AT5G51170

Phosphodiesterase responsible for the U6 snRNA 3' end processing. Acts as an exoribonuclease (RNase) responsible for trimming the poly(U) tract of the last nucleotides in the pre-U6 snRNA molecule, leading to the formation of mature U6 snRNA

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
arabidopsis_thaliana
5
OG0006090
Physical Location & Seq
Reverse (-)
20793794 .. 20795399
1606 bp
Loading structure...
UTR
Exon/CDS
Intron
AT5G51170.3

Sequence Viewer

Length: 858 bp
ATGGAAGCATTGAGAGCGTCCTACGGCGACTCTTCATCGGATTCCGATACCGATGATCTTTCTCCGGCGAGTCCCGTTACTGCAAATTCTGGAGAGAAAGATTCGATTTCCTTGCCTCCTCCACCGCTTGCGCTTCTCGATTCCATTGTATCCACAGGTTCACTGGATTTCTTCTCAACAGAGCCTGGAGTTCGTGTAAGAAACTTTCCTCATGTCGATGGAAATTACGCTTTGCACGTTTACGTACCTGTTTGTATACCTCCACTGCCAAAGAAGGAGATTGTATGTTTTTTAAAGAAGGTTGCATCAGTTGTTCCTCATCTTCATTTGGTAGAGGCTGATGTGCCACTCAGCATTCTATGCAAGGATGATCAGAAGTTTGAGCGTGCCTTGGGGAGAGAGTTCCACATAAGCTTAGGAAGAAACGTTCCACTACGTGTTCATCAGATTAACTCGGTGATTTCTATGCTTCGGCAAAAGCTTCAGTTGCAGAAGAGATACTTGATAGATTTCAATAAGTGGGAAGTCTTTGTGAATGATGACCATACTCGCTCTTTCCTTTCTTTGGAAATCACTACTTCAGGACTATCCGAGATAAGTAAGCAAATTGATGCTGTTAATGAAGTTTACAAGCTCCACAATCTGCCGGAGTTCTACAAGGATCCGCGGCCGCATATATCCTTGGTCTGGGCGTTGGGTGATATTAGAACTTCCCTAAAGGGAGCTGTTGACGTGGAACTTAGGAAGCTTAGAGCAGGTGGTTGTGTGCAGAATCGTATCTTCACCTCTAAGTTTTGTGGGATCGAGTGTAAGATAGGAAACAAAACACACAAAATATGTAAACTCCCAGATGAATAA
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
HVSL

Protein Analysis

285

Amino Acids

31.85

Weight (kDa)

7.13

Isoelectric Point (pI)

