pycom04g10040

nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay

Design Primers CRISPR Design

Basic Information

Type: gene
Biological Identity
pyrus_communis
Chr4
OG0028693
Physical Location & Seq
Forward (+)
12761367 .. 12762762
1396 bp
Loading structure...
UTR
Exon/CDS
Intron
N/A

Sequence Viewer

Length: 486 bp
ATGGAGAGTGGTGTAGAGTTGACGCGCAAAAAGTCACCAGAAAAGGCTCTTTACTTTTCCCAACCCTCAAACGTCCTCTCTCTGTACTTTTCCGTGCTTTTATCATATCCAGGGTTTCATCTCCTACACACCATTTCCTGCCTCTCGTCTCCTCCTTTTCCGTCGCACGCTGTAAGTCTCAAAATCATGACTGAAATCGAAGAGAAAACGTGTCCGATATGTGCCGAGGAGATGGATTTGACGGATCAGCAACTGAAGCCGTGGAAATGCGGTTACGAGGTATGTGTTTGGTGCTGGCATCACATTATGGAAATGGCAGAGAAGGATGGAAAGGATGGCTGCTGTCCAGTATGCCGTACACCTTATGACAAGAAATTGTTGGAGTGGCAGCACATGGTTTCGTTTCAGGTTAATGTATGTTGTTCTGTGACAACTGACAAGTTGAGGATAGAAACTGTTTCGCTCCTTGAACAGGTTGGTGGCTGA
Functional Annotation
Gene Ontology
Molecular Function
Biological Process
Cellular Component
No ontology terms assigned.
KEGG Pathways
Metabolic & Signaling
ko03018 map03018
Pfam Domains
Protein Families
RRM_1 zf-RING_4

Protein Analysis

162

Amino Acids

18.32

Weight (kDa)

5.65

Isoelectric Point (pI)

49.08

Instability Index
Protein Domains (Pfam)
Domain Name Pfam ID Position E-value Description
zf-RING_4 PF14570 71 - 123 3e-16 RING/Ubox like zinc-binding domain
Hydrophobicity Profile (Kyte-Doolittle)
AI Structure Prediction Report
Calculating structure properties...

Genomic Context

Gene Family Tree

Species Filter
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Publication-ready
iTOL Interactive Tree Of Life · Most popular EvolView Flexible annotations MEGA Desktop phylogenetics suite FigTree Desktop tree editor

Orthologous Genes (Group: OG0028693)

Species Orthologous Gene IDs
malus_domestica MD04G1105000.v1.1
pyrus_communis pycom04g10040

