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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: GNPDA1 (CAeditome ID:10007)

Gene summary for GNPDA1

check button Gene summary
Gene informationGene symbol

GNPDA1

Gene ID

10007

Gene nameglucosamine-6-phosphate deaminase 1
SynonymsGNP1|GNPDA|GNPI|GPI|HLN
Cytomap

5q31.3

Type of geneprotein-coding
Descriptionglucosamine-6-phosphate isomerase 1GNPDA 1glcN6P deaminase 1oscillin
Modification date20210518
UniProtAcc

P46926

Context

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

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RNA A-to-I events for GNPDA1

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: ENSG00000113552.14

check button RNA A-to-I editing events in Cancer.
CAediting_438008(141993621, -), CAediting_438009(141993644, -), CAediting_438010(141993648, -), CAediting_438011(141993649, -), CAediting_438012(141993663, -), CAediting_438013(141993797, -), CAediting_438014(141993829, -), CAediting_438015(141996656, -), CAediting_438016(141996712, -), CAediting_438017(141999588, -), CAediting_438018(141999595, -), CAediting_438019(141999610, -), CAediting_438020(141999745, -), CAediting_438021(141999754, -), CAediting_438022(141999797, -), CAediting_438023(141999821, -), CAediting_438024(141999998, -), CAediting_438025(141999999, -), CAediting_438026(142000004, -), CAediting_438027(142000005, -), CAediting_438028(142000043, -), CAediting_438029(142000048, -), CAediting_438030(142000054, -), CAediting_438031(142000071, -), CAediting_438032(142000089, -), CAediting_438033(142000097, -), CAediting_438034(142000100, -), CAediting_438035(142000101, -), CAediting_438036(142000102, -), CAediting_438037(142000152, -), CAediting_438038(142000170, -), CAediting_438039(142000182, -), CAediting_438040(142000205, -), CAediting_438041(142000206, -), CAediting_438042(142000208, -), CAediting_438043(142000222, -), CAediting_438044(142010509, -), CAediting_438045(142010514, -), CAediting_438046(142010582, -), CAediting_438047(142010583, -), CAediting_438048(142010674, -), CAediting_438049(142010682, -), CAediting_438050(142010687, -), CAediting_438051(142010710, -), CAediting_438052(142011020, -), CAediting_438053(142011085, -), CAediting_438054(142011984, -),

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RNA editing positional annotations for GNPDA1 using Annovar

check button Protein coding RNA editing(s).
CAeditome IDPositionVariant typeENSTNTchangeAAchangeSIFT_scorePolyphen2_HVAR_scorePROVEAN_pred
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000311337.9c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000500692.5c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000503229.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000503794.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000504139.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000504424.1c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000505689.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000508177.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000510194.4c.A52Gp.K18EDBD
CAediting_438054chr5_142011984_-nonsynonymous SNVENST00000513454.4c.A52Gp.K18EDBD

