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Center for Computational Systems Medicine
Soverview

Gene summary

Soverview

RNA A-to-I events

Soverview

Differntial gene expression between RNA A-to-I edited versus non-edited samples

Soverview

Protein coding region RNA A-to-I editings

Soverview

The effects of the RNA editing to the miRNA binding sites

Soverview

The effects of the RNA editing to the stability of the RNA structures

Soverview

Relation with ADAR

Soverview

Relation with AD stages

Soverview

Related drugs with this gene

Soverview

Related diseases with this gene


Gene summary for SON

check button Gene summary
Gene informationGene symbol

SON

Gene ID

6651

Gene nameSON DNA and RNA binding protein
SynonymsBASS1|C21orf50|DBP-5|NREBP|SON3|TOKIMS
Cytomap

21q22.11

Type of geneprotein-coding
Descriptionprotein SONBax antagonist selected in Saccharomyces 1NRE-binding proteinSON DNA binding proteinnegative regulatory element-binding protein
Modification date20200313
UniProtAcc

P18583,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
SON

GO:0006397

mRNA processing

21504830

SON

GO:0043066

negative regulation of apoptotic process

10509013

SON

GO:0048024

regulation of mRNA splicing, via spliceosome

21504830


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RNA A-to-I events for SON

check buttonRNA A-to-I editing events in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure.
* This pie chart shows the number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
all structure

check button RNA editing frequencies across three data sets.
boxplot

check buttonThe number of RNA A-to-I editing events in different types of transcripts (# event, percentage).
boxplot

check button RNA A-to-I editing events in AD.
ADediting_957027(33546666, +), ADediting_957028(33546722, +), ADediting_957029(33547068, +), ADediting_957030(33547074, +), ADediting_957031(33547075, +), ADediting_957032(33547101, +), ADediting_957033(33547104, +), ADediting_957034(33547162, +), ADediting_957035(33547165, +), ADediting_957036(33547243, +), ADediting_957037(33547244, +), ADediting_957038(33547256, +), ADediting_957039(33547930, +), ADediting_957040(33550495, +), ADediting_957041(33550950, +), ADediting_957042(33550969, +), ADediting_957043(33551013, +), ADediting_957044(33551799, +), ADediting_957045(33556593, +), ADediting_957046(33557386, +), ADediting_957047(33557387, +), ADediting_957048(33557388, +), ADediting_1641784(33546594, +), ADediting_1641785(33546603, +), ADediting_1641786(33546610, +), ADediting_1641787(33546625, +), ADediting_1641788(33546660, +), ADediting_1641789(33546661, +), ADediting_1641790(33546670, +), ADediting_1641791(33546678, +), ADediting_1641792(33546706, +),

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RNA editing positional annotations for SON using Annovar

check button Protein coding RNA editing(s).
ADeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred
ADediting_957040chr21_33550495_+nonsynonymous SNVENST00000356577.9c.A1264Gp.T422A0.0060.282-1.65
ADediting_957040chr21_33550495_+nonsynonymous SNVENST00000455528.5c.A1264Gp.T422A0.0060.282-1.65
ADediting_957040chr21_33550495_+nonsynonymous SNVENST00000300278.8c.A1264Gp.T422A0.0060.282-1.65
ADediting_957040chr21_33550495_+nonsynonymous SNVENST00000381679.8c.A1264Gp.T422A0.0060.282-1.65
ADediting_957041chr21_33550950_+synonymous SNVENST00000356577.9c.A1719Gp.P573P...
ADediting_957041chr21_33550950_+synonymous SNVENST00000455528.5c.A1719Gp.P573P...
ADediting_957041chr21_33550950_+synonymous SNVENST00000300278.8c.A1719Gp.P573P...
ADediting_957041chr21_33550950_+synonymous SNVENST00000381679.8c.A1719Gp.P573P...
ADediting_957042chr21_33550969_+nonsynonymous SNVENST00000356577.9c.A1738Gp.R580G0.1550.008-1.89
ADediting_957042chr21_33550969_+nonsynonymous SNVENST00000455528.5c.A1738Gp.R580G0.1550.008-1.89
ADediting_957042chr21_33550969_+nonsynonymous SNVENST00000300278.8c.A1738Gp.R580G0.1550.008-1.89
ADediting_957042chr21_33550969_+nonsynonymous SNVENST00000381679.8c.A1738Gp.R580G0.1550.008-1.89
ADediting_957043chr21_33551013_+synonymous SNVENST00000356577.9c.A1782Gp.L594L...
ADediting_957043chr21_33551013_+synonymous SNVENST00000455528.5c.A1782Gp.L594L...
ADediting_957043chr21_33551013_+synonymous SNVENST00000300278.8c.A1782Gp.L594L...
ADediting_957043chr21_33551013_+synonymous SNVENST00000381679.8c.A1782Gp.L594L...
ADediting_957044chr21_33551799_+synonymous SNVENST00000356577.9c.A2568Gp.L856L...
ADediting_957044chr21_33551799_+synonymous SNVENST00000455528.5c.A2568Gp.L856L...
ADediting_957044chr21_33551799_+synonymous SNVENST00000300278.8c.A2568Gp.L856L...
ADediting_957044chr21_33551799_+synonymous SNVENST00000381679.8c.A2568Gp.L856L...

