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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: PALMD (CAeditome ID:54873)

Gene summary for PALMD

check button Gene summary
Gene informationGene symbol

PALMD

Gene ID

54873

Gene namepalmdelphin
SynonymsC1orf11|PALML
Cytomap

1p21.2

Type of geneprotein-coding
Descriptionpalmdelphinparalemmin-like proteinparalemnin-like protein
Modification date20210518
UniProtAcc

Q9NP74

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 PALMD

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: ENSG00000099260.9
boxplot

check button RNA A-to-I editing events in Cancer.
CAediting_83116(99667982, +), CAediting_83117(99678184, +), CAediting_83118(99678197, +), CAediting_83119(99678295, +), CAediting_83120(99678326, +), CAediting_83121(99678327, +), CAediting_83122(99678334, +), CAediting_83123(99678367, +), CAediting_83124(99678379, +), CAediting_83125(99678852, +), CAediting_83126(99678870, +), CAediting_83127(99678871, +), CAediting_83128(99678892, +), CAediting_83129(99678929, +), CAediting_83130(99682750, +), CAediting_83131(99682751, +), CAediting_83132(99682756, +), CAediting_83133(99682759, +), CAediting_83134(99682765, +), CAediting_83135(99682773, +), CAediting_83136(99682777, +), CAediting_83137(99682778, +), CAediting_83138(99682786, +), CAediting_83139(99682791, +), CAediting_83140(99682796, +), CAediting_83141(99682805, +), CAediting_83142(99682810, +), CAediting_83143(99682829, +), CAediting_83144(99682835, +), CAediting_83145(99682844, +), CAediting_83146(99682847, +), CAediting_83147(99682848, +), CAediting_83148(99682850, +), CAediting_83149(99682854, +), CAediting_83150(99682855, +), CAediting_83151(99682856, +), CAediting_83152(99682859, +), CAediting_83153(99682863, +), CAediting_83154(99682885, +), CAediting_83155(99682895, +), CAediting_83156(99682899, +), CAediting_83157(99682908, +), CAediting_83158(99682912, +), CAediting_83159(99682917, +), CAediting_83160(99682918, +), CAediting_83161(99682926, +), CAediting_83162(99682927, +), CAediting_83163(99682938, +), CAediting_83164(99682956, +), CAediting_83165(99682969, +), CAediting_83166(99682993, +), CAediting_83167(99684554, +), CAediting_83168(99684578, +), CAediting_83169(99684584, +), CAediting_83170(99684590, +), CAediting_83171(99684597, +), CAediting_83172(99684602, +), CAediting_83173(99684603, +), CAediting_83174(99684622, +), CAediting_83175(99684623, +), CAediting_83176(99684624, +), CAediting_83177(99684626, +), CAediting_83178(99684635, +), CAediting_83179(99684640, +), CAediting_83180(99684648, +), CAediting_83181(99684652, +), CAediting_83182(99684699, +), CAediting_83183(99684707, +), CAediting_83184(99684726, +), CAediting_83185(99684738, +), CAediting_83186(99684739, +), CAediting_83187(99684752, +), CAediting_83188(99684755, +), CAediting_83189(99684769, +), CAediting_83190(99684778, +), CAediting_83191(99684779, +),