45.21

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HVSL PF09749 66 - 217 1.6e-42 Uncharacterised conserved protein
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) 746
Acc36I ACCTGC 1 cut(s) 746
AccI GTMKAC 1 cut(s) 256
AccII CGCG 1 cut(s) 667
AciI CCGC 4 cut(s) 125, 665, 667, 671
AclI AACGTT 1 cut(s) 426
AclWI GGATC 3 cut(s) 656, 669, 809
AcoI YGGCCR 1 cut(s) 668
AcsI RAATTY 1 cut(s) 85
AcuI CTGAAG 2 cut(s) 467, 564
AdeI CACNNNGTG 1 cut(s) 437
AfaI GTAC 1 cut(s) 246
AfiI CCNNNNNNNGG 2 cut(s) 565, 687
AflIII ACRYGT 1 cut(s) 436
AgsI TTSAA 1 cut(s) 514
AjiI CACGTC 1 cut(s) 733
AjnI CCWGG 1 cut(s) 184
AloI GAACNNNNNNTCC 2 cut(s) 411, 443
AluBI AGCT 5 cut(s) 414, 481, 634, 725, 748
AluI AGCT 5 cut(s) 414, 481, 634, 725, 748
AlwI GGATC 3 cut(s) 656, 669, 809
AlwNI CAGNNNCTG 1 cut(s) 185
AoxI GGCC 1 cut(s) 668
ApoI RAATTY 1 cut(s) 85
AspLEI GCGC 1 cut(s) 133
AsuHPI GGTGA 3 cut(s) 469, 710, 775
BamHI GGATCC 1 cut(s) 661
BccI CCATC 1 cut(s) 212
BceAI ACGGC 1 cut(s) 40
BcgI CGANNNNNNTGC 2 cut(s) 94, 128
BciT130I CCWGG 1 cut(s) 186
BciVI GTATCC 1 cut(s) 160
BclI TGATCA 1 cut(s) 370
BfuAI ACCTGC 1 cut(s) 746
BfuI GTATCC 1 cut(s) 160
BisI GCNGC 2 cut(s) 668, 671
BlsI GCNGC 2 cut(s) 669, 672
Bme1390I CCNGG 1 cut(s) 186
BmgBI CACGTC 1 cut(s) 733
BmiI GGNNCC 1 cut(s) 663
BmrFI CCNGG 1 cut(s) 186
BmsI GCATC 2 cut(s) 314, 601
BpmI CTGGAG 2 cut(s) 111, 207
Bpu10I CCTNAGC 1 cut(s) 415
BsaAI YACGTR 2 cut(s) 244, 437
BsaJI CCNNGG 3 cut(s) 390, 665, 681
BsaXI ACNNNNNCTCC 2 cut(s) 180, 210
Bsc4I CCNNNNNNNGG 2 cut(s) 565, 687
Bse1I ACTGG 1 cut(s) 168
BseBI CCWGG 1 cut(s) 186
BseDI CCNNGG 3 cut(s) 390, 665, 681
BseGI GGATG 1 cut(s) 373
BseLI CCNNNNNNNGG 2 cut(s) 565, 687
BseMII CTCAG 1 cut(s) 364
BseNI ACTGG 1 cut(s) 168
BseRI GAGGAG 1 cut(s) 108
BseX3I CGGCCG 1 cut(s) 668
BsgI GTGCAG 1 cut(s) 788
Bsh1236I CGCG 1 cut(s) 667
Bsh1285I CGRYCG 1 cut(s) 671
BshFI GGCC 1 cut(s) 670
BsiEI CGRYCG 1 cut(s) 671
BsiSI CCGG 2 cut(s) 65, 647
BslFI GGGAC 1 cut(s) 57
BslI CCNNNNNNNGG 2 cut(s) 565, 687
BsmFI GGGAC 1 cut(s) 57
BsmI GAATGC 1 cut(s) 354
BsnI GGCC 1 cut(s) 670
Bsp143I GATC 4 cut(s) 55, 370, 661, 801
BspACI CCGC 4 cut(s) 125, 665, 667, 671
BspANI GGCC 1 cut(s) 670
BspCNI CTCAG 1 cut(s) 363
BspFNI CGCG 1 cut(s) 667
BspLI GGNNCC 1 cut(s) 663
BspMI ACCTGC 1 cut(s) 746
BspPI GGATC 3 cut(s) 656, 669, 809
BsrI ACTGG 1 cut(s) 168
BssECI CCNNGG 3 cut(s) 390, 665, 681
BssMI GATC 4 cut(s) 55, 370, 661, 801
BssNAI GTATAC 1 cut(s) 257
BssT1I CCWWGG 2 cut(s) 390, 681
Bst1107I GTATAC 1 cut(s) 257
Bst2UI CCWGG 1 cut(s) 186
Bst6I CTCTTC 2 cut(s) 37, 488
