 1313
BcgI CGANNNNNNTGC 4 cut(s) 26, 60, 1157, 1191
BciT130I CCWGG 2 cut(s) 94, 618
BcoDI GTCTC 1 cut(s) 743
BfaI CTAG 1 cut(s) 1364
BfmI CTRYAG 1 cut(s) 1239
BfuAI ACCTGC 1 cut(s) 1232
BisI GCNGC 4 cut(s) 417, 612, 1236, 1239
BlsI GCNGC 4 cut(s) 418, 613, 1237, 1240
Bme1390I CCNGG 2 cut(s) 94, 618
Bme18I GGWCC 3 cut(s) 313, 435, 997
BmeT110I CYCGRG 1 cut(s) 1028
BmgBI CACGTC 1 cut(s) 1292
BmgT120I GGNCC 3 cut(s) 313, 435, 997
BmiI GGNNCC 2 cut(s) 286, 998
BmrFI CCNGG 2 cut(s) 94, 618
BmsI GCATC 4 cut(s) 372, 586, 947, 1267
BpiI GAAGAC 2 cut(s) 908, 1011
BpmI CTGGAG 1 cut(s) 774
BpuEI CTTGAG 1 cut(s) 567
BsaAI YACGTR 1 cut(s) 656
BsaJI CCNNGG 4 cut(s) 66, 98, 887, 991
BsaWI WCCGGW 1 cut(s) 310
Bsc4I CCNNNNNNNGG 6 cut(s) 99, 294, 410, 687, 1227, 1319
Bse1I ACTGG 3 cut(s) 79, 757, 1176
Bse3DI GCAATG 3 cut(s) 751, 829, 1259
BseBI CCWGG 2 cut(s) 94, 618
BseDI CCNNGG 4 cut(s) 66, 98, 887, 991
BseGI GGATG 5 cut(s) 577, 664, 897, 1203, 1282
BseLI CCNNNNNNNGG 6 cut(s) 99, 294, 410, 687, 1227, 1319
BseMI GCAATG 3 cut(s) 751, 829, 1259
BseMII CTCAG 3 cut(s) 636, 640, 867
BseNI ACTGG 3 cut(s) 79, 757, 1176
BsePI GCGCGC 1 cut(s) 53
BseRI GAGGAG 2 cut(s) 740, 743
BseXI GCAGC 3 cut(s) 403, 623, 1225
BseYI CCCAGC 1 cut(s) 1306
BsgI GTGCAG 2 cut(s) 630, 1266
Bsh1236I CGCG 1 cut(s) 55
BshFI GGCC 1 cut(s) 97
BsiHKCI CYCGRG 1 cut(s) 1028
BsiSI CCGG 2 cut(s) 311, 429
BslI CCNNNNNNNGG 6 cut(s) 99, 294, 410, 687, 1227, 1319
BsmAI GTCTC 1 cut(s) 743
BsmI GAATGC 1 cut(s) 509
BsnI GGCC 1 cut(s) 97
BsoBI CYCGRG 1 cut(s) 1028
Bsp143I GATC 2 cut(s) 37, 1357
BspACI CCGC 2 cut(s) 1236, 1361
BspANI GGCC 1 cut(s) 97
BspCNI CTCAG 3 cut(s) 637, 639, 868
BspFNI CGCG 1 cut(s) 55
BspLI GGNNCC 2 cut(s) 286, 998
BspMAI CTGCAG 1 cut(s) 1243
BspMI ACCTGC 1 cut(s) 1232
BspPI GGATC 2 cut(s) 32, 1352
BsrDI GCAATG 3 cut(s) 751, 829, 1259
BsrI ACTGG 3 cut(s) 79, 757, 1176
BssECI CCNNGG 4 cut(s) 66, 98, 887, 991
BssHII GCGCGC 1 cut(s) 53
BssMI GATC 2 cut(s) 37, 1357
BssT1I CCWWGG 3 cut(s) 66, 98, 991
Bst2UI CCWGG 2 cut(s) 94, 618
