FvH4_3g33250

tRNA pseudouridine

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
fragaria_vesca
Fvb3
OG0004793
Physical Location & Seq
Reverse (-)
28639005 .. 28644210
5206 bp
Loading structure...
UTR
Exon/CDS
Intron
FvH4_3g33250.t1

Sequence Viewer

Length: 1053 bp
ATGTCAGAAAATCTTAAGCACTCACTAGAGAGCCGCTCCCAATCTCCCAAAAGACCTTCAAAGATTTCCAAAACCACAAGCGAAGAAGCAGAAGCAGAATCCATGAGCAAACCCCAGGGAATCCAACGCTATCTGATCGCAATAGAGTACATTGGCACTCGCTTCTCTGGCTCTCAGCAACAGTCCAATTGCCGCACTGTTGTTGGCGTTCTTGAGGAGGCTTTTCGCAAATTTATTGGGCAGCCAGTGTCAATCTTCTGTTCGAGTCGAACTGATGCTGGAGTTCATGCTTTATCCAATGTTTGTCATGTAGATATTGAGCGCATAAGCAAAAGAAAGCCTGGTGAAGTGTTACCACCTCATGAACCTATAGTGGTCCAAAGAGCTGTAAACCATTTCTTACAGAAGAATGAAGGTGATGTAATGGTGGTTGATGTTCGAAGTGTTCCAGCTGATTTTCATGCTAGATTTAAAGCCCAAGAACGCACGTACTTCTATCGCTTGCTATCTGGGCCAGAGCCTTTGTCAACCTTTGAAAAAGACCGCGCATGGCATATACCTGAGGAGCTGGATGTTTTGGCTATGCAGGAAGCCTGCAAAATTCTGGTTGGACACCATGATTTTAGTTCATTTAGAGCAGCAGGTTGTCAGGCGAAGTCACCGATCAGAACACTAGATGAGTTAAATGTGTCTGAGGTTGTCTCATCTCCAAACTTTCCAACAATAGCAGAGAGGACAAGAAATTTAGTGCAGAAAGATATTCAGTGCACCAACAATCCCGAGGCCGACTGCCACTCTAGTTTCAATGGAGGAACTGATCAAGGATTTGGCTTGAGGAAAAAACACAGATGCATTGTTGTAACCGCACGAGCACGTGCCTTTCTATACCACCAGGTAAGACTGCTTGTTGGTGTCCTCAAATGTGTTGGAACTGGAGATCTAAAAATACCTGACGTGGAGAGGATTTTGAATGCAAAGACAGTGACTGCTGCTAGCCCCATGGCGCCTGCTTGTGGTCTATATCTTGGACATGTGAGATACGATTTGCCATGA
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

351

Amino Acids

38.98

Weight (kDa)

8.76

Isoelectric Point (pI)

49.97

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
PseudoU_synth_1 PF01416 46 - 119 2e-07 tRNA pseudouridine synthase
PseudoU_synth_1 PF01416 198 - 348 2.7e-25 tRNA pseudouridine synthase
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

