MD01G1175500.v1.1

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
malus_domestica
Chr01
OG0006090
Physical Location & Seq
Forward (+)
27658757 .. 27661706
2950 bp
Loading structure...
UTR
Exon/CDS
Intron
MD01G1175500.v1.1.491

Sequence Viewer

Length: 942 bp
ATGGAGGCCCTGATCGCCTCGTACGGAAACTCGTCGTCGGCCTCAGGCTCCAAGTCGCCGGTTCCACCTTCAGATCTGAACAACTCTCAAAACCCGGCCCCAGCTCGGCCTCTGCCACCTCTACCACTTCGCGAAAGCCCCAATTCCTCAGGTAACCTCCAATTCCCATCAACTTTCTCTCTTTTTTTACTTTCTATTGAGATAGCTTTCTGCCAACCAAGTGTTTGGTCCTCCGAAGGATTTCTGGACTTGTCACTAAGCGATCGGCCGAGCAGAGTCAGGAACTTCCCTCACGTCAAGGGGAACTACGTAGTATATGTATACATCCCAGTTTATATACCGCCAGCACCGAGGAAAGAGATGGCCTTGTTTTTTAACAAGCTAGCTTCGCTGGTGCCTGGTCTCCATGCCGTTGACGTTAACGTCCCGTTTGACATTCTGCGGAATGACAAGCACAAGCTCGAACAAGTTGCTTTAGGTAGAAAATTGCATATAAGTCTGGGAAGAACTGTCCAGGTTCAGGTACACCAGATTGATTCCTTGGTGACAATGCTGCGGCAGAAGCTTCAGAATCAGAGGCGATATTGGATTGATTTTAGCAAATGGGAAGTTTTTGTTAACGATGATCGGACCCGGACATTTGTGTCGATAGAAGTCACTGATGCTGGGTTAGCTGAGATAACAAAGCAGATTCAAGCTGTCAATGAGGTGTATAAGCTTCACAATCTTCCTGAATTTTACAAGGTTCCACGCCCTCATATATCGGTAGCTTGGGCATTGGGTGACATAAGCAATTCCCTGAAGAAAGTGTTTGAAGGAGAAAGAAGAAGATCTGCAGTTGGAAGATCATTACAGAAAAGTATTTTTACCAGTAAATTCAACGGCATCGAATGTAGGATTGGGAATAAAATACACAAAATATGTAAATTTTCTGAAGAATAA
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

314

Amino Acids

35.33

Weight (kDa)

9.59

Isoelectric Point (pI)