Bst4CI ACNGT 4 cut(s) 325, 424, 634, 1052
BstBAI YACGTR 1 cut(s) 656
BstC8I GCNNGC 1 cut(s) 55
BstDEI CTNAG 3 cut(s) 626, 645, 876
BstDSI CCRYGG 1 cut(s) 887
BstENI CCTNNNNNAGG 1 cut(s) 1225
BstF5I GGATG 5 cut(s) 577, 664, 897, 1203, 1282
BstFNI CGCG 1 cut(s) 55
BstHHI GCGC 2 cut(s) 55, 57
BstKTI GATC 2 cut(s) 40, 1360
BstMAI GTCTC 1 cut(s) 743
BstMBI GATC 2 cut(s) 37, 1357
BstMWI GCNNNNNNNGC 3 cut(s) 425, 1244, 1307
BstNI CCWGG 2 cut(s) 94, 618
BstNSI RCATGY 1 cut(s) 1287
BstSCI CCNGG 2 cut(s) 92, 616
BstSFI CTRYAG 1 cut(s) 1239
BstUI CGCG 1 cut(s) 55
BstV1I GCAGC 3 cut(s) 403, 623, 1225
BstV2I GAAGAC 2 cut(s) 908, 1011
BsuRI GGCC 1 cut(s) 97
BtgI CCRYGG 1 cut(s) 887
BtrI CACGTC 1 cut(s) 1292
BtsCI GGATG 5 cut(s) 577, 664, 897, 1203, 1282
BtsIMutI CAGTG 3 cut(s) 321, 498, 852
BveI ACCTGC 1 cut(s) 1232
Cac8I GCNNGC 1 cut(s) 55
CaiI CAGNNNCTG 2 cut(s) 385, 644
CfoI GCGC 2 cut(s) 55, 57
Cfr13I GGNCC 3 cut(s) 313, 435, 997
CpoI CGGWCCG 1 cut(s) 435
CseI GACGC 1 cut(s) 1265
Csp6I GTAC 2 cut(s) 168, 1041
CspI CGGWCCG 1 cut(s) 435
CviAII CATG 7 cut(s) 85, 278, 800, 1024, 1139, 1159, 1284
CviQI GTAC 2 cut(s) 168, 1041
DdeI CTNAG 3 cut(s) 626, 645, 876
DpnI GATC 2 cut(s) 39, 1359
DpnII GATC 2 cut(s) 37, 1357
Eco130I CCWWGG 3 cut(s) 66, 98, 991
Eco147I AGGCCT 1 cut(s) 97
Eco47I GGWCC 3 cut(s) 313, 435, 997
Eco72I CACGTG 1 cut(s) 656
Eco88I CYCGRG 1 cut(s) 1028
EcoNI CCTNNNNNAGG 1 cut(s) 1225
EcoRI GAATTC 2 cut(s) 1087, 1352
EcoRII CCWGG 2 cut(s) 92, 616
EcoT14I CCWWGG 3 cut(s) 66, 98, 991
EcoT22I ATGCAT 1 cut(s) 509
ErhI CCWWGG 3 cut(s) 66, 98, 991
FaeI CATG 7 cut(s) 88, 281, 803, 1027, 1142, 1162, 1287
FalI AAGNNNNNCTT 4 cut(s) 59, 91, 456, 488
FatI CATG 7 cut(s) 84, 277, 799, 1023, 1138, 1158, 1283
Fnu4HI GCNGC 4 cut(s) 417, 612, 1236, 1239
FokI GGATG 5 cut(s) 584, 651, 904, 1210, 1289
Fsp4HI GCNGC 4 cut(s) 417, 612, 1236, 1239
FspBI CTAG 1 cut(s) 1364
GlaI GCGC 2 cut(s) 54, 56
GluI GCNGC 4 cut(s) 417, 612, 1236, 1239
GsaI CCCAGC 1 cut(s) 1310
GsuI CTGGAG 1 cut(s) 774
HaeIII GGCC 1 cut(s) 97