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Publication-ready
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Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
Acc36I ACCTGC 1 cut(s) 632
AccB1I GGYRCC 1 cut(s) 1003
AccBSI CCGCTC 1 cut(s) 36
AccII CGCG 1 cut(s) 546
AciI CCGC 4 cut(s) 34, 193, 544, 864
AcsI RAATTY 3 cut(s) 230, 600, 742
AcvI CACGTG 1 cut(s) 875
AcyI GRCGYC 1 cut(s) 1004
AfaI GTAC 2 cut(s) 149, 491
AfiI CCNNNNNNNGG 1 cut(s) 1013
AflII CTTAAG 1 cut(s) 14
AflIII ACRYGT 1 cut(s) 1030
AgsI TTSAA 4 cut(s) 60, 536, 805, 970
AjiI CACGTC 1 cut(s) 955
AjnI CCWGG 3 cut(s) 114, 340, 891
AluBI AGCT 3 cut(s) 386, 452, 568
AluI AGCT 3 cut(s) 386, 452, 568
Alw21I GWGCWC 2 cut(s) 770, 874
Alw26I GTCTC 1 cut(s) 706
Alw44I GTGCAC 1 cut(s) 766
AlwNI CAGNNNCTG 1 cut(s) 986
Ama87I CYCGRG 1 cut(s) 779
AoxI GGCC 2 cut(s) 512, 783
ApaLI GTGCAC 1 cut(s) 766
ApeKI GCWGC 3 cut(s) 241, 638, 989
ApoI RAATTY 3 cut(s) 230, 600, 742
AspLEI GCGC 3 cut(s) 324, 548, 1006
AspS9I GGNCC 2 cut(s) 376, 512
AsuHPI GGTGA 3 cut(s) 356, 428, 651
AsuII TTCGAA 1 cut(s) 439
AsuNHI GCTAGC 1 cut(s) 992
AvaI CYCGRG 1 cut(s) 779
AvaII GGWCC 1 cut(s) 376
AxyI CCTNAGG 1 cut(s) 561
BaeGI GKGCMC 1 cut(s) 770
BanI GGYRCC 1 cut(s) 1003
BauI CACGAG 1 cut(s) 867
BbrPI CACGTG 1 cut(s) 875
Bbv12I GWGCWC 2 cut(s) 770, 874
BbvI GCAGC 3 cut(s) 253, 650, 976
BciT130I CCWGG 3 cut(s) 116, 342, 893
BclI TGATCA 1 cut(s) 817
BcoDI GTCTC 1 cut(s) 706
BfaI CTAG 5 cut(s) 26, 465, 674, 798, 993
BfmI CTRYAG 1 cut(s) 369
BfoI RGCGCY 1 cut(s) 1007
BfrI CTTAAG 1 cut(s) 14
BfuAI ACCTGC 1 cut(s) 632
BglII AGATCT 1 cut(s) 937
BisI GCNGC 5 cut(s) 34, 193, 242, 639, 990
BlsI GCNGC 5 cut(s) 35, 194, 243, 640, 991
Bme1390I CCNGG 3 cut(s) 116, 342, 893
Bme18I GGWCC 1 cut(s) 376
BmeT110I CYCGRG 1 cut(s) 779
BmgBI CACGTC 1 cut(s) 955
BmgT120I GGNCC 2 cut(s) 376, 512
BmiI GGNNCC 1 cut(s) 1005
BmrFI CCNGG 3 cut(s) 116, 342, 893
BmsI GCATC 2 cut(s) 265, 839
BmtI GCTAGC 1 cut(s) 996
BplI GAGNNNNNCTC 4 cut(s) 20, 52, 686, 718
BpmI CTGGAG 2 cut(s) 300, 954
Bpu14I TTCGAA 1 cut(s) 439
BpuEI CTTGAG 2 cut(s) 233, 853
BsaAI YACGTR 2 cut(s) 489, 875
BsaHI GRCGYC 1 cut(s) 1004
BsaJI CCNNGG 4 cut(s) 114, 115, 780, 999
Bsc4I CCNNNNNNNGG 1 cut(s) 1013
Bse1I ACTGG 2 cut(s) 245, 937
Bse21I CCTNAGG 1 cut(s) 561
BseBI CCWGG 3 cut(s) 116, 342, 893
BseDI CCNNGG 4 cut(s) 114, 115, 780, 999
BseGI GGATG 1 cut(s) 577
BseLI CCNNNNNNNGG 1 cut(s) 1013