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RNA editing positional annotations for PALMD 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_83116chr1_99667982_+ncRNA_exonic
CAediting_83117chr1_99678184_+intronic
CAediting_83118chr1_99678197_+intronic
CAediting_83119chr1_99678295_+intronic
CAediting_83120chr1_99678326_+intronic
CAediting_83121chr1_99678327_+intronic
CAediting_83122chr1_99678334_+intronic
CAediting_83123chr1_99678367_+intronic
CAediting_83124chr1_99678379_+intronic
CAediting_83125chr1_99678852_+intronic
CAediting_83126chr1_99678870_+intronic
CAediting_83127chr1_99678871_+intronic
CAediting_83128chr1_99678892_+intronic
CAediting_83129chr1_99678929_+intronic
CAediting_83130chr1_99682750_+intronic
CAediting_83131chr1_99682751_+intronic
CAediting_83132chr1_99682756_+intronic
CAediting_83133chr1_99682759_+intronic
CAediting_83134chr1_99682765_+intronic
CAediting_83135chr1_99682773_+intronic
CAediting_83136chr1_99682777_+intronic
CAediting_83137chr1_99682778_+intronic
CAediting_83138chr1_99682786_+intronic
CAediting_83139chr1_99682791_+intronic
CAediting_83140chr1_99682796_+intronic
CAediting_83141chr1_99682805_+intronic
CAediting_83142chr1_99682810_+intronic
CAediting_83143chr1_99682829_+intronic
CAediting_83144chr1_99682835_+intronic
CAediting_83145chr1_99682844_+intronic
CAediting_83146chr1_99682847_+intronic
CAediting_83147chr1_99682848_+intronic
CAediting_83148chr1_99682850_+intronic
CAediting_83149chr1_99682854_+intronic
CAediting_83150chr1_99682855_+intronic
CAediting_83151chr1_99682856_+intronic
CAediting_83152chr1_99682859_+intronic
CAediting_83153chr1_99682863_+intronic
CAediting_83154chr1_99682885_+intronic
CAediting_83155chr1_99682895_+intronic
CAediting_83156chr1_99682899_+intronic
CAediting_83157chr1_99682908_+intronic
CAediting_83158chr1_99682912_+intronic
CAediting_83159chr1_99682917_+intronic
CAediting_83160chr1_99682918_+intronic
CAediting_83161chr1_99682926_+intronic
CAediting_83162chr1_99682927_+intronic
CAediting_83163chr1_99682938_+intronic
CAediting_83164chr1_99682956_+intronic
CAediting_83165chr1_99682969_+intronic
CAediting_83166chr1_99682993_+intronic
CAediting_83167chr1_99684554_+ncRNA_exonic
CAediting_83168chr1_99684578_+ncRNA_exonic
CAediting_83169chr1_99684584_+ncRNA_exonic
CAediting_83170chr1_99684590_+ncRNA_exonic
CAediting_83171chr1_99684597_+ncRNA_exonic
CAediting_83172chr1_99684602_+ncRNA_exonic
CAediting_83173chr1_99684603_+ncRNA_exonic
CAediting_83174chr1_99684622_+ncRNA_exonic
CAediting_83175chr1_99684623_+ncRNA_exonic
CAediting_83176chr1_99684624_+ncRNA_exonic
CAediting_83177chr1_99684626_+ncRNA_exonic
CAediting_83178chr1_99684635_+ncRNA_exonic
CAediting_83179chr1_99684640_+ncRNA_exonic
CAediting_83180chr1_99684648_+ncRNA_exonic
CAediting_83181chr1_99684652_+ncRNA_exonic
CAediting_83182chr1_99684699_+ncRNA_exonic
CAediting_83183chr1_99684707_+ncRNA_exonic
CAediting_83184chr1_99684726_+ncRNA_exonic
CAediting_83185chr1_99684738_+ncRNA_exonic
CAediting_83186chr1_99684739_+ncRNA_exonic
CAediting_83187chr1_99684752_+ncRNA_exonic
CAediting_83188chr1_99684755_+ncRNA_exonic
CAediting_83189chr1_99684769_+ncRNA_exonic
CAediting_83190chr1_99684778_+ncRNA_exonic
CAediting_83191chr1_99684779_+ncRNA_exonic

