MD07G1245400.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
Chr07
OG0006090
Physical Location & Seq
Forward (+)
31541997 .. 31543401
1405 bp
Loading structure...
UTR
Exon/CDS
Intron
MD07G1245400.v1.1.491

Sequence Viewer

Length: 528 bp
ATGTATACATCCCAGGTAATCAAAATTCTCGAAATTTTCAGCTCCATTAGCAAATGCGATCCCTTTGCACTTAGATTTTGCTTGTTTAATTGTGTGGTTCCAGTTTATATACCACCAGCACCAAGGAAAGAGATGGCCTTGTTTTTGAACAAGCTTGCTTCTCTGGTGCCTGGTCTCCACGCCGTTGACGTTGACGTCCCGCTTGACATTCTGCGTAAGGACGAGCATAAGCTTGAACAAGTTGCTTTAGGCAGAGAGTTCCATATAAGTCTCGGAAGAACTGTTCCGATTCGGGTGCACCAGATTAATTCCTTGGTGACAATGCTGCGGCAGAAGCTTCAGATTCAGAGGCGATATTTTGAGGTTTTTGTTAACGATGATCAGACCCGGACCTTTGTGTCGATCGAAGTCATTGCTGCTGGGTTAGCTGAGATAACAAAGCAGATTCAAGCTGTCAATGAGGTGTATATGCTTCACAATCTTCCTGAATTTTACAAGGATCCGCGTCCTCATATTTCGGTAGCTTAG
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

176

Amino Acids

20.08

Weight (kDa)

8.45

Isoelectric Point (pI)