check button Gene structure information of RNA editing(s).
ADeditome IDPositionVariant type
ADediting_957027chr21_33546666_+intronic
ADediting_957028chr21_33546722_+intronic
ADediting_957029chr21_33547068_+intronic
ADediting_957030chr21_33547074_+intronic
ADediting_957031chr21_33547075_+intronic
ADediting_957032chr21_33547101_+intronic
ADediting_957033chr21_33547104_+intronic
ADediting_957034chr21_33547162_+intronic
ADediting_957035chr21_33547165_+intronic
ADediting_957036chr21_33547243_+intronic
ADediting_957037chr21_33547244_+intronic
ADediting_957038chr21_33547256_+intronic
ADediting_957039chr21_33547930_+intronic
ADediting_957040chr21_33550495_+exonic
ADediting_957041chr21_33550950_+exonic
ADediting_957042chr21_33550969_+exonic
ADediting_957043chr21_33551013_+exonic
ADediting_957044chr21_33551799_+exonic
ADediting_957045chr21_33556593_+intronic
ADediting_957046chr21_33557386_+intronic
ADediting_957047chr21_33557387_+intronic
ADediting_957048chr21_33557388_+intronic
ADediting_1641784chr21_33546594_+intronic
ADediting_1641785chr21_33546603_+intronic
ADediting_1641786chr21_33546610_+intronic
ADediting_1641787chr21_33546625_+intronic
ADediting_1641788chr21_33546660_+intronic
ADediting_1641789chr21_33546661_+intronic
ADediting_1641790chr21_33546670_+intronic
ADediting_1641791chr21_33546678_+intronic
ADediting_1641792chr21_33546706_+intronic

check button Repat-regional RNA editing(s).
ADeditome IDPositionRepeat familyRepeat sub familyRepeat name
ADediting_957027chr21_33546666_+SINEAluName=AluSq2
ADediting_957028chr21_33546722_+SINEAluName=AluSq2
ADediting_957029chr21_33547068_+SINEAluName=AluSq2
ADediting_957030chr21_33547074_+SINEAluName=AluSq2
ADediting_957031chr21_33547075_+SINEAluName=AluSq2
ADediting_957032chr21_33547101_+SINEAluName=AluSq2
ADediting_957033chr21_33547104_+SINEAluName=AluSq2
ADediting_957034chr21_33547162_+SINEAluName=AluSq2
ADediting_957035chr21_33547165_+SINEAluName=AluSq2
ADediting_957036chr21_33547243_+SINEAluName=AluSq2
ADediting_957037chr21_33547244_+SINEAluName=AluSq2
ADediting_957038chr21_33547256_+SINEAluName=AluSq2
ADediting_957039chr21_33547930_+SINEAluName=AluY
ADediting_957045chr21_33556593_+SINEAluName=AluSx3
ADediting_1641784chr21_33546594_+SINEAluName=AluSq2
ADediting_1641785chr21_33546603_+SINEAluName=AluSq2
ADediting_1641786chr21_33546610_+SINEAluName=AluSq2
ADediting_1641787chr21_33546625_+SINEAluName=AluSq2
ADediting_1641788chr21_33546660_+SINEAluName=AluSq2
ADediting_1641789chr21_33546661_+SINEAluName=AluSq2
ADediting_1641790chr21_33546670_+SINEAluName=AluSq2
ADediting_1641791chr21_33546678_+SINEAluName=AluSq2
ADediting_1641792chr21_33546706_+SINEAluName=AluSq2