Restriction Enzyme Sites

1 / 10
Enzyme Recognition Site Cut Count Positions (bp)
AccII CGCG 1 cut(s) 25
AciI CCGC 1 cut(s) 270
AclWI GGATC 1 cut(s) 252
AcuI CTGAAG 1 cut(s) 275
AfaI GTAC 2 cut(s) 86, 358
AfiI CCNNNNNNNGG 1 cut(s) 472
AflIII ACRYGT 1 cut(s) 209
AgsI TTSAA 1 cut(s) 470
AjnI CCWGG 1 cut(s) 109
Alw26I GTCTC 2 cut(s) 153, 182
AlwI GGATC 1 cut(s) 252
AlwNI CAGNNNCTG 1 cut(s) 253
ApeKI GCWGC 2 cut(s) 339, 388
AspLEI GCGC 1 cut(s) 27
AsuHPI GGTGA 1 cut(s) 27
BbvI GCAGC 2 cut(s) 326, 400
BccI CCATC 3 cut(s) 226, 320, 329
BceAI ACGGC 2 cut(s) 244, 339
BciT130I CCWGG 1 cut(s) 111
BcoDI GTCTC 2 cut(s) 153, 182
BisI GCNGC 2 cut(s) 340, 389
BlsI GCNGC 2 cut(s) 341, 390
Bme1390I CCNGG 1 cut(s) 111
BmrFI CCNGG 1 cut(s) 111
BmsI GCATC 1 cut(s) 307
BsaJI CCNNGG 3 cut(s) 110, 225, 260
Bsc4I CCNNNNNNNGG 1 cut(s) 472
Bse1I ACTGG 1 cut(s) 347
BseBI CCWGG 1 cut(s) 111
BseDI CCNNGG 3 cut(s) 110, 225, 260
BseGI GGATG 2 cut(s) 331, 340
BseLI CCNNNNNNNGG 1 cut(s) 472
BseNI ACTGG 1 cut(s) 347
BseRI GAGGAG 2 cut(s) 141, 242
BseXI GCAGC 2 cut(s) 326, 400
Bsh1236I CGCG 1 cut(s) 25
BslI CCNNNNNNNGG 1 cut(s) 472
BsmAI GTCTC 2 cut(s) 153, 182
BsmBI CGTCTC 1 cut(s) 153
Bsp143I GATC 1 cut(s) 244
BspACI CCGC 1 cut(s) 270
BspFNI CGCG 1 cut(s) 25
BspHI TCATGA 1 cut(s) 186
BspPI GGATC 1 cut(s) 252
BsrI ACTGG 1 cut(s) 347
BssECI CCNNGG 3 cut(s) 110, 225, 260
BssMI GATC 1 cut(s) 244
Bst2UI CCWGG 1 cut(s) 111
Bst4CI ACNGT 1 cut(s) 457
Bst6I CTCTTC 1 cut(s) 195
BstC8I GCNNGC 2 cut(s) 168, 296
BstDSI CCRYGG 1 cut(s) 260
BstENI CCTNNNNNAGG 1 cut(s) 470
BstF5I GGATG 2 cut(s) 331, 340
BstFNI CGCG 1 cut(s) 25
BstHHI GCGC 1 cut(s) 27
BstKTI GATC 1 cut(s) 247
BstMAI GTCTC 2 cut(s) 153, 182
BstMBI GATC 1 cut(s) 244
BstMWI GCNNNNNNNGC 1 cut(s) 256
BstNI CCWGG 1 cut(s) 111
BstSCI CCNGG 1 cut(s) 109
BstUI CGCG 1 cut(s) 25
BstV1I GCAGC 2 cut(s) 326, 400
BtgI CCRYGG 1 cut(s) 260
BtsCI GGATG 2 cut(s) 331, 340
Cac8I GCNNGC 2 cut(s) 168, 296
CaiI CAGNNNCTG 1 cut(s) 253
CciI TCATGA 1 cut(s) 186
CfoI GCGC 1 cut(s) 27
CseI GACGC 1 cut(s) 31
Csp6I GTAC 2 cut(s) 85, 357
CviAII CATG 2 cut(s) 187, 394
CviJI RGCY 4 cut(s) 47, 259, 339, 483
CviKI_1 RGCY 4 cut(s) 47, 259, 339, 483
CviQI GTAC 2 cut(s) 85, 357
DpnI GATC 1 cut(s) 246
DpnII GATC 1 cut(s) 244
Eam1104I CTCTTC 1 cut(s) 195
EarI CTCTTC 1 cut(s) 195
Eco57I CTGAAG 1 cut(s) 275
EcoNI CCTNNNNNAGG 1 cut(s) 470