HapII CCGG 2 cut(s) 311, 429
HgaI GACGC 1 cut(s) 1265
HhaI GCGC 2 cut(s) 55, 57
Hin1II CATG 7 cut(s) 88, 281, 803, 1027, 1142, 1162, 1287
Hin6I GCGC 2 cut(s) 53, 55
HinP1I GCGC 2 cut(s) 53, 55
HindIII AAGCTT 1 cut(s) 73
HinfI GANTC 4 cut(s) 447, 469, 913, 1185
HpaII CCGG 2 cut(s) 311, 429
Hpy166II GTNNAC 2 cut(s) 1000, 1062
Hpy188I TCNGA 4 cut(s) 127, 144, 514, 814
Hpy188III TCNNGA 6 cut(s) 259, 464, 584, 628, 1133, 1378
Hpy8I GTNNAC 2 cut(s) 1000, 1062
HpyAV CCTTC 3 cut(s) 404, 1146, 1375
HpyCH4III ACNGT 4 cut(s) 325, 424, 634, 1052
HpyCH4IV ACGT 4 cut(s) 254, 655, 861, 1291
HpyF10VI GCNNNNNNNGC 3 cut(s) 425, 1244, 1307
HpyF3I CTNAG 3 cut(s) 626, 645, 876
HpySE526I ACGT 4 cut(s) 254, 655, 861, 1291
Hsp92II CATG 7 cut(s) 88, 281, 803, 1027, 1142, 1162, 1287
HspAI GCGC 2 cut(s) 53, 55
Kzo9I GATC 2 cut(s) 37, 1357
LmnI GCTCC 3 cut(s) 543, 1135, 1315
Lsp1109I GCAGC 3 cut(s) 403, 623, 1225
LweI GCATC 4 cut(s) 372, 586, 947, 1267
MaeI CTAG 1 cut(s) 1364
MaeII ACGT 4 cut(s) 254, 655, 861, 1291
MaeIII GTNAC 2 cut(s) 448, 640
MalI GATC 2 cut(s) 39, 1359
MboI GATC 2 cut(s) 37, 1357
MboII GAAGA 5 cut(s) 518, 892, 908, 1011, 1361
MfeI CAATTG 1 cut(s) 486
MlyI GAGTC 2 cut(s) 456, 922
MmeI TCCRAC 2 cut(s) 817, 1057
Mph1103I ATGCAT 1 cut(s) 509
MseI TTAA 5 cut(s) 459, 714, 774, 780, 845
MspA1I CMGCKG 1 cut(s) 1238
MspI CCGG 2 cut(s) 311, 429
MspR9I CCNGG 2 cut(s) 94, 618
MunI CAATTG 1 cut(s) 486
Mva1269I GAATGC 1 cut(s) 509
MvaI CCWGG 2 cut(s) 94, 618
MvnI CGCG 1 cut(s) 55
MwoI GCNNNNNNNGC 3 cut(s) 425, 1244, 1307
NdeII GATC 2 cut(s) 37, 1357
NlaIII CATG 7 cut(s) 88, 281, 803, 1027, 1142, 1162, 1287
NlaIV GGNNCC 2 cut(s) 286, 998
NmuCI GTSAC 1 cut(s) 448
NsiI ATGCAT 1 cut(s) 509
NspI RCATGY 1 cut(s) 1287
PaeR7I CTCGAG 1 cut(s) 1028
PaqCI CACCTGC 1 cut(s) 1232
PauI GCGCGC 1 cut(s) 53
PceI AGGCCT 1 cut(s) 97
PctI GAATGC 1 cut(s) 509
PfeI GAWTC 2 cut(s) 469, 1185
PflMI CCANNNNNTGG 2 cut(s) 99, 1319
PkrI GCNGC 4 cut(s) 418, 613, 1237, 1240
PleI GAGTC 2 cut(s) 455, 921
PmaCI CACGTG 1 cut(s) 656