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RNA A-to-I editing events in the alternative splicing sites for SON

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeADeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength
ESADediting_957029chr21_33547068_+33547067:335470755ss2eCAGGTTCAA1.19CGGGTTCAA-6.26
ESADediting_957030chr21_33547074_+33547067:335470755ss5iCAGGTTCAA1.19CAGGTTCGA5.36
ESADediting_957031chr21_33547075_+33547067:335470755ss6iCAGGTTCAA1.19CAGGTTCAG2.78

check button Differential pencent of spliced in (PSI) between RNA A-to-I edited and non-edited samples

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for SON

check button Distribution of the averaged gene expression in AD and control with or without RNA A-to-I editing event.
* The grey color means N/A.

check button Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event.
boxplot
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check button - Differentially expressed gene between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.
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check button - Differentially expressed transcript between RNA A-to-I edited samples versus non-edited samples.
* Click on the image to enlarge it in a new window.

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ADeditome IDChrPositoingSkipped exonENSGENSTs

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Protein coding region RNA A-to-I editings for SON

check button- Lollipop plot for RNA A-to-I editings across protein structure.
* Click on the image to enlarge it in a new window.
all structure


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The effects of the RNA editing to the miRNA binding sites for SON


check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA gained miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in lncRNA lost miRNA binding sites.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1337757chr7_5495852_-ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-589-3pchr2133558865335588717mer-m83355884933558872145-17.06
ADediting_98289chr1_32086992_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-5585-3pchr2133557641335576477mer-m83355762533557648151-21.24

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
ADeditom_IDPositionENSGENSTTranscript namemiRNA IDChromosomeTargtTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
ADediting_1471003chr9_63819626_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-4477bchr2133558361335583688mer-1a3355834633558368152-9.23
ADediting_1471004chr9_63819627_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-4477bchr2133558361335583688mer-1a3355834633558368152-9.23
ADediting_1535953chr14_101045971_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-381-3pchr2133558202335582098mer-1a3355818833558209146-9.84
ADediting_1535954chr14_101045974_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-381-3pchr2133558202335582098mer-1a3355818833558209146-9.84
ADediting_1556067chr19_40282625_-ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-641chr2133558948335589547mer-m83355893233558955142-14.91
ADediting_1631458chr19_40282624_-ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-641chr2133558948335589547mer-m83355893233558955142-14.91
ADediting_843620chr2_207754818_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-4775chr2133557737335577437mer-1a3355772133557743145-17.11
ADediting_843620chr2_207754818_+ENSG00000159140.20ENST00000381679.8SON-203hsa-miR-4775chr2133558531335585388mer-1a3355851733558538151-7.56

check button Differentially expressed gene-miRNA network

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The effects of the RNA editing to the stability of the RNA structures for SON

check button - RNA A-to-I editing in mRNA.
* Click on the image to enlarge it in a new window.
ENSTENST typeRNA structure without RNA A-to-I editing.RNA structure with RNA A-to-I editing.
ENST00000356577.9protein_codingSoverviewSoverview
ENST00000300278.8protein_codingSoverviewSoverview
ENST00000381679.8protein_codingSoverviewSoverview

check button RNA A-to-I editing in miRNA.
ADeditom_IDENSTmir_IDEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

check button RNA A-to-I editing in mRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
ADediting_957040ENST00000356577.9chr21_33550495_+1319-2741.90-2737.70-2752.60
ADediting_957041ENST00000356577.9chr21_33550950_+1774-2738.90-2737.70-2752.60
ADediting_957042ENST00000356577.9chr21_33550969_+1793-2740.30-2737.70-2752.60
ADediting_957043ENST00000356577.9chr21_33551013_+1837-2742.80-2737.70-2752.60
ADediting_957044ENST00000356577.9chr21_33551799_+2623-2739.50-2737.70-2752.60
ADediting_957040ENST00000300278.8chr21_33550495_+1293-2493.90-2489.70-2504.60
ADediting_957041ENST00000300278.8chr21_33550950_+1748-2490.90-2489.70-2504.60
ADediting_957042ENST00000300278.8chr21_33550969_+1767-2492.30-2489.70-2504.60
ADediting_957043ENST00000300278.8chr21_33551013_+1811-2494.80-2489.70-2504.60
ADediting_957044ENST00000300278.8chr21_33551799_+2597-2491.50-2489.70-2504.60
ADediting_957040ENST00000381679.8chr21_33550495_+1292-2584.60-2580.40-2595.30
ADediting_957041ENST00000381679.8chr21_33550950_+1747-2581.60-2580.40-2595.30
ADediting_957042ENST00000381679.8chr21_33550969_+1766-2583.00-2580.40-2595.30
ADediting_957043ENST00000381679.8chr21_33551013_+1810-2585.50-2580.40-2595.30
ADediting_957044ENST00000381679.8chr21_33551799_+2596-2582.20-2580.40-2595.30