BseMII CTCAG 3 cut(s) 188, 552, 684
BseNI ACTGG 2 cut(s) 245, 937
BseRI GAGGAG 2 cut(s) 230, 578
BseSI GKGCMC 1 cut(s) 770
BseXI GCAGC 3 cut(s) 253, 650, 976
BsgI GTGCAG 1 cut(s) 770
Bsh1236I CGCG 1 cut(s) 546
BshFI GGCC 2 cut(s) 514, 785
BshNI GGYRCC 1 cut(s) 1003
BsiHKAI GWGCWC 2 cut(s) 770, 874
BsiHKCI CYCGRG 1 cut(s) 779
BslI CCNNNNNNNGG 1 cut(s) 1013
BsmAI GTCTC 1 cut(s) 706
BsmI GAATGC 1 cut(s) 976
BsnI GGCC 2 cut(s) 514, 785
BsoBI CYCGRG 1 cut(s) 779
Bsp119I TTCGAA 1 cut(s) 439
Bsp1286I GDGCHC 2 cut(s) 770, 874
Bsp143I GATC 4 cut(s) 135, 663, 817, 937
Bsp19I CCATGG 1 cut(s) 999
BspACI CCGC 4 cut(s) 34, 193, 544, 864
BspANI GGCC 2 cut(s) 514, 785
BspCNI CTCAG 3 cut(s) 187, 553, 685
BspFNI CGCG 1 cut(s) 546
BspHI TCATGA 1 cut(s) 361
BspLI GGNNCC 1 cut(s) 1005
BspMI ACCTGC 1 cut(s) 632
BspOI GCTAGC 1 cut(s) 996
BspT104I TTCGAA 1 cut(s) 439
BspT107I GGYRCC 1 cut(s) 1003
BspTI CTTAAG 1 cut(s) 14
BsrBI CCGCTC 1 cut(s) 36
BsrI ACTGG 2 cut(s) 245, 937
BssECI CCNNGG 4 cut(s) 114, 115, 780, 999
BssMI GATC 4 cut(s) 135, 663, 817, 937
BssNI GRCGYC 1 cut(s) 1004
BssSI CACGAG 1 cut(s) 867
BssT1I CCWWGG 1 cut(s) 999
Bst2BI CACGAG 1 cut(s) 867
Bst2UI CCWGG 3 cut(s) 116, 342, 893
Bst4CI ACNGT 3 cut(s) 183, 199, 982
BstACI GRCGYC 1 cut(s) 1004
BstAFI CTTAAG 1 cut(s) 14
BstBAI YACGTR 2 cut(s) 489, 875
BstBI TTCGAA 1 cut(s) 439
BstC8I GCNNGC 4 cut(s) 503, 595, 994, 1008
BstDEI CTNAG 3 cut(s) 174, 561, 693
BstDSI CCRYGG 1 cut(s) 999
BstF5I GGATG 1 cut(s) 577
BstFNI CGCG 1 cut(s) 546
BstH2I RGCGCY 1 cut(s) 1007
BstHHI GCGC 3 cut(s) 324, 548, 1006
BstKTI GATC 4 cut(s) 138, 666, 820, 940
BstMAI GTCTC 1 cut(s) 706
BstMBI GATC 4 cut(s) 135, 663, 817, 937
BstMWI GCNNNNNNNGC 2 cut(s) 168, 511
BstNI CCWGG 3 cut(s) 116, 342, 893
BstNSI RCATGY 1 cut(s) 1034
BstSCI CCNGG 3 cut(s) 114, 340, 891
BstSFI CTRYAG 1 cut(s) 369
BstSLI GKGCMC 1 cut(s) 770
BstUI CGCG 1 cut(s) 546
BstV1I GCAGC 3 cut(s) 253, 650, 976
BstX2I RGATCY 1 cut(s) 937
BstYI RGATCY 1 cut(s) 937
Bsu36I CCTNAGG 1 cut(s) 561
BsuRI GGCC 2 cut(s) 514, 785
BtgI CCRYGG 1 cut(s) 999
BtrI CACGTC 1 cut(s) 955
BtsCI GGATG 1 cut(s) 577
BtsIMutI CAGTG 4 cut(s) 195, 252, 770, 987
BveI ACCTGC 1 cut(s) 632
Cac8I GCNNGC 4 cut(s) 503, 595, 994, 1008
CaiI CAGNNNCTG 1 cut(s) 986
CciI TCATGA 1 cut(s) 361
CfoI GCGC 3 cut(s) 324, 548, 1006
Cfr13I GGNCC 2 cut(s) 376, 512
CsiI ACCWGGT 1 cut(s) 891
Csp6I GTAC 2 cut(s) 148, 490
CviQI GTAC 2 cut(s) 148, 490
DdeI CTNAG 3 cut(s) 174, 561, 693