53.25

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
HVSL PF09749 35 - 175 1.3e-25 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) 194, 397
AatII GACGTC 1 cut(s) 198
AccB1I GGYRCC 1 cut(s) 166
AccI GTMKAC 1 cut(s) 5
AccII CGCG 1 cut(s) 505
AciI CCGC 3 cut(s) 200, 328, 503
AclWI GGATC 3 cut(s) 53, 494, 507
AcsI RAATTY 3 cut(s) 24, 33, 488
AcuI CTGAAG 1 cut(s) 323
AcyI GRCGYC 1 cut(s) 195
AgsI TTSAA 3 cut(s) 148, 236, 449
AjnI CCWGG 2 cut(s) 12, 169
AloI GAACNNNNNNTCC 2 cut(s) 267, 299
AluBI AGCT 7 cut(s) 42, 154, 232, 337, 428, 452, 524
AluI AGCT 7 cut(s) 42, 154, 232, 337, 428, 452, 524
Alw21I GWGCWC 1 cut(s) 300
Alw26I GTCTC 2 cut(s) 179, 275
Alw44I GTGCAC 1 cut(s) 296
AlwI GGATC 3 cut(s) 53, 494, 507
AoxI GGCC 1 cut(s) 135
ApaLI GTGCAC 1 cut(s) 296
ApeKI GCWGC 2 cut(s) 325, 416
ApoI RAATTY 3 cut(s) 24, 33, 488
AseI ATTAAT 1 cut(s) 306
AspS9I GGNCC 1 cut(s) 390
AsuC2I CCSGG 1 cut(s) 388
AsuHPI GGTGA 1 cut(s) 328
AvaII GGWCC 1 cut(s) 390
BaeGI GKGCMC 1 cut(s) 300
BamHI GGATCC 1 cut(s) 499
BanI GGYRCC 1 cut(s) 166
Bbv12I GWGCWC 1 cut(s) 300
BbvI GCAGC 2 cut(s) 312, 403
BccI CCATC 1 cut(s) 127
BceAI ACGGC 1 cut(s) 167
BcgI CGANNNNNNTGC 6 cut(s) 47, 81, 277, 311, 395, 429
BciT130I CCWGG 2 cut(s) 14, 171
BclI TGATCA 1 cut(s) 379
BcnI CCSGG 1 cut(s) 388
BcoDI GTCTC 2 cut(s) 179, 275
BisI GCNGC 3 cut(s) 326, 329, 417
BlsI GCNGC 3 cut(s) 327, 330, 418
Bme1390I CCNGG 3 cut(s) 14, 171, 388
Bme18I GGWCC 1 cut(s) 390
BmgT120I GGNCC 1 cut(s) 390
BmiI GGNNCC 3 cut(s) 99, 168, 501
BmrFI CCNGG 3 cut(s) 14, 171, 388
BpuMI CCSGG 1 cut(s) 388
BsaHI GRCGYC 1 cut(s) 195
BsaI GGTCTC 1 cut(s) 179
BsaJI CCNNGG 3 cut(s) 12, 122, 312
Bse1I ACTGG 1 cut(s) 101
Bse3DI GCAATG 1 cut(s) 411
BseBI CCWGG 2 cut(s) 14, 171
BseDI CCNNGG 3 cut(s) 12, 122, 312
BseGI GGATG 1 cut(s) 8
BseMI GCAATG 1 cut(s) 411
BseMII CTCAG 1 cut(s) 420
BseNI ACTGG 1 cut(s) 101
BseSI GKGCMC 1 cut(s) 300
BseXI GCAGC 2 cut(s) 312, 403
BseYI CCCAGC 1 cut(s) 419
Bsh1236I CGCG 1 cut(s) 505
Bsh1285I CGRYCG 1 cut(s) 405
BshFI GGCC 1 cut(s) 137
BshNI GGYRCC 1 cut(s) 166
BsiEI CGRYCG 1 cut(s) 405
BsiHKAI GWGCWC 1 cut(s) 300
BsiSI CCGG 1 cut(s) 388
BslFI GGGAC 1 cut(s) 182
BsmAI GTCTC 2 cut(s) 179, 275
BsmFI GGGAC 1 cut(s) 182
BsnI GGCC 1 cut(s) 137
Bso31I GGTCTC 1 cut(s) 179
Bsp1286I GDGCHC 1 cut(s) 300
Bsp143I GATC 4 cut(s) 58, 379, 402, 499
BspACI CCGC 3 cut(s) 200, 328, 503
BspANI GGCC 1 cut(s) 137
BspCNI CTCAG 1 cut(s) 421
BspFNI CGCG 1 cut(s) 505
BspLI GGNNCC 3 cut(s) 99, 168, 501
BspPI GGATC 3 cut(s) 53, 494, 507
BspT107I GGYRCC 1 cut(s) 166
BspTNI GGTCTC 1 cut(s) 179
BsrDI GCAATG 1 cut(s) 411
BsrI ACTGG 1 cut(s) 101
BssECI CCNNGG 3 cut(s) 12, 122, 312
BssMI GATC 4 cut(s) 58, 379, 402, 499
BssNAI GTATAC 1 cut(s) 6
BssNI GRCGYC 1 cut(s) 195
BssT1I CCWWGG 2 cut(s) 122, 312
Bst1107I GTATAC 1 cut(s) 6
Bst2UI CCWGG 2 cut(s) 14, 171
Bst4CI ACNGT 1 cut(s) 283
BstACI GRCGYC 1 cut(s) 195
BstC8I GCNNGC 1 cut(s) 156
BstDEI CTNAG 3 cut(s) 71, 429, 525
BstF5I GGATG 1 cut(s) 8
BstFNI CGCG 1 cut(s) 505
BstKTI GATC 4 cut(s) 61, 382, 405, 502
BstMAI GTCTC 2 cut(s) 179, 275
BstMBI GATC 4 cut(s) 58, 379, 402, 499
BstMCI CGRYCG 1 cut(s) 405
BstMWI GCNNNNNNNGC 3 cut(s) 48, 334, 425
BstNI CCWGG 2 cut(s) 14, 171
BstSCI CCNGG 3 cut(s) 12, 169, 386
BstSLI GKGCMC 1 cut(s) 300
BstUI CGCG 1 cut(s) 505
BstV1I GCAGC 2 cut(s) 312, 403
BstX2I RGATCY 1 cut(s) 499
BstYI RGATCY 1 cut(s) 499
BstZ17I GTATAC 1 cut(s) 6
BsuRI GGCC 1 cut(s) 137
BtsCI GGATG 1 cut(s) 8
Cac8I GCNNGC 1 cut(s) 156
Cfr13I GGNCC 1 cut(s) 390