58.45

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HVSL PF09749 88 - 308 2.2e-52 Uncharacterised conserved protein
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)
AasI GACNNNNNNGTC 2 cut(s) 422, 643
AccB1I GGYRCC 1 cut(s) 394
AccI GTMKAC 1 cut(s) 321
AccII CGCG 1 cut(s) 132
AciI CCGC 3 cut(s) 341, 442, 556
AcoI YGGCCR 1 cut(s) 266
AcsI RAATTY 3 cut(s) 734, 875, 926
AcuI CTGAAG 3 cut(s) 54, 551, 821
AfaI GTAC 2 cut(s) 23, 525
AfiI CCNNNNNNNGG 2 cut(s) 105, 520
AgsI TTSAA 3 cut(s) 695, 815, 880
AjiI CACGTC 1 cut(s) 295
AjnI CCWGG 2 cut(s) 397, 513
AjuI GAANNNNNNNTTGG 2 cut(s) 882, 914
Alw26I GTCTC 1 cut(s) 407
AoxI GGCC 6 cut(s) 6, 39, 96, 107, 266, 363
ApeKI GCWGC 1 cut(s) 553
ApoI RAATTY 3 cut(s) 734, 875, 926
Asp700I GAANNNNTTC 1 cut(s) 240
AspS9I GGNCC 4 cut(s) 7, 97, 228, 630
AsuC2I CCSGG 2 cut(s) 95, 634
AsuHPI GGTGA 2 cut(s) 556, 794
AsuNHI GCTAGC 1 cut(s) 382
AvaII GGWCC 2 cut(s) 228, 630
AxyI CCTNAGG 2 cut(s) 43, 148
BanI GGYRCC 1 cut(s) 394
BbvI GCAGC 1 cut(s) 540
BccI CCATC 2 cut(s) 175, 355
BceAI ACGGC 2 cut(s) 395, 898
BcgI CGANNNNNNTGC 2 cut(s) 452, 486
BciT130I CCWGG 2 cut(s) 399, 515
BcnI CCSGG 2 cut(s) 95, 634
BcoDI GTCTC 1 cut(s) 407
BfaI CTAG 1 cut(s) 383
BfmI CTRYAG 1 cut(s) 834
BglII AGATCT 2 cut(s) 73, 830
BisI GCNGC 2 cut(s) 554, 557
BlsI GCNGC 2 cut(s) 555, 558
Bme1390I CCNGG 4 cut(s) 95, 399, 515, 634
Bme18I GGWCC 2 cut(s) 228, 630
BmgBI CACGTC 1 cut(s) 295
BmgT120I GGNCC 4 cut(s) 7, 97, 228, 630
BmiI GGNNCC 6 cut(s) 49, 63, 99, 396, 632, 747
BmrFI CCNGG 4 cut(s) 95, 399, 515, 634
BmrI ACTGGG 1 cut(s) 323
BmsI GCATC 2 cut(s) 652, 894
BmtI GCTAGC 1 cut(s) 386
BmuI ACTGGG 1 cut(s) 323
BpuMI CCSGG 2 cut(s) 95, 634
BsaAI YACGTR 1 cut(s) 310
BsaI GGTCTC 1 cut(s) 407
BsaJI CCNNGG 2 cut(s) 350, 540
Bsc4I CCNNNNNNNGG 2 cut(s) 105, 520
Bse118I RCCGGY 1 cut(s) 58
Bse1I ACTGG 2 cut(s) 329, 870
Bse21I CCTNAGG 2 cut(s) 43, 148
BseBI CCWGG 2 cut(s) 399, 515
BseDI CCNNGG 2 cut(s) 350, 540
BseGI GGATG 1 cut(s) 324
BseLI CCNNNNNNNGG 2 cut(s) 105, 520
BseMII CTCAG 3 cut(s) 57, 162, 666
BseNI ACTGG 2 cut(s) 329, 870
BseX3I CGGCCG 1 cut(s) 266
BseXI GCAGC 1 cut(s) 540
BseYI CCCAGC 2 cut(s) 100, 665
Bsh1236I CGCG 1 cut(s) 132
Bsh1285I CGRYCG 2 cut(s) 265, 269