BstAPI GCANNNNNTGC 1 cut(s) 360
BstBAI YACGTR 2 cut(s) 244, 437
BstC8I GCNNGC 2 cut(s) 129, 387
BstDEI CTNAG 5 cut(s) 350, 415, 740, 749, 789
BstDSI CCRYGG 1 cut(s) 665
BstF5I GGATG 1 cut(s) 373
BstFNI CGCG 1 cut(s) 667
BstHHI GCGC 1 cut(s) 133
BstKTI GATC 4 cut(s) 58, 373, 664, 804
BstMBI GATC 4 cut(s) 55, 370, 661, 801
BstMCI CGRYCG 1 cut(s) 671
BstMWI GCNNNNNNNGC 3 cut(s) 14, 360, 487
BstNI CCWGG 1 cut(s) 186
BstSCI CCNGG 1 cut(s) 184
BstSNI TACGTA 1 cut(s) 244
BstUI CGCG 1 cut(s) 667
BstX2I RGATCY 1 cut(s) 661
BstYI RGATCY 1 cut(s) 661
BstZ17I GTATAC 1 cut(s) 257
BstZI CGGCCG 1 cut(s) 668
BsuI GTATCC 1 cut(s) 160
BsuRI GGCC 1 cut(s) 670
BtgI CCRYGG 1 cut(s) 665
BtrI CACGTC 1 cut(s) 733
BtsCI GGATG 1 cut(s) 373
BtsI GCAGTG 1 cut(s) 263
BtsIMutI CAGTG 2 cut(s) 161, 263
BveI ACCTGC 1 cut(s) 746
Cac8I GCNNGC 2 cut(s) 129, 387
CaiI CAGNNNCTG 1 cut(s) 185
CciNI GCGGCCGC 1 cut(s) 668
CfoI GCGC 1 cut(s) 133
Cfr42I CCGCGG 1 cut(s) 668
CseI GACGC 1 cut(s) 6
Csp6I GTAC 1 cut(s) 245
CviAII CATG 1 cut(s) 212
CviJI RGCY 8 cut(s) 184, 338, 414, 481, 634, 670, 725, 748
CviKI_1 RGCY 8 cut(s) 184, 338, 414, 481, 634, 670, 725, 748
CviQI GTAC 1 cut(s) 245
DdeI CTNAG 5 cut(s) 350, 415, 740, 749, 789
DpnI GATC 4 cut(s) 57, 372, 663, 803
DpnII GATC 4 cut(s) 55, 370, 661, 801
DraI TTTAAA 1 cut(s) 294
DraIII CACNNNGTG 1 cut(s) 437
EaeI YGGCCR 1 cut(s) 668
EagI CGGCCG 1 cut(s) 668
Eam1104I CTCTTC 2 cut(s) 37, 488
EarI CTCTTC 2 cut(s) 37, 488
EclXI CGGCCG 1 cut(s) 668
Eco105I TACGTA 1 cut(s) 244
Eco130I CCWWGG 2 cut(s) 390, 681
Eco52I CGGCCG 1 cut(s) 668
Eco57I CTGAAG 2 cut(s) 467, 564
EcoRII CCWGG 1 cut(s) 184
EcoT14I CCWWGG 2 cut(s) 390, 681
ErhI CCWWGG 2 cut(s) 390, 681
FaeI CATG 1 cut(s) 215
FalI AAGNNNNNCTT 2 cut(s) 485, 517
FaqI GGGAC 1 cut(s) 57
FatI CATG 1 cut(s) 211
FbaI TGATCA 1 cut(s) 370
FblI GTMKAC 1 cut(s) 256
Fnu4HI GCNGC 2 cut(s) 668, 671
FokI GGATG 1 cut(s) 380
Fsp4HI GCNGC 2 cut(s) 668, 671
GlaI GCGC 1 cut(s) 132
GluI GCNGC 2 cut(s) 668, 671
GsuI CTGGAG 2 cut(s) 111, 207
HaeIII GGCC 1 cut(s) 670
HapII CCGG 2 cut(s) 65, 647
HgaI GACGC 1 cut(s) 6
HhaI GCGC 1 cut(s) 133
Hin1II CATG 1 cut(s) 215
Hin6I GCGC 1 cut(s) 131
HinP1I GCGC 1 cut(s) 131
HincII GTYRAC 1 cut(s) 730
HindII GTYRAC 1 cut(s) 730
HindIII AAGCTT 3 cut(s) 412, 479, 746
HinfI GANTC 6 cut(s) 29, 41, 70, 101, 140, 772
HpaII CCGG 2 cut(s) 65, 647
HphI GGTGA 3 cut(s) 469, 710, 775
Hpy166II GTNNAC 6 cut(s) 161, 241, 257, 628, 730, 842
Hpy188I TCNGA 5 cut(s) 40, 46, 375, 447, 592
Hpy188III TCNNGA 3 cut(s) 90, 137, 582
Hpy8I GTNNAC 6 cut(s) 161, 241, 257, 628, 730, 842