check button Gene structure information of RNA editing(s).
CAeditome IDPositionVariant type
CAediting_438008chr5_141993621_-intronic
CAediting_438009chr5_141993644_-intronic
CAediting_438010chr5_141993648_-intronic
CAediting_438011chr5_141993649_-intronic
CAediting_438012chr5_141993663_-intronic
CAediting_438013chr5_141993797_-intronic
CAediting_438014chr5_141993829_-intronic
CAediting_438015chr5_141996656_-intronic
CAediting_438016chr5_141996712_-intronic
CAediting_438017chr5_141999588_-intronic
CAediting_438018chr5_141999595_-intronic
CAediting_438019chr5_141999610_-intronic
CAediting_438020chr5_141999745_-intronic
CAediting_438021chr5_141999754_-intronic
CAediting_438022chr5_141999797_-intronic
CAediting_438023chr5_141999821_-intronic
CAediting_438024chr5_141999998_-intronic
CAediting_438025chr5_141999999_-intronic
CAediting_438026chr5_142000004_-intronic
CAediting_438027chr5_142000005_-intronic
CAediting_438028chr5_142000043_-intronic
CAediting_438029chr5_142000048_-intronic
CAediting_438030chr5_142000054_-intronic
CAediting_438031chr5_142000071_-intronic
CAediting_438032chr5_142000089_-intronic
CAediting_438033chr5_142000097_-intronic
CAediting_438034chr5_142000100_-intronic
CAediting_438035chr5_142000101_-intronic
CAediting_438036chr5_142000102_-intronic
CAediting_438037chr5_142000152_-intronic
CAediting_438038chr5_142000170_-intronic
CAediting_438039chr5_142000182_-intronic
CAediting_438040chr5_142000205_-intronic
CAediting_438041chr5_142000206_-intronic
CAediting_438042chr5_142000208_-intronic
CAediting_438043chr5_142000222_-intronic
CAediting_438044chr5_142010509_-ncRNA_intronic
CAediting_438045chr5_142010514_-ncRNA_intronic
CAediting_438046chr5_142010582_-ncRNA_intronic
CAediting_438047chr5_142010583_-ncRNA_intronic
CAediting_438048chr5_142010674_-ncRNA_intronic
CAediting_438049chr5_142010682_-ncRNA_intronic
CAediting_438050chr5_142010687_-ncRNA_intronic
CAediting_438051chr5_142010710_-ncRNA_intronic
CAediting_438052chr5_142011020_-ncRNA_intronic
CAediting_438053chr5_142011085_-ncRNA_intronic
CAediting_438054chr5_142011984_-exonic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_438008chr5_141993621_-SINEAluAluJb
CAediting_438009chr5_141993644_-SINEAluAluJb
CAediting_438010chr5_141993648_-SINEAluAluJb
CAediting_438011chr5_141993649_-SINEAluAluJb
CAediting_438012chr5_141993663_-SINEAluAluJb
CAediting_438013chr5_141993797_-SINEAluAluJb
CAediting_438014chr5_141993829_-SINEAluAluJb
CAediting_438015chr5_141996656_-SINEAluAluSz6
CAediting_438016chr5_141996712_-SINEAluAluSz6
CAediting_438017chr5_141999588_-SINEAluAluSz
CAediting_438018chr5_141999595_-SINEAluAluSz
CAediting_438019chr5_141999610_-SINEAluAluSz
CAediting_438020chr5_141999745_-SINEAluAluSz
CAediting_438021chr5_141999754_-SINEAluAluSz
CAediting_438022chr5_141999797_-SINEAluAluSz
CAediting_438023chr5_141999821_-SINEAluAluSz
CAediting_438024chr5_141999998_-SINEAluFRAM
CAediting_438025chr5_141999999_-SINEAluFRAM
CAediting_438026chr5_142000004_-SINEAluAluJr
CAediting_438027chr5_142000005_-SINEAluAluJr
CAediting_438028chr5_142000043_-SINEAluAluJr
CAediting_438029chr5_142000048_-SINEAluAluJr
CAediting_438030chr5_142000054_-SINEAluAluJr
CAediting_438031chr5_142000071_-SINEAluAluJr
CAediting_438032chr5_142000089_-SINEAluAluJr
CAediting_438033chr5_142000097_-SINEAluAluJr
CAediting_438034chr5_142000100_-SINEAluAluJr
CAediting_438035chr5_142000101_-SINEAluAluJr
CAediting_438036chr5_142000102_-SINEAluAluJr
CAediting_438037chr5_142000152_-SINEAluAluJr
CAediting_438038chr5_142000170_-SINEAluAluJr
CAediting_438039chr5_142000182_-SINEAluAluJr
CAediting_438040chr5_142000205_-SINEAluAluJr
CAediting_438041chr5_142000206_-SINEAluAluJr
CAediting_438042chr5_142000208_-SINEAluAluJr
CAediting_438043chr5_142000222_-SINEAluAluJr
CAediting_438044chr5_142010509_-SINEAluAluJb
CAediting_438045chr5_142010514_-SINEAluAluJb
CAediting_438046chr5_142010582_-SINEAluAluJb
CAediting_438047chr5_142010583_-SINEAluAluJb
CAediting_438048chr5_142010674_-SINEAluAluJb
CAediting_438049chr5_142010682_-SINEAluAluJb
CAediting_438050chr5_142010687_-SINEAluAluJb
CAediting_438051chr5_142010710_-SINEAluAluJb
CAediting_438052chr5_142011020_-SINEAluAluJb
CAediting_438053chr5_142011085_-SINEAluAluJb

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RNA A-to-I editing events in the alternative splicing sites for GNPDA1

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 ENSG00000113552.14.GNPDA1.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000113552.14.GNPDA1.

