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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 tumor samples versus normal 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 cancer stages

Soverview

Relation with survival state

Soverview

Related drugs with this gene

Soverview

Related diseases with this gene

Editing gene: SYNPO (CAeditome ID:11346)

Gene summary for SYNPO

check button Gene summary
Gene informationGene symbol

SYNPO

Gene ID

11346

Gene namesynaptopodin
Synonyms-
Cytomap

5q33.1

Type of geneprotein-coding
Descriptionsynaptopodin
Modification date20210518
UniProtAcc

Q8N3V7

Context

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

GO:0098886

Synaptopodin

25164660

SYNPO

GO:0005829

Synaptopodin

30661770

SYNPO

GO:0015629

Synaptopodin

0000054


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RNA A-to-I events for SYNPO

check buttonRNA A-to-I editing events across TCGA 33 cancers data sets based on Ensembl gene isoform structure.
all structure

check button RNA editing frequencies across 33 cancers of gene: ENSG00000171992.11

check button RNA A-to-I editing events in Cancer.
CAediting_441362(150628747, +), CAediting_441363(150628814, +), CAediting_441364(150628828, +), CAediting_441365(150628932, +), CAediting_441366(150629050, +), CAediting_441367(150629138, +), CAediting_441368(150629139, +), CAediting_441369(150629152, +), CAediting_441370(150629178, +), CAediting_441371(150629193, +), CAediting_441372(150629247, +), CAediting_441373(150633880, +), CAediting_441374(150633888, +), CAediting_441375(150643652, +), CAediting_441376(150643661, +), CAediting_441377(150643664, +), CAediting_441378(150643795, +), CAediting_441379(150643796, +), CAediting_441380(150643801, +), CAediting_441381(150643991, +), CAediting_441382(150643993, +), CAediting_441383(150644052, +), CAediting_441384(150644054, +), CAediting_441385(150644068, +), CAediting_441386(150644114, +), CAediting_441387(150644116, +), CAediting_441388(150644121, +), CAediting_441389(150651180, +), CAediting_441390(150654862, +), CAediting_441391(150654870, +), CAediting_441392(150655057, +), CAediting_441393(150655077, +), CAediting_441394(150655121, +), CAediting_441395(150655676, +), CAediting_441396(150655714, +), CAediting_441397(150655733, +), CAediting_441398(150655746, +), CAediting_441399(150655752, +), CAediting_441400(150655753, +), CAediting_441401(150655757, +), CAediting_441402(150655770, +), CAediting_441403(150655792, +), CAediting_441404(150655798, +), CAediting_441405(150655816, +), CAediting_441406(150655817, +), CAediting_441407(150655825, +), CAediting_441408(150655831, +), CAediting_441409(150655834, +), CAediting_441410(150655840, +), CAediting_441411(150655860, +), CAediting_441412(150655873, +), CAediting_441413(150655894, +), CAediting_441414(150655912, +), CAediting_441415(150655925, +), CAediting_441416(150656041, +), CAediting_441417(150656057, +), CAediting_441418(150656063, +), CAediting_441419(150656068, +), CAediting_441420(150656070, +), CAediting_441421(150656071, +), CAediting_441422(150656076, +), CAediting_441423(150656077, +), CAediting_441424(150656101, +), CAediting_441425(150656103, +), CAediting_441426(150656106, +), CAediting_441427(150656112, +),