PmlI CACGTG 1 cut(s) 656
PpsI GAGTC 2 cut(s) 455, 921
Ppu21I YACGTR 1 cut(s) 656
PshBI ATTAAT 1 cut(s) 780
Psp6I CCWGG 2 cut(s) 92, 616
PspCI CACGTG 1 cut(s) 656
PspFI CCCAGC 1 cut(s) 1306
PspGI CCWGG 2 cut(s) 92, 616
PspN4I GGNNCC 2 cut(s) 286, 998
PspPI GGNCC 3 cut(s) 313, 435, 997
PspXI VCTCGAGB 1 cut(s) 1028
PstI CTGCAG 1 cut(s) 1243
PstNI CAGNNNCTG 2 cut(s) 385, 644
PteI GCGCGC 1 cut(s) 53
RsaI GTAC 2 cut(s) 169, 1042
RsaNI GTAC 2 cut(s) 168, 1041
Rsr2I CGGWCCG 1 cut(s) 435
RsrII CGGWCCG 1 cut(s) 435
SaqAI TTAA 5 cut(s) 459, 714, 774, 780, 845
SatI GCNGC 4 cut(s) 417, 612, 1236, 1239
Sau3AI GATC 2 cut(s) 37, 1357
Sau96I GGNCC 3 cut(s) 313, 435, 997
SchI GAGTC 2 cut(s) 456, 922
ScrFI CCNGG 2 cut(s) 94, 618
SfaNI GCATC 4 cut(s) 372, 586, 947, 1267
SfcI CTRYAG 1 cut(s) 1239
Sfr274I CTCGAG 1 cut(s) 1028
SinI GGWCC 3 cut(s) 313, 435, 997
SlaI CTCGAG 1 cut(s) 1028
SmlI CTYRAG 2 cut(s) 582, 1028
SmoI CTYRAG 2 cut(s) 582, 1028
SseBI AGGCCT 1 cut(s) 97
SsiI CCGC 2 cut(s) 1236, 1361
SspMI CTAG 1 cut(s) 1364
StuI AGGCCT 1 cut(s) 97
StyD4I CCNGG 2 cut(s) 92, 616
StyI CCWWGG 3 cut(s) 66, 98, 991
TaaI ACNGT 4 cut(s) 325, 424, 634, 1052
TaiI ACGT 4 cut(s) 257, 658, 864, 1294
TaqI TCGA 5 cut(s) 114, 1029, 1167, 1356, 1379
TaqII GACCGA 1 cut(s) 452
TatI WGTACW 1 cut(s) 1040
TauI GCSGC 1 cut(s) 1238
TfiI GAWTC 2 cut(s) 469, 1185
Tru1I TTAA 5 cut(s) 459, 714, 774, 780, 845
Tru9I TTAA 5 cut(s) 459, 714, 774, 780, 845
TscAI CASTG 3 cut(s) 328, 505, 859
TseFI GTSAC 1 cut(s) 448
TseI GCWGC 3 cut(s) 416, 611, 1238
Tsp45I GTSAC 1 cut(s) 448
TspDTI ATGAA 4 cut(s) 73, 816, 1155, 1362
TspGWI ACGGA 3 cut(s) 448, 904, 1081
TspRI CASTG 3 cut(s) 328, 505, 859
Van91I CCANNNNNTGG 2 cut(s) 99, 1319
VpaK11BI GGWCC 3 cut(s) 313, 435, 997
VspI ATTAAT 1 cut(s) 780
XagI CCTNNNNNAGG 1 cut(s) 1225
XapI RAATTY 7 cut(s) 192, 217, 356, 670, 770, 1087, 1352
XceI RCATGY 1 cut(s) 1287
XhoI CTCGAG 1 cut(s) 1028
XspI CTAG 1 cut(s) 1364
Zsp2I ATGCAT 1 cut(s) 509
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.