BshFI GGCC 6 cut(s) 8, 41, 98, 109, 268, 365
BshNI GGYRCC 1 cut(s) 394
BsiEI CGRYCG 2 cut(s) 265, 269
BsiSI CCGG 3 cut(s) 59, 95, 634
BsiWI CGTACG 1 cut(s) 21
BslFI GGGAC 1 cut(s) 410
BslI CCNNNNNNNGG 2 cut(s) 105, 520
BsmAI GTCTC 1 cut(s) 407
BsmFI GGGAC 1 cut(s) 410
BsnI GGCC 6 cut(s) 8, 41, 98, 109, 268, 365
Bso31I GGTCTC 1 cut(s) 407
Bsp143I GATC 6 cut(s) 12, 73, 262, 625, 830, 845
Bsp68I TCGCGA 1 cut(s) 132
BspACI CCGC 3 cut(s) 341, 442, 556
BspANI GGCC 6 cut(s) 8, 41, 98, 109, 268, 365
BspCNI CTCAG 3 cut(s) 56, 161, 667
BspFNI CGCG 1 cut(s) 132
BspLI GGNNCC 6 cut(s) 49, 63, 99, 396, 632, 747
BspMAI CTGCAG 1 cut(s) 838
BspOI GCTAGC 1 cut(s) 386
BspT107I GGYRCC 1 cut(s) 394
BspTNI GGTCTC 1 cut(s) 407
BsrFI RCCGGY 1 cut(s) 58
BsrI ACTGG 2 cut(s) 329, 870
BssAI RCCGGY 1 cut(s) 58
BssECI CCNNGG 2 cut(s) 350, 540
BssMI GATC 6 cut(s) 12, 73, 262, 625, 830, 845
BssNAI GTATAC 1 cut(s) 322
BssT1I CCWWGG 1 cut(s) 540
Bst1107I GTATAC 1 cut(s) 322
Bst2UI CCWGG 2 cut(s) 399, 515
Bst4CI ACNGT 1 cut(s) 511
BstBAI YACGTR 1 cut(s) 310
BstC8I GCNNGC 2 cut(s) 345, 384
BstDEI CTNAG 4 cut(s) 43, 148, 257, 675
BstEII GGTNACC 1 cut(s) 152
BstF5I GGATG 1 cut(s) 324
BstFNI CGCG 1 cut(s) 132
BstKTI GATC 6 cut(s) 15, 76, 265, 628, 833, 848
BstMAI GTCTC 1 cut(s) 407
BstMBI GATC 6 cut(s) 12, 73, 262, 625, 830, 845
BstMCI CGRYCG 2 cut(s) 265, 269
BstMWI GCNNNNNNNGC 4 cut(s) 14, 388, 562, 671
BstNI CCWGG 2 cut(s) 399, 515
BstPI GGTNACC 1 cut(s) 152
BstSCI CCNGG 4 cut(s) 93, 397, 513, 632
BstSFI CTRYAG 1 cut(s) 834
BstSNI TACGTA 1 cut(s) 310
BstUI CGCG 1 cut(s) 132
BstV1I GCAGC 1 cut(s) 540
BstX2I RGATCY 2 cut(s) 73, 830
BstXI CCANNNNNNTGG 1 cut(s) 225
BstYI RGATCY 2 cut(s) 73, 830
BstZ17I GTATAC 1 cut(s) 322
BstZI CGGCCG 1 cut(s) 266
Bsu36I CCTNAGG 2 cut(s) 43, 148
BsuRI GGCC 6 cut(s) 8, 41, 98, 109, 268, 365
BtrI CACGTC 1 cut(s) 295
BtsCI GGATG 1 cut(s) 324
BtsIMutI CAGTG 1 cut(s) 657
BtuMI TCGCGA 1 cut(s) 132
Cac8I GCNNGC 2 cut(s) 345, 384
Cfr10I RCCGGY 1 cut(s) 58
Cfr13I GGNCC 4 cut(s) 7, 97, 228, 630
Csp6I GTAC 2 cut(s) 22, 524
CviAII CATG 1 cut(s) 407
CviQI GTAC 2 cut(s) 22, 524
DdeI CTNAG 4 cut(s) 43, 148, 257, 675
DpnI GATC 6 cut(s) 14, 75, 264, 627, 832, 847
DpnII GATC 6 cut(s) 12, 73, 262, 625, 830, 845