check button RNA A-to-I editing in lncRNA.
ADeditom_IDENSTEditing_InformationEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI

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Relation with ADAR for SON

check button Correlation between ADAR gene expression and RNA editing frequency
TissueADeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
DLPFCADediting_957040chr21_33550495_+2.99366957095091e-060.2617276643974281.65217450813129e-080.3137481760474870.317138596793604-0.057000424841945
CERADediting_957040chr21_33550495_+3.78140625620148e-110.5064727399420381.44565411520741e-120.5367161672095270.03371362017962190.173515570603164
DLPFCADediting_957042chr21_33550969_+3.71694326835735e-060.2593129543330712.47239387552213e-080.310064945783390.170268694346063-0.078083407267865
CERADediting_957042chr21_33550969_+2.8805330094077e-100.4860411562981698.94128629435396e-130.5409253541465110.9464335378775190.00553195901617054
TCXADediting_957042chr21_33550969_+0.2307028921478370.09844685066800824.35756943973561e-070.3986485658377780.00177066615374376-0.253200544060075
FPADediting_957042chr21_33550969_+0.007100944140425080.2011301529645542.22480964481359e-050.3121017230210070.00529362748368189-0.208186048760734
STGADediting_957042chr21_33550969_+0.0002080418990332930.3940879740326941.9411131166308e-050.4478449025315280.0762052663746795-0.194527672412881
CERADediting_957043chr21_33551013_+9.76044043969585e-090.4470465342552822.64883273162989e-120.5313267098262270.01244829432381940.203617695058008
TCXADediting_957043chr21_33551013_+8.54991083946114e-060.3545084124734732.84959661171647e-070.4044535138679780.0450649765252944-0.163892667437494

check button Correlation between ADAR gene expression and this gene's expression
TissueADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
DLPFC0.0006721939784984920.1921192428574597.12623160252476e-110.359218224064520.001323492975080630.181578492263994
AC5.20790952761511e-700.8470082898192923.16013296153743e-460.7489686309784352.68274763178603e-210.551523535681374
PCC1.29337895681591e-240.653227424661881.13826725414081e-230.6430044903527730.0007746395051866850.241225459000546
CER2.09979408877095e-570.9068460294058723.81630405458505e-350.8034267965120740.0004382016255803050.2835327961893
TCX4.82548713666475e-280.7471605927401310.0007095506260189620.2734535093442062.56470101611593e-150.587960224471203
FP5.28809772097241e-340.7543944325957951.24434050081171e-250.6813195956386452.79159520539887e-050.308519547749415
IFG6.14448486609407e-070.817324603256860.00174481471328030.5939768915152040.002207483527811810.58334385920557
PG6.3741350120505e-450.8121404702384533.30812570918382e-280.6954079142848560.2354080877346610.0874241936590068
STG1.58576007680701e-200.8079261097109898.9040805699845e-150.7222605221605390.02589300653262520.243058628105823

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Relation with AD stages for SON

check button Correlation between AD stages and RNA editing frequency
TissueADeditomIDpositionP-valCoeff.
CERADediting_957040chr21_33550495_+8.93690409515281e-050.367955277077954
CERADediting_957043chr21_33551013_+1.22370321696711e-050.407176684526004

check button Correlation between AD stages and this gene's expression
TissueP-valCoeff.
CER1.27773994954881e-060.446470661497967
TCX9.64977265611241e-130.623288111341868

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RelatedDrugs for SON

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SON

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
SONC4310696ZTTK SYNDROME4CTD_human;ORPHANET;UNIPROT
SONC0010606Adenoid Cystic Carcinoma1CTD_human
SONC0036095Salivary Gland Neoplasms1CTD_human
SONC0220636Malignant neoplasm of salivary gland1CTD_human