EcoRII CCWGG 1 cut(s) 109
Esp3I CGTCTC 1 cut(s) 153
FaeI CATG 2 cut(s) 190, 397
FaiI YATR 9 cut(s) 106, 188, 220, 283, 308, 352, 366, 395, 418
FatI CATG 2 cut(s) 186, 393
Fnu4HI GCNGC 2 cut(s) 340, 389
FokI GGATG 2 cut(s) 338, 347
Fsp4HI GCNGC 2 cut(s) 340, 389
GlaI GCGC 1 cut(s) 26
GluI GCNGC 2 cut(s) 340, 389
HgaI GACGC 1 cut(s) 31
HhaI GCGC 1 cut(s) 27
Hin1II CATG 2 cut(s) 190, 397
Hin6I GCGC 1 cut(s) 25
HinP1I GCGC 1 cut(s) 25
HincII GTYRAC 1 cut(s) 21
HindII GTYRAC 1 cut(s) 21
HphI GGTGA 1 cut(s) 27
Hpy166II GTNNAC 2 cut(s) 21, 359
Hpy188I TCNGA 1 cut(s) 216
Hpy188III TCNNGA 1 cut(s) 187
Hpy8I GTNNAC 2 cut(s) 21, 359
Hpy99I CGWCG 1 cut(s) 166
HpyAV CCTTC 1 cut(s) 316
HpyCH4III ACNGT 1 cut(s) 457
HpyCH4IV ACGT 2 cut(s) 72, 209
HpyF10VI GCNNNNNNNGC 1 cut(s) 256
HpySE526I ACGT 2 cut(s) 72, 209
Hsp92II CATG 2 cut(s) 190, 397
HspAI GCGC 1 cut(s) 25
Kzo9I GATC 1 cut(s) 244
LmnI GCTCC 1 cut(s) 468
LpnPI CCDG 8 cut(s) 51, 96, 123, 151, 280, 360, 392, 458
Lsp1109I GCAGC 2 cut(s) 326, 400
LweI GCATC 1 cut(s) 307
MaeII ACGT 2 cut(s) 72, 209
MaeIII GTNAC 3 cut(s) 33, 272, 427
MalI GATC 1 cut(s) 246
MboI GATC 1 cut(s) 244
MboII GAAGA 1 cut(s) 212
MluCI AATT 1 cut(s) 374
MmeI TCCRAC 1 cut(s) 360
MnlI CCTC 7 cut(s) 76, 86, 152, 162, 220, 271, 438
MseI TTAA 1 cut(s) 411
MspR9I CCNGG 1 cut(s) 111
MvaI CCWGG 1 cut(s) 111
MvnI CGCG 1 cut(s) 25
MwoI GCNNNNNNNGC 1 cut(s) 256
NdeII GATC 1 cut(s) 244
NlaIII CATG 2 cut(s) 190, 397
NmeAIII GCCGAG 1 cut(s) 250
NmuCI GTSAC 2 cut(s) 33, 427
PagI TCATGA 1 cut(s) 186
PkrI GCNGC 2 cut(s) 341, 390
Psp6I CCWGG 1 cut(s) 109
PspGI CCWGG 1 cut(s) 109
PstNI CAGNNNCTG 1 cut(s) 253
RsaI GTAC 2 cut(s) 86, 358
RsaNI GTAC 2 cut(s) 85, 357
SaqAI TTAA 1 cut(s) 411
SatI GCNGC 2 cut(s) 340, 389
Sau3AI GATC 1 cut(s) 244
ScrFI CCNGG 1 cut(s) 111
SetI ASST 6 cut(s) 75, 212, 282, 364, 411, 477
SfaNI GCATC 1 cut(s) 307
Sse9I AATT 1 cut(s) 374
SsiI CCGC 1 cut(s) 270
StyD4I CCNGG 1 cut(s) 109
TaaI ACNGT 1 cut(s) 457
TaiI ACGT 2 cut(s) 75, 212
TaqI TCGA 1 cut(s) 198
TasI AATT 1 cut(s) 374
TatI WGTACW 1 cut(s) 84
Tru1I TTAA 1 cut(s) 411
Tru9I TTAA 1 cut(s) 411
TseFI GTSAC 2 cut(s) 33, 427
TseI GCWGC 2 cut(s) 339, 388
Tsp45I GTSAC 2 cut(s) 33, 427
TspDTI ATGAA 1 cut(s) 107
TspGWI ACGGA 3 cut(s) 82, 150, 257
XagI CCTNNNNNAGG 1 cut(s) 470
Using CommOnly database (standard laboratory enzymes). Scanned on CDS sequence.