CseI GACGC 1 cut(s) 494
CviJI RGCY 8 cut(s) 42, 137, 154, 232, 337, 428, 452, 524
CviKI_1 RGCY 8 cut(s) 42, 137, 154, 232, 337, 428, 452, 524
DdeI CTNAG 3 cut(s) 71, 429, 525
DpnI GATC 4 cut(s) 60, 381, 404, 501
DpnII GATC 4 cut(s) 58, 379, 402, 499
DrdI GACNNNNNNGTC 2 cut(s) 194, 397
DseDI GACNNNNNNGTC 2 cut(s) 194, 397
Eco130I CCWWGG 2 cut(s) 122, 312
Eco31I GGTCTC 1 cut(s) 179
Eco47I GGWCC 1 cut(s) 390
Eco57I CTGAAG 1 cut(s) 323
EcoRII CCWGG 2 cut(s) 12, 169
EcoT14I CCWWGG 2 cut(s) 122, 312
ErhI CCWWGG 2 cut(s) 122, 312
FaiI YATR 9 cut(s) 6, 108, 110, 228, 264, 266, 468, 470, 513
FaqI GGGAC 1 cut(s) 182
FauI CCCGC 1 cut(s) 207
FbaI TGATCA 1 cut(s) 379
FblI GTMKAC 1 cut(s) 5
Fnu4HI GCNGC 3 cut(s) 326, 329, 417
Fsp4HI GCNGC 3 cut(s) 326, 329, 417
GluI GCNGC 3 cut(s) 326, 329, 417
GsaI CCCAGC 1 cut(s) 423
HaeIII GGCC 1 cut(s) 137
HapII CCGG 1 cut(s) 388
HgaI GACGC 1 cut(s) 494
Hin1I GRCGYC 1 cut(s) 195
HincII GTYRAC 3 cut(s) 187, 193, 373
HindII GTYRAC 3 cut(s) 187, 193, 373
HindIII AAGCTT 3 cut(s) 152, 230, 335
HinfI GANTC 3 cut(s) 289, 343, 445
HpaI GTTAAC 1 cut(s) 373
HpaII CCGG 1 cut(s) 388
HphI GGTGA 1 cut(s) 328
Hpy166II GTNNAC 5 cut(s) 6, 187, 193, 298, 373
Hpy188I TCNGA 5 cut(s) 275, 288, 342, 348, 384
Hpy188III TCNNGA 2 cut(s) 29, 485
Hpy8I GTNNAC 5 cut(s) 6, 187, 193, 298, 373
HpyCH4III ACNGT 1 cut(s) 283
HpyCH4IV ACGT 2 cut(s) 189, 195
HpyCH4V TGCA 2 cut(s) 68, 298
HpyF10VI GCNNNNNNNGC 3 cut(s) 48, 334, 425
HpyF3I CTNAG 3 cut(s) 71, 429, 525
HpySE526I ACGT 2 cut(s) 189, 195
Hsp92I GRCGYC 1 cut(s) 195
Ksp22I TGATCA 1 cut(s) 379
KspAI GTTAAC 1 cut(s) 373
Kzo9I GATC 4 cut(s) 58, 379, 402, 499
LmnI GCTCC 1 cut(s) 47
Lsp1109I GCAGC 2 cut(s) 312, 403
MaeII ACGT 2 cut(s) 189, 195
MaeIII GTNAC 1 cut(s) 316
MalI GATC 4 cut(s) 60, 381, 404, 501
MboI GATC 4 cut(s) 58, 379, 402, 499
MboII GAAGA 2 cut(s) 288, 473
MflI RGATCY 1 cut(s) 499
MhlI GDGCHC 1 cut(s) 300
MluCI AATT 5 cut(s) 24, 33, 88, 307, 488
MnlI CCTC 4 cut(s) 342, 355, 454, 519
MseI TTAA 3 cut(s) 87, 306, 372
MspI CCGG 1 cut(s) 388
MspR9I CCNGG 3 cut(s) 14, 171, 388
MvaI CCWGG 2 cut(s) 14, 171
MvnI CGCG 1 cut(s) 505
MwoI GCNNNNNNNGC 3 cut(s) 48, 334, 425
NciI CCSGG 1 cut(s) 388
NdeII GATC 4 cut(s) 58, 379, 402, 499
NlaIV GGNNCC 3 cut(s) 99, 168, 501
NmuCI GTSAC 1 cut(s) 316
PcsI WCGNNNNNNNCGW 1 cut(s) 186
PfeI GAWTC 3 cut(s) 289, 343, 445
PkrI GCNGC 3 cut(s) 327, 330, 418
Ple19I CGATCG 1 cut(s) 405
PshBI ATTAAT 1 cut(s) 306
Psp6I CCWGG 2 cut(s) 12, 169
PspFI CCCAGC 1 cut(s) 419
PspGI CCWGG 2 cut(s) 12, 169
PspN4I GGNNCC 3 cut(s) 99, 168, 501
PspPI GGNCC 1 cut(s) 390
PsuI RGATCY 1 cut(s) 499
PvuI CGATCG 1 cut(s) 405
SaqAI TTAA 3 cut(s) 87, 306, 372
SatI GCNGC 3 cut(s) 326, 329, 417
Sau3AI GATC 4 cut(s) 58, 379, 402, 499
Sau96I GGNCC 1 cut(s) 390
ScrFI CCNGG 3 cut(s) 14, 171, 388
SduI GDGCHC 1 cut(s) 300
SinI GGWCC 1 cut(s) 390
Sse9I AATT 5 cut(s) 24, 33, 88, 307, 488
SsiI CCGC 3 cut(s) 200, 328, 503
StyD4I CCNGG 3 cut(s) 12, 169, 386
StyI CCWWGG 2 cut(s) 122, 312
TaaI ACNGT 1 cut(s) 283
TaiI ACGT 2 cut(s) 192, 198
TaqI TCGA 3 cut(s) 30, 401, 405
TasI AATT 5 cut(s) 24, 33, 88, 307, 488
TauI GCSGC 1 cut(s) 331
TfiI GAWTC 3 cut(s) 289, 343, 445
Tru1I TTAA 3 cut(s) 87, 306, 372
Tru9I TTAA 3 cut(s) 87, 306, 372
TseFI GTSAC 1 cut(s) 316
TseI GCWGC 2 cut(s) 325, 416
Tsp45I GTSAC 1 cut(s) 316
VneI GTGCAC 1 cut(s) 296
VpaK11BI GGWCC 1 cut(s) 390
VspI ATTAAT 1 cut(s) 306
XapI RAATTY 3 cut(s) 24, 33, 488
XmiI GTMKAC 1 cut(s) 5
ZraI GACGTC 1 cut(s) 196
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.