DinI GGCGCC 1 cut(s) 1005
DpnI GATC 4 cut(s) 137, 665, 819, 939
DpnII GATC 4 cut(s) 135, 663, 817, 937
DraI TTTAAA 1 cut(s) 472
Eco130I CCWWGG 1 cut(s) 999
Eco47I GGWCC 1 cut(s) 376
Eco72I CACGTG 1 cut(s) 875
Eco81I CCTNAGG 1 cut(s) 561
Eco88I CYCGRG 1 cut(s) 779
EcoRII CCWGG 3 cut(s) 114, 340, 891
EcoT14I CCWWGG 1 cut(s) 999
EcoT22I ATGCAT 1 cut(s) 854
EgeI GGCGCC 1 cut(s) 1005
EheI GGCGCC 1 cut(s) 1005
ErhI CCWWGG 1 cut(s) 999
FbaI TGATCA 1 cut(s) 817
Fnu4HI GCNGC 5 cut(s) 34, 193, 242, 639, 990
FokI GGATG 1 cut(s) 584
Fsp4HI GCNGC 5 cut(s) 34, 193, 242, 639, 990
FspBI CTAG 5 cut(s) 26, 465, 674, 798, 993
GlaI GCGC 3 cut(s) 323, 547, 1005
GluI GCNGC 5 cut(s) 34, 193, 242, 639, 990
GsuI CTGGAG 2 cut(s) 300, 954
HaeII RGCGCY 1 cut(s) 1007
HaeIII GGCC 2 cut(s) 514, 785
HhaI GCGC 3 cut(s) 324, 548, 1006
Hin1I GRCGYC 1 cut(s) 1004
Hin6I GCGC 3 cut(s) 322, 546, 1004
HinP1I GCGC 3 cut(s) 322, 546, 1004
HincII GTYRAC 1 cut(s) 528
HindII GTYRAC 1 cut(s) 528
HinfI GANTC 3 cut(s) 98, 120, 265
HphI GGTGA 3 cut(s) 356, 428, 651
Hpy166II GTNNAC 3 cut(s) 391, 528, 768
Hpy188I TCNGA 4 cut(s) 7, 135, 668, 694
Hpy188III TCNNGA 3 cut(s) 212, 362, 779
Hpy8I GTNNAC 3 cut(s) 391, 528, 768
HpyAV CCTTC 2 cut(s) 66, 407
HpyCH4III ACNGT 3 cut(s) 183, 199, 982
HpyCH4IV ACGT 3 cut(s) 488, 874, 954
HpyCH4V TGCA 6 cut(s) 586, 597, 751, 768, 852, 974
HpyF10VI GCNNNNNNNGC 2 cut(s) 168, 511
HpyF3I CTNAG 3 cut(s) 174, 561, 693
HpySE526I ACGT 3 cut(s) 488, 874, 954
Hsp92I GRCGYC 1 cut(s) 1004
HspAI GCGC 3 cut(s) 322, 546, 1004
KasI GGCGCC 1 cut(s) 1003
Ksp22I TGATCA 1 cut(s) 817
Kzo9I GATC 4 cut(s) 135, 663, 817, 937
LmnI GCTCC 2 cut(s) 41, 565
Lsp1109I GCAGC 3 cut(s) 253, 650, 976
LweI GCATC 2 cut(s) 265, 839
MabI ACCWGGT 1 cut(s) 891
MaeI CTAG 5 cut(s) 26, 465, 674, 798, 993
MaeII ACGT 3 cut(s) 488, 874, 954
MaeIII GTNAC 4 cut(s) 351, 657, 859, 982
MalI GATC 4 cut(s) 137, 665, 819, 939
MbiI CCGCTC 1 cut(s) 36
MboI GATC 4 cut(s) 135, 663, 817, 937
MboII GAAGA 3 cut(s) 95, 247, 418
MfeI CAATTG 1 cut(s) 187
MflI RGATCY 1 cut(s) 937
MhlI GDGCHC 2 cut(s) 770, 874
MluCI AATT 4 cut(s) 187, 230, 600, 742
Mly113I GGCGCC 1 cut(s) 1004
MlyI GAGTC 1 cut(s) 274
MmeI TCCRAC 4 cut(s) 148, 589, 743, 907
Mph1103I ATGCAT 1 cut(s) 854
MseI TTAA 3 cut(s) 15, 471, 683
MspA1I CMGCKG 1 cut(s) 452
MspCI CTTAAG 1 cut(s) 14
MspR9I CCNGG 3 cut(s) 116, 342, 893
MunI CAATTG 1 cut(s) 187
Mva1269I GAATGC 1 cut(s) 976