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RNA editing positional annotations for SYNPO using Annovar

check button Protein coding RNA editing(s).
CAeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred

check button Gene structure information of RNA editing(s).
CAeditome IDPositionVariant type
CAediting_441362chr5_150628747_+ncRNA_intronic
CAediting_441363chr5_150628814_+ncRNA_intronic
CAediting_441364chr5_150628828_+ncRNA_intronic
CAediting_441365chr5_150628932_+ncRNA_intronic
CAediting_441366chr5_150629050_+ncRNA_intronic
CAediting_441367chr5_150629138_+ncRNA_intronic
CAediting_441368chr5_150629139_+ncRNA_intronic
CAediting_441369chr5_150629152_+ncRNA_intronic
CAediting_441370chr5_150629178_+ncRNA_intronic
CAediting_441371chr5_150629193_+ncRNA_intronic
CAediting_441372chr5_150629247_+ncRNA_intronic
CAediting_441373chr5_150633880_+ncRNA_intronic
CAediting_441374chr5_150633888_+ncRNA_intronic
CAediting_441375chr5_150643652_+ncRNA_intronic
CAediting_441376chr5_150643661_+ncRNA_intronic
CAediting_441377chr5_150643664_+ncRNA_intronic
CAediting_441378chr5_150643795_+ncRNA_intronic
CAediting_441379chr5_150643796_+ncRNA_intronic
CAediting_441380chr5_150643801_+ncRNA_intronic
CAediting_441381chr5_150643991_+ncRNA_intronic
CAediting_441382chr5_150643993_+ncRNA_intronic
CAediting_441383chr5_150644052_+ncRNA_intronic
CAediting_441384chr5_150644054_+ncRNA_intronic
CAediting_441385chr5_150644068_+ncRNA_intronic
CAediting_441386chr5_150644114_+ncRNA_intronic
CAediting_441387chr5_150644116_+ncRNA_intronic
CAediting_441388chr5_150644121_+ncRNA_intronic
CAediting_441389chr5_150651180_+UTR3
CAediting_441390chr5_150654862_+intronic
CAediting_441391chr5_150654870_+intronic
CAediting_441392chr5_150655057_+intronic
CAediting_441393chr5_150655077_+intronic
CAediting_441394chr5_150655121_+intronic
CAediting_441395chr5_150655676_+intronic
CAediting_441396chr5_150655714_+intronic
CAediting_441397chr5_150655733_+intronic
CAediting_441398chr5_150655746_+intronic
CAediting_441399chr5_150655752_+intronic
CAediting_441400chr5_150655753_+intronic
CAediting_441401chr5_150655757_+intronic
CAediting_441402chr5_150655770_+intronic
CAediting_441403chr5_150655792_+intronic
CAediting_441404chr5_150655798_+intronic
CAediting_441405chr5_150655816_+intronic
CAediting_441406chr5_150655817_+intronic
CAediting_441407chr5_150655825_+intronic
CAediting_441408chr5_150655831_+intronic
CAediting_441409chr5_150655834_+intronic
CAediting_441410chr5_150655840_+intronic
CAediting_441411chr5_150655860_+intronic
CAediting_441412chr5_150655873_+intronic
CAediting_441413chr5_150655894_+intronic
CAediting_441414chr5_150655912_+intronic
CAediting_441415chr5_150655925_+intronic
CAediting_441416chr5_150656041_+intronic
CAediting_441417chr5_150656057_+intronic
CAediting_441418chr5_150656063_+intronic
CAediting_441419chr5_150656068_+intronic
CAediting_441420chr5_150656070_+intronic
CAediting_441421chr5_150656071_+intronic
CAediting_441422chr5_150656076_+intronic
CAediting_441423chr5_150656077_+intronic
CAediting_441424chr5_150656101_+intronic