HpyAV CCTTC 2 cut(s) 268, 292
HpyCH4IV ACGT 5 cut(s) 237, 243, 426, 436, 732
HpyCH4V TGCA 6 cut(s) 83, 235, 305, 363, 490, 769
HpyF10VI GCNNNNNNNGC 3 cut(s) 14, 360, 487
HpyF3I CTNAG 5 cut(s) 350, 415, 740, 749, 789
HpySE526I ACGT 5 cut(s) 237, 243, 426, 436, 732
Hsp92II CATG 1 cut(s) 215
HspAI GCGC 1 cut(s) 131
Ksp22I TGATCA 1 cut(s) 370
KspI CCGCGG 1 cut(s) 668
Kzo9I GATC 4 cut(s) 55, 370, 661, 801
LmnI GCTCC 2 cut(s) 639, 722
LweI GCATC 2 cut(s) 314, 601
MaeII ACGT 5 cut(s) 237, 243, 426, 436, 732
MaeIII GTNAC 1 cut(s) 76
MalI GATC 4 cut(s) 57, 372, 663, 803
MboI GATC 4 cut(s) 55, 370, 661, 801
MboII GAAGA 6 cut(s) 24, 163, 314, 432, 505, 772
MflI RGATCY 1 cut(s) 661
MluCI AATT 3 cut(s) 85, 223, 606
MlyI GAGTC 2 cut(s) 23, 79
MnlI CCTC 7 cut(s) 126, 129, 219, 270, 327, 328, 796
MseI TTAA 3 cut(s) 293, 450, 618
MslI CAYNNNNRTG 1 cut(s) 216
MspA1I CMGCKG 1 cut(s) 667
MspI CCGG 2 cut(s) 65, 647
MspR9I CCNGG 1 cut(s) 186
Mva1269I GAATGC 1 cut(s) 354
MvaI CCWGG 1 cut(s) 186
MvnI CGCG 1 cut(s) 667
MwoI GCNNNNNNNGC 3 cut(s) 14, 360, 487
NdeII GATC 4 cut(s) 55, 370, 661, 801
NlaIII CATG 1 cut(s) 215
NlaIV GGNNCC 1 cut(s) 663
NotI GCGGCCGC 1 cut(s) 668
PaqCI CACCTGC 1 cut(s) 746
PcsI WCGNNNNNNNCGW 1 cut(s) 234
PctI GAATGC 1 cut(s) 354
PfeI GAWTC 4 cut(s) 41, 101, 140, 772
PkrI GCNGC 2 cut(s) 669, 672
PleI GAGTC 2 cut(s) 23, 78
PpsI GAGTC 2 cut(s) 23, 78
Ppu21I YACGTR 2 cut(s) 244, 437
Psp1406I AACGTT 1 cut(s) 426
Psp6I CCWGG 1 cut(s) 184
PspGI CCWGG 1 cut(s) 184
PspN4I GGNNCC 1 cut(s) 663
PstNI CAGNNNCTG 1 cut(s) 185
PsuI RGATCY 1 cut(s) 661
RsaI GTAC 1 cut(s) 246
RsaNI GTAC 1 cut(s) 245
RseI CAYNNNNRTG 1 cut(s) 216
SacII CCGCGG 1 cut(s) 668
SaqAI TTAA 3 cut(s) 293, 450, 618
SatI GCNGC 2 cut(s) 668, 671
Sau3AI GATC 4 cut(s) 55, 370, 661, 801
SchI GAGTC 2 cut(s) 23, 79
ScrFI CCNGG 1 cut(s) 186
SfaNI GCATC 2 cut(s) 314, 601
Sfr303I CCGCGG 1 cut(s) 668
SgrBI CCGCGG 1 cut(s) 668
SmiMI CAYNNNNRTG 1 cut(s) 216
SnaBI TACGTA 1 cut(s) 244
Sse9I AATT 3 cut(s) 85, 223, 606
SsiI CCGC 4 cut(s) 125, 665, 667, 671
StyD4I CCNGG 1 cut(s) 184
StyI CCWWGG 2 cut(s) 390, 681
TaiI ACGT 5 cut(s) 240, 246, 429, 439, 735
TaqI TCGA 4 cut(s) 104, 138, 216, 804
TasI AATT 3 cut(s) 85, 223, 606
TauI GCSGC 2 cut(s) 670, 673
TfiI GAWTC 4 cut(s) 41, 101, 140, 772
Tru1I TTAA 3 cut(s) 293, 450, 618
Tru9I TTAA 3 cut(s) 293, 450, 618
TscAI CASTG 2 cut(s) 168, 270
TspDTI ATGAA 4 cut(s) 24, 314, 431, 636
TspRI CASTG 2 cut(s) 168, 270
XapI RAATTY 1 cut(s) 85
XcmI CCANNNNNNNNNTGG 1 cut(s) 160
XmiI GTMKAC 1 cut(s) 256
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.