DrdI GACNNNNNNGTC 2 cut(s) 422, 643
DseDI GACNNNNNNGTC 2 cut(s) 422, 643
EaeI YGGCCR 1 cut(s) 266
EagI CGGCCG 1 cut(s) 266
EclXI CGGCCG 1 cut(s) 266
Eco105I TACGTA 1 cut(s) 310
Eco130I CCWWGG 1 cut(s) 540
Eco31I GGTCTC 1 cut(s) 407
Eco47I GGWCC 2 cut(s) 228, 630
Eco52I CGGCCG 1 cut(s) 266
Eco57I CTGAAG 3 cut(s) 54, 551, 821
Eco81I CCTNAGG 2 cut(s) 43, 148
Eco91I GGTNACC 1 cut(s) 152
EcoO109I RGGNCCY 1 cut(s) 7
EcoO65I GGTNACC 1 cut(s) 152
EcoRII CCWGG 2 cut(s) 397, 513
EcoT14I CCWWGG 1 cut(s) 540
ErhI CCWWGG 1 cut(s) 540
FaeI CATG 1 cut(s) 410
FaqI GGGAC 1 cut(s) 410
FatI CATG 1 cut(s) 406
FblI GTMKAC 1 cut(s) 321
Fnu4HI GCNGC 2 cut(s) 554, 557
FokI GGATG 1 cut(s) 311
Fsp4HI GCNGC 2 cut(s) 554, 557
FspBI CTAG 1 cut(s) 383
GluI GCNGC 2 cut(s) 554, 557
GsaI CCCAGC 2 cut(s) 104, 669
HaeIII GGCC 6 cut(s) 8, 41, 98, 109, 268, 365
HapII CCGG 3 cut(s) 59, 95, 634
Hin1II CATG 1 cut(s) 410
HincII GTYRAC 3 cut(s) 415, 421, 619
HindII GTYRAC 3 cut(s) 415, 421, 619
HindIII AAGCTT 2 cut(s) 563, 716
HinfI GANTC 4 cut(s) 276, 536, 571, 691
HpaI GTTAAC 2 cut(s) 421, 619
HpaII CCGG 3 cut(s) 59, 95, 634
HphI GGTGA 2 cut(s) 556, 794
Hpy166II GTNNAC 5 cut(s) 322, 415, 421, 526, 619
Hpy188I TCNGA 7 cut(s) 73, 78, 235, 570, 576, 630, 934
Hpy188III TCNNGA 4 cut(s) 131, 245, 280, 731
Hpy8I GTNNAC 5 cut(s) 322, 415, 421, 526, 619
Hpy99I CGWCG 2 cut(s) 37, 40
HpyAV CCTTC 3 cut(s) 78, 230, 809
HpyCH4III ACNGT 1 cut(s) 511
HpyCH4IV ACGT 4 cut(s) 294, 309, 417, 423
HpyCH4V TGCA 2 cut(s) 490, 836
HpyF10VI GCNNNNNNNGC 4 cut(s) 14, 388, 562, 671
HpyF3I CTNAG 4 cut(s) 43, 148, 257, 675
HpySE526I ACGT 4 cut(s) 294, 309, 417, 423
Hsp92II CATG 1 cut(s) 410
KspAI GTTAAC 2 cut(s) 421, 619
Kzo9I GATC 6 cut(s) 12, 73, 262, 625, 830, 845
LmnI GCTCC 1 cut(s) 53
Lsp1109I GCAGC 1 cut(s) 540
LweI GCATC 2 cut(s) 652, 894
MaeI CTAG 1 cut(s) 383
MaeII ACGT 4 cut(s) 294, 309, 417, 423
MaeIII GTNAC 5 cut(s) 152, 252, 544, 655, 782
MalI GATC 6 cut(s) 14, 75, 264, 627, 832, 847
MboI GATC 6 cut(s) 12, 73, 262, 625, 830, 845
MboII GAAGA 6 cut(s) 516, 719, 814, 837, 840, 855
MflI RGATCY 2 cut(s) 73, 830
MluCI AATT 7 cut(s) 142, 161, 485, 734, 793, 875, 926
MlyI GAGTC 1 cut(s) 285
MmeI TCCRAC 1 cut(s) 820
MroXI GAANNNNTTC 1 cut(s) 240