CAediting_441425chr5_150656103_+intronic
CAediting_441426chr5_150656106_+intronic
CAediting_441427chr5_150656112_+intronic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_441362chr5_150628747_+SINEAluAluSx
CAediting_441363chr5_150628814_+SINEAluAluSx
CAediting_441364chr5_150628828_+SINEAluAluSx
CAediting_441366chr5_150629050_+SINEAluAluJo
CAediting_441367chr5_150629138_+SINEAluAluJo
CAediting_441368chr5_150629139_+SINEAluAluJo
CAediting_441369chr5_150629152_+SINEAluAluJo
CAediting_441370chr5_150629178_+SINEAluAluJo
CAediting_441371chr5_150629193_+SINEAluAluJo
CAediting_441372chr5_150629247_+SINEAluAluJo
CAediting_441373chr5_150633880_+SINEAluAluJo
CAediting_441374chr5_150633888_+SINEAluAluJo
CAediting_441375chr5_150643652_+SINEAluAluSg4
CAediting_441376chr5_150643661_+SINEAluAluSg4
CAediting_441377chr5_150643664_+SINEAluAluSg4
CAediting_441378chr5_150643795_+SINEAluAluSg4
CAediting_441379chr5_150643796_+SINEAluAluSg4
CAediting_441380chr5_150643801_+SINEAluAluSg4
CAediting_441381chr5_150643991_+SINEAluAluJb
CAediting_441382chr5_150643993_+SINEAluAluJb
CAediting_441383chr5_150644052_+SINEAluAluJb
CAediting_441384chr5_150644054_+SINEAluAluJb
CAediting_441385chr5_150644068_+SINEAluAluJb
CAediting_441386chr5_150644114_+SINEAluAluJb
CAediting_441387chr5_150644116_+SINEAluAluJb
CAediting_441388chr5_150644121_+SINEAluAluJb
CAediting_441390chr5_150654862_+SINEAluAluSp
CAediting_441391chr5_150654870_+SINEAluAluSp
CAediting_441392chr5_150655057_+SINEAluAluSp
CAediting_441393chr5_150655077_+SINEAluAluSp
CAediting_441394chr5_150655121_+SINEAluAluSp
CAediting_441395chr5_150655676_+SINEAluAluSx
CAediting_441396chr5_150655714_+SINEAluAluSx
CAediting_441397chr5_150655733_+SINEAluAluSx
CAediting_441398chr5_150655746_+SINEAluAluSx
CAediting_441399chr5_150655752_+SINEAluAluSx
CAediting_441400chr5_150655753_+SINEAluAluSx
CAediting_441401chr5_150655757_+SINEAluAluSx
CAediting_441402chr5_150655770_+SINEAluAluSx
CAediting_441403chr5_150655792_+SINEAluAluSx
CAediting_441404chr5_150655798_+SINEAluAluSx
CAediting_441405chr5_150655816_+SINEAluAluSx
CAediting_441406chr5_150655817_+SINEAluAluSx
CAediting_441407chr5_150655825_+SINEAluAluSx
CAediting_441408chr5_150655831_+SINEAluAluSx
CAediting_441409chr5_150655834_+SINEAluAluSx
CAediting_441410chr5_150655840_+SINEAluAluSx
CAediting_441411chr5_150655860_+SINEAluAluSx
CAediting_441412chr5_150655873_+SINEAluAluSx
CAediting_441413chr5_150655894_+SINEAluAluSx
CAediting_441414chr5_150655912_+SINEAluAluSx
CAediting_441415chr5_150655925_+SINEAluAluSx
CAediting_441416chr5_150656041_+SINEMIRMIR
CAediting_441417chr5_150656057_+SINEMIRMIR
CAediting_441418chr5_150656063_+SINEMIRMIR
CAediting_441419chr5_150656068_+SINEMIRMIR
CAediting_441420chr5_150656070_+SINEMIRMIR
CAediting_441421chr5_150656071_+SINEMIRMIR
CAediting_441422chr5_150656076_+SINEMIRMIR
CAediting_441423chr5_150656077_+SINEMIRMIR
CAediting_441424chr5_150656101_+SINEMIRMIR
CAediting_441425chr5_150656103_+SINEMIRMIR
CAediting_441426chr5_150656106_+SINEMIRMIR
CAediting_441427chr5_150656112_+SINEMIRMIR