MvaI CCWGG 3 cut(s) 116, 342, 893
MvnI CGCG 1 cut(s) 546
MwoI GCNNNNNNNGC 2 cut(s) 168, 511
NarI GGCGCC 1 cut(s) 1004
NcoI CCATGG 1 cut(s) 999
NdeII GATC 4 cut(s) 135, 663, 817, 937
NheI GCTAGC 1 cut(s) 992
NlaIV GGNNCC 1 cut(s) 1005
NmuCI GTSAC 2 cut(s) 657, 982
NsiI ATGCAT 1 cut(s) 854
NspI RCATGY 1 cut(s) 1034
NspV TTCGAA 1 cut(s) 439
PagI TCATGA 1 cut(s) 361
PasI CCCWGGG 1 cut(s) 115
PciI ACATGT 1 cut(s) 1030
PctI GAATGC 1 cut(s) 976
PfeI GAWTC 2 cut(s) 98, 120
PkrI GCNGC 5 cut(s) 35, 194, 243, 640, 991
PleI GAGTC 1 cut(s) 273
PluTI GGCGCC 1 cut(s) 1007
PmaCI CACGTG 1 cut(s) 875
PmlI CACGTG 1 cut(s) 875
PpsI GAGTC 1 cut(s) 273
Ppu21I YACGTR 2 cut(s) 489, 875
PscI ACATGT 1 cut(s) 1030
Psp6I CCWGG 3 cut(s) 114, 340, 891
PspCI CACGTG 1 cut(s) 875
PspGI CCWGG 3 cut(s) 114, 340, 891
PspN4I GGNNCC 1 cut(s) 1005
PspPI GGNCC 2 cut(s) 376, 512
PstNI CAGNNNCTG 1 cut(s) 986
PsuI RGATCY 1 cut(s) 937
PvuII CAGCTG 1 cut(s) 452
RsaI GTAC 2 cut(s) 149, 491
RsaNI GTAC 2 cut(s) 148, 490
SaqAI TTAA 3 cut(s) 15, 471, 683
SatI GCNGC 5 cut(s) 34, 193, 242, 639, 990
Sau3AI GATC 4 cut(s) 135, 663, 817, 937
Sau96I GGNCC 2 cut(s) 376, 512
SchI GAGTC 1 cut(s) 274
ScrFI CCNGG 3 cut(s) 116, 342, 893
SduI GDGCHC 2 cut(s) 770, 874
SexAI ACCWGGT 1 cut(s) 891
SfaNI GCATC 2 cut(s) 265, 839
SfcI CTRYAG 1 cut(s) 369
SfoI GGCGCC 1 cut(s) 1005
SfuI TTCGAA 1 cut(s) 439
SinI GGWCC 1 cut(s) 376
SmlI CTYRAG 3 cut(s) 14, 212, 832
SmoI CTYRAG 3 cut(s) 14, 212, 832
Sse9I AATT 4 cut(s) 187, 230, 600, 742
SsiI CCGC 4 cut(s) 34, 193, 544, 864
SspDI GGCGCC 1 cut(s) 1003
SspMI CTAG 5 cut(s) 26, 465, 674, 798, 993
StyD4I CCNGG 3 cut(s) 114, 340, 891
StyI CCWWGG 1 cut(s) 999
TaaI ACNGT 3 cut(s) 183, 199, 982
TaiI ACGT 3 cut(s) 491, 877, 957
TaqI TCGA 3 cut(s) 263, 268, 439
TasI AATT 4 cut(s) 187, 230, 600, 742
TatI WGTACW 1 cut(s) 147
TauI GCSGC 2 cut(s) 36, 195
TfiI GAWTC 2 cut(s) 98, 120
Tru1I TTAA 3 cut(s) 15, 471, 683
Tru9I TTAA 3 cut(s) 15, 471, 683
TscAI CASTG 4 cut(s) 202, 252, 770, 987
TseFI GTSAC 2 cut(s) 657, 982
TseI GCWGC 3 cut(s) 241, 638, 989
Tsp45I GTSAC 2 cut(s) 657, 982
TspDTI ATGAA 5 cut(s) 275, 378, 426, 449, 618
TspRI CASTG 4 cut(s) 202, 252, 770, 987
Vha464I CTTAAG 1 cut(s) 14
VneI GTGCAC 1 cut(s) 766
VpaK11BI GGWCC 1 cut(s) 376
XapI RAATTY 3 cut(s) 230, 600, 742
XceI RCATGY 1 cut(s) 1034
XspI CTAG 5 cut(s) 26, 465, 674, 798, 993
Zsp2I ATGCAT 1 cut(s) 854
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.