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Differntial gene expression between RNA A-to-I edited versus non-edited samples for GNPDA1

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

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

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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Protein coding region RNA A-to-I editings for GNPDA1

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 GNPDA1

**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

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

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_604450chr7_133034877_-ENSG00000113552.14ENST00000513454hsa-miR-36541419918141419918207mer-m8141991813141991831140-16.64
CAediting_228905chr2_188297554_+ENSG00000113552.14ENST00000500692hsa-miR-561-3p1420015571420015637mer-m8142001556142001575148-11.48
CAediting_396018chr5_1062918_-ENSG00000113552.14ENST00000500692hsa-miR-46351420013761420013827mer-m8142001375142001396145-14.16
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000500692hsa-miR-589-3p1420009321420009387mer-m8142000931142000955153-20.69
CAediting_228905chr2_188297554_+ENSG00000113552.14ENST00000508177hsa-miR-561-3p1420015571420015637mer-m8142001556142001575148-11.48
CAediting_396018chr5_1062918_-ENSG00000113552.14ENST00000508177hsa-miR-46351420013761420013827mer-m8142001375142001396145-14.16
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000508177hsa-miR-589-3p1420009321420009387mer-m8142000931142000955153-20.69
CAediting_228905chr2_188297554_+ENSG00000113552.14ENST00000503794hsa-miR-561-3p1420015571420015637mer-m8142001556142001575148-11.48
CAediting_396018chr5_1062918_-ENSG00000113552.14ENST00000503794hsa-miR-46351420013761420013827mer-m8142001375142001396145-14.16
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000503794hsa-miR-589-3p1420009321420009387mer-m8142000931142000955153-20.69
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000500692hsa-miR-6891-5p1420008841420008907mer-m8142000883142000902144-17.18
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000508177hsa-miR-6891-5p1420008841420008907mer-m8142000883142000902144-17.18
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000503794hsa-miR-6891-5p1420008841420008907mer-m8142000883142000902144-17.18

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_524911chr7_5495852_-ENSG00000113552.14ENST00000500692hsa-miR-589-3p1420010031420010108mer-1a142001003142001026144-18.01
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000500692hsa-miR-589-3p1420017511420017577mer-m8142001750142001777153-22.08
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000500692hsa-miR-6891-5p1420016971420017037mer-1a142001697142001715141-18.97
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000508177hsa-miR-589-3p1420010031420010108mer-1a142001003142001026144-18.01
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000508177hsa-miR-589-3p1420017511420017577mer-m8142001750142001777153-22.08
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000508177hsa-miR-6891-5p1420016971420017037mer-1a142001697142001715141-18.97
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000503794hsa-miR-589-3p1420010031420010108mer-1a142001003142001026144-18.01
CAediting_524911chr7_5495852_-ENSG00000113552.14ENST00000503794hsa-miR-589-3p1420017511420017577mer-m8142001750142001777153-22.08
CAediting_468389chr6_31355314_-ENSG00000113552.14ENST00000503794hsa-miR-6891-5p1420016971420017037mer-1a142001697142001715141-18.97

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 GNPDA1

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.
ENST00000513454.4protein_codingSoverviewSoverview
ENST00000311337.9protein_codingSoverviewSoverview
ENST00000500692.5protein_codingSoverviewSoverview
ENST00000503229.4protein_codingSoverviewSoverview
ENST00000503794.4protein_codingSoverviewSoverview
ENST00000504139.4protein_codingSoverviewSoverview
ENST00000505689.4protein_codingSoverviewSoverview
ENST00000507107.1retained_intronSoverviewSoverview
ENST00000508177.4protein_codingSoverviewSoverview
ENST00000510194.4protein_codingSoverviewSoverview
ENST00000504424.1protein_codingSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_438054ENST00000513454.4chr5_142011984_--357.40-354.30-357.40
CAediting_438054ENST00000311337.9chr5_142011984_--775.70-771.80-775.70
CAediting_438054ENST00000500692.5chr5_142011984_--790.50-787.10-790.50
CAediting_438054ENST00000503229.4chr5_142011984_--180.30-176.40-180.30
CAediting_438054ENST00000503794.4chr5_142011984_--920.90-920.60-920.90
CAediting_438054ENST00000504139.4chr5_142011984_--270.10-266.40-270.10
CAediting_438054ENST00000505689.4chr5_142011984_--354.30-350.40-354.30
CAediting_438054ENST00000507107.1chr5_142011984_--187.30-185.80-187.30
CAediting_438054ENST00000508177.4chr5_142011984_--1032.20-1031.90-1032.20
CAediting_438054ENST00000510194.4chr5_142011984_--211.60-207.70-211.60
CAediting_438054ENST00000504424.1chr5_142011984_--204.40-201.00-204.40

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Relation with ADAR for GNPDA1

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.)

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Relation with cancer stages for GNPDA1

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

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Relation with survival for GNPDA1

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

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RelatedDrugs for GNPDA1

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 GNPDA1

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource
GNPDA1C0023893Liver Cirrhosis, Experimental1CTD_human