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

check button RNA A-to-I editing(s) in the alternative splicing sites.
AStypeCAeditomIDEditing positionAS positionAS directionExonic locationWildtype sequenceWildtype splicing strengthRNA edited sequenceRNA edited splicing strength

check button Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000171992.11.SYNPO.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000171992.11.SYNPO.

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

check button Differential gene expressions between RNA A-to-I edited and non-edited tumor samples.
* The grey color means N/A.
boxplot

check button Correlation between RNA A-to-I editing and gene expression.
boxplot

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.
KIRC.CAediting_441424.ENSG00000171992.SYNPO.png
Soverview

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

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


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

**If you are searching a miRNA gene with RNA editing events in its seed regions, please see the search pages of miRNA targets to discover the effects of this RNA editing event to miRNA regulations. For more information, please check the files in the Download page.

check button RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000394243hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000394243hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000522122hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000522122hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000519664hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000519664hsa-miR-44351506511771506511837mer-m8150651163150651184157.00-20.75

check button RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000394243hsa-miR-6789-5p1506511731506511797mer-m8150651151150651180150-32.68
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000522122hsa-miR-6789-5p1506511731506511797mer-m8150651151150651180150-32.68
CAediting_441389chr5_150651180_+ENSG00000171992.11ENST00000519664hsa-miR-6789-5p1506511731506511797mer-m8150651151150651180150-32.68

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

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

check button RNA A-to-I editing in miRNAs gained binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs lost binding to lncRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy

check button RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_748296chr10_51299626_+ENSG00000171992.11ENST00000394243hsa-miR-605-3p1506533111506533188mer-1a150653296150653318146-16.11
CAediting_980496chr14_31014685_-ENSG00000171992.11ENST00000394243hsa-miR-624-3p1506525641506525707mer-m8150652551150652571154-26.28
CAediting_393chr1_1167164_+ENSG00000171992.11ENST00000394243hsa-miR-200b-3p1506527101506527167mer-m8150652697150652717154-13.36
CAediting_393chr1_1167164_+ENSG00000171992.11ENST00000394243hsa-miR-200b-3p1506533911506533977mer-m8150653378150653398145-10.88
CAediting_393chr1_1167164_+ENSG00000171992.11ENST00000394243hsa-miR-200b-3p1506538751506538828mer-1a150653861150653882140-11.54
CAediting_688081chr9_63819627_+ENSG00000171992.11ENST00000394243hsa-miR-4477b1506536751506536828mer-1a150653661150653682142-9.79
CAediting_1229415chr17_67471547_+ENSG00000171992.11ENST00000394243hsa-miR-548aa1506504721506504787mer-m8150650455150650479140-11.93
CAediting_1368054chr19_46709310_-ENSG00000171992.11ENST00000394243hsa-miR-320e1506536651506536717mer-m8150653655150653672150-25.22
CAediting_77128chr1_85133844_+ENSG00000171992.11ENST00000394243hsa-miR-4423-3p1506520221506520287mer-m8150652009150652029140-14.9
CAediting_77128chr1_85133844_+ENSG00000171992.11ENST00000394243hsa-miR-4423-3p1506532391506532457mer-m8150653226150653246140-12.68
CAediting_228905chr2_188297554_+ENSG00000171992.11ENST00000394243hsa-miR-561-3p1506535381506535447mer-1a150653523150653544147-17.94
CAediting_1229415chr17_67471547_+ENSG00000171992.11ENST00000522122hsa-miR-548aa1506504721506504787mer-m8150650455150650479140-11.93
CAediting_77128chr1_85133844_+ENSG00000171992.11ENST00000522122hsa-miR-4423-3p1506520221506520287mer-m8150652009150652029140-14.9
CAediting_1229415chr17_67471547_+ENSG00000171992.11ENST00000519664hsa-miR-548aa1506504721506504787mer-m8150650455150650479140-11.93
CAediting_77128chr1_85133844_+ENSG00000171992.11ENST00000519664hsa-miR-4423-3p1506520221506520287mer-m8150652009150652029140-14.9
CAediting_468389chr6_31355314_-ENSG00000171992.11ENST00000394243hsa-miR-6891-5p1506536301506536367mer-m8150653619150653637146-24.39
CAediting_468389chr6_31355314_-ENSG00000171992.11ENST00000394243hsa-miR-6891-5p1506507641506507718mer-1a150650753150650771149-21.78
CAediting_1524209chrX_134546392_-ENSG00000171992.11ENST00000394243hsa-miR-503-5p1506535011506535077mer-m8150653484150653508156-24.42
CAediting_468389chr6_31355314_-ENSG00000171992.11ENST00000522122hsa-miR-6891-5p1506507641506507718mer-1a150650753150650771149-21.78
CAediting_468389chr6_31355314_-ENSG00000171992.11ENST00000519664hsa-miR-6891-5p1506507641506507718mer-1a150650753150650771149-21.78