MseI TTAA 3 cut(s) 375, 420, 618
MspI CCGG 3 cut(s) 59, 95, 634
MspR9I CCNGG 4 cut(s) 95, 399, 515, 634
MvaI CCWGG 2 cut(s) 399, 515
MvnI CGCG 1 cut(s) 132
MwoI GCNNNNNNNGC 4 cut(s) 14, 388, 562, 671
NciI CCSGG 2 cut(s) 95, 634
NdeII GATC 6 cut(s) 12, 73, 262, 625, 830, 845
NheI GCTAGC 1 cut(s) 382
NlaIII CATG 1 cut(s) 410
NlaIV GGNNCC 6 cut(s) 49, 63, 99, 396, 632, 747
NmeAIII GCCGAG 2 cut(s) 85, 294
NmuCI GTSAC 4 cut(s) 252, 544, 655, 782
NruI TCGCGA 1 cut(s) 132
PdmI GAANNNNTTC 1 cut(s) 240
PfeI GAWTC 3 cut(s) 536, 571, 691
Pfl23II CGTACG 1 cut(s) 21
PkrI GCNGC 2 cut(s) 555, 558
Ple19I CGATCG 1 cut(s) 265
PleI GAGTC 1 cut(s) 284
PpsI GAGTC 1 cut(s) 284
Ppu21I YACGTR 1 cut(s) 310
Psp6I CCWGG 2 cut(s) 397, 513
PspEI GGTNACC 1 cut(s) 152
PspFI CCCAGC 2 cut(s) 100, 665
PspGI CCWGG 2 cut(s) 397, 513
PspLI CGTACG 1 cut(s) 21
PspN4I GGNNCC 6 cut(s) 49, 63, 99, 396, 632, 747
PspPI GGNCC 4 cut(s) 7, 97, 228, 630
PstI CTGCAG 1 cut(s) 838
PsuI RGATCY 2 cut(s) 73, 830
PvuI CGATCG 1 cut(s) 265
RruI TCGCGA 1 cut(s) 132
RsaI GTAC 2 cut(s) 23, 525
RsaNI GTAC 2 cut(s) 22, 524
SaqAI TTAA 3 cut(s) 375, 420, 618
SatI GCNGC 2 cut(s) 554, 557
Sau3AI GATC 6 cut(s) 12, 73, 262, 625, 830, 845
Sau96I GGNCC 4 cut(s) 7, 97, 228, 630
SchI GAGTC 1 cut(s) 285
ScrFI CCNGG 4 cut(s) 95, 399, 515, 634
SfaNI GCATC 2 cut(s) 652, 894
SfcI CTRYAG 1 cut(s) 834
SinI GGWCC 2 cut(s) 228, 630
SnaBI TACGTA 1 cut(s) 310
Sse9I AATT 7 cut(s) 142, 161, 485, 734, 793, 875, 926
SsiI CCGC 3 cut(s) 341, 442, 556
SspMI CTAG 1 cut(s) 383
StyD4I CCNGG 4 cut(s) 93, 397, 513, 632
StyI CCWWGG 1 cut(s) 540
TaaI ACNGT 1 cut(s) 511
TaiI ACGT 4 cut(s) 297, 312, 420, 426
TaqI TCGA 3 cut(s) 462, 647, 888
TasI AATT 7 cut(s) 142, 161, 485, 734, 793, 875, 926
TauI GCSGC 1 cut(s) 559
TfiI GAWTC 3 cut(s) 536, 571, 691
Tru1I TTAA 3 cut(s) 375, 420, 618
Tru9I TTAA 3 cut(s) 375, 420, 618
TscAI CASTG 1 cut(s) 664
TseFI GTSAC 4 cut(s) 252, 544, 655, 782
TseI GCWGC 1 cut(s) 553
Tsp45I GTSAC 4 cut(s) 252, 544, 655, 782
TspGWI ACGGA 1 cut(s) 39
TspRI CASTG 1 cut(s) 664
VpaK11BI GGWCC 2 cut(s) 228, 630
XapI RAATTY 3 cut(s) 734, 875, 926
XmiI GTMKAC 1 cut(s) 321
XmnI GAANNNNTTC 1 cut(s) 240
XspI CTAG 1 cut(s) 383
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.