check button RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA.
CAeditom_IDPositionENSGENSTmiRNATargetscan startTargetscan endTargetscan scoreMiranda startMiranda endMiranda scoreMiranda energy
CAediting_442554chr5_154685830_+ENSG00000171992.11ENST00000394243hsa-miR-13031506538591506538657mer-m8150653845150653866145-16.31
CAediting_1054808chr15_66496985_-ENSG00000171992.11ENST00000394243hsa-miR-45121506535441506535518mer-1a150653529150653551151-20.96
CAediting_1524209chrX_134546392_-ENSG00000171992.11ENST00000394243hsa-miR-503-5p1506508941506509007mer-m8150650879150650901148-18.12
CAediting_748296chr10_51299626_+ENSG00000171992.11ENST00000394243hsa-miR-605-3p1506520871506520937mer-m8150652073150652094146-18.49
CAediting_748296chr10_51299626_+ENSG00000171992.11ENST00000394243hsa-miR-605-3p1506536931506536997mer-m8150653677150653700147-18.07
CAediting_748296chr10_51299626_+ENSG00000171992.11ENST00000394243hsa-miR-605-3p1506508691506508757mer-m8150650855150650876141-15.54
CAediting_1524209chrX_134546392_-ENSG00000171992.11ENST00000522122hsa-miR-503-5p1506508941506509007mer-m8150650879150650901148-18.12
CAediting_1524209chrX_134546392_-ENSG00000171992.11ENST00000519664hsa-miR-503-5p1506508941506509007mer-m8150650879150650901148-18.12

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 SYNPO

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.
ENST00000394243.4protein_codingSoverviewSoverview
ENST00000522122.1protein_codingSoverviewSoverview
ENST00000519664.1protein_codingSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_441389ENST00000394243.4chr5_150651180_+-2913.50-2910.90-2913.50
CAediting_441389ENST00000522122.1chr5_150651180_+-2182.30-2179.70-2182.30
CAediting_441389ENST00000519664.1chr5_150651180_+-1938.50-1935.90-1938.50

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Relation with ADAR for SYNPO

check button Correlation between ADAR gene expression and RNA editing frequency
CancerCAeditomIDpositionADAR1 (p-val)ADAR1 (coeff.)ADAR2 (p-val)ADAR2 (coeff.)ADAR3 (p-val)ADAR3 (coeff.)
OVCAediting_441420chr5_150656070_+0.003195151682816170.401276695224957....

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Relation with cancer stages for SYNPO

check button Correlation between Cancer stages and RNA editing frequency
CancerStage_typeCAeditomIDpositionP-valCoeff.
KIRCpathologic_stageCAediting_441424chr5_150656101_+0.0377879083880840.158074311527986

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Relation with survival for SYNPO

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

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RelatedDrugs for SYNPO

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.8 2021-01-03)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for SYNPO

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource
SYNPOC0017668Focal glomerulosclerosis1GENOMICS_ENGLAND
SYNPOC4049702Focal Segmental Glomerulosclerosis, Not Otherwise Specified1GENOMICS_ENGLAND