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_83116chr1_99667982_+SINEAluAluSx1
CAediting_83117chr1_99678184_+SINEAluAluSz
CAediting_83118chr1_99678197_+SINEAluAluSz
CAediting_83119chr1_99678295_+SINEAluAluSz
CAediting_83120chr1_99678326_+SINEAluAluSz
CAediting_83121chr1_99678327_+SINEAluAluSz
CAediting_83122chr1_99678334_+SINEAluAluSz
CAediting_83123chr1_99678367_+SINEAluAluSz
CAediting_83124chr1_99678379_+SINEAluAluSz
CAediting_83125chr1_99678852_+SINEAluFLAM_C
CAediting_83126chr1_99678870_+SINEAluFLAM_C
CAediting_83127chr1_99678871_+SINEAluFLAM_C
CAediting_83128chr1_99678892_+SINEAluFLAM_C
CAediting_83129chr1_99678929_+SINEAluFLAM_C
CAediting_83130chr1_99682750_+SINEAluAluSz
CAediting_83131chr1_99682751_+SINEAluAluSz
CAediting_83132chr1_99682756_+SINEAluAluSz
CAediting_83133chr1_99682759_+SINEAluAluSz
CAediting_83134chr1_99682765_+SINEAluAluSz
CAediting_83135chr1_99682773_+SINEAluAluSz
CAediting_83136chr1_99682777_+SINEAluAluSz
CAediting_83137chr1_99682778_+SINEAluAluSz
CAediting_83138chr1_99682786_+SINEAluAluSz
CAediting_83139chr1_99682791_+SINEAluAluSz
CAediting_83140chr1_99682796_+SINEAluAluSz
CAediting_83141chr1_99682805_+SINEAluAluSz
CAediting_83142chr1_99682810_+SINEAluAluSz
CAediting_83143chr1_99682829_+SINEAluAluSz
CAediting_83144chr1_99682835_+SINEAluAluSz
CAediting_83145chr1_99682844_+SINEAluAluSz
CAediting_83146chr1_99682847_+SINEAluAluSz
CAediting_83147chr1_99682848_+SINEAluAluSz
CAediting_83148chr1_99682850_+SINEAluAluSz
CAediting_83149chr1_99682854_+SINEAluAluSz
CAediting_83150chr1_99682855_+SINEAluAluSz
CAediting_83151chr1_99682856_+SINEAluAluSz
CAediting_83152chr1_99682859_+SINEAluAluSz
CAediting_83153chr1_99682863_+SINEAluAluSz
CAediting_83154chr1_99682885_+SINEAluAluSz
CAediting_83155chr1_99682895_+SINEAluAluSz
CAediting_83156chr1_99682899_+SINEAluAluSz
CAediting_83157chr1_99682908_+SINEAluAluSz
CAediting_83158chr1_99682912_+SINEAluAluSz
CAediting_83159chr1_99682917_+SINEAluAluSz
CAediting_83160chr1_99682918_+SINEAluAluSz
CAediting_83161chr1_99682926_+SINEAluAluSz
CAediting_83162chr1_99682927_+SINEAluAluSz
CAediting_83163chr1_99682938_+SINEAluAluSz
CAediting_83164chr1_99682956_+SINEAluAluSz
CAediting_83165chr1_99682969_+SINEAluAluSz
CAediting_83166chr1_99682993_+SINEAluAluSz
CAediting_83167chr1_99684554_+SINEAluAluJb
CAediting_83168chr1_99684578_+SINEAluAluJb
CAediting_83169chr1_99684584_+SINEAluAluJb
CAediting_83170chr1_99684590_+SINEAluAluJb
CAediting_83171chr1_99684597_+SINEAluAluJb
CAediting_83172chr1_99684602_+SINEAluAluJb
CAediting_83173chr1_99684603_+SINEAluAluJb
CAediting_83174chr1_99684622_+SINEAluAluJb
CAediting_83175chr1_99684623_+SINEAluAluJb
CAediting_83176chr1_99684624_+SINEAluAluJb
CAediting_83177chr1_99684626_+SINEAluAluJb
CAediting_83178chr1_99684635_+SINEAluAluJb
CAediting_83179chr1_99684640_+SINEAluAluJb
CAediting_83180chr1_99684648_+SINEAluAluJb
CAediting_83181chr1_99684652_+SINEAluAluJb
CAediting_83182chr1_99684699_+SINEAluAluJb
CAediting_83183chr1_99684707_+SINEAluAluJb
CAediting_83184chr1_99684726_+SINEAluAluJb
CAediting_83185chr1_99684738_+SINEAluAluJb
CAediting_83186chr1_99684739_+SINEAluAluJb
CAediting_83187chr1_99684752_+SINEAluAluJb
CAediting_83188chr1_99684755_+SINEAluAluJb
CAediting_83189chr1_99684769_+SINEAluAluJb
CAediting_83190chr1_99684778_+SINEAluAluJb
CAediting_83191chr1_99684779_+SINEAluAluJb

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

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 ENSG00000099260.9.PALMD.

check button Correlation between RNA A-to-I editing and PSI for ENSG00000099260.9.PALMD.

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

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.

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

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 PALMD

**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_393chr1_1167164_+ENSG00000099260.9ENST00000615664hsa-miR-200b-3p99694296996943027mer-m89969428299694303140-9.25

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

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 PALMD

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.
ENST00000605613.1retained_intronSoverviewSoverview
ENST00000496843.1retained_intronSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_83116ENST00000605613.1chr1_99667982_+-517.71-515.81-517.71
CAediting_83167ENST00000496843.1chr1_99684554_+-1335.27-1335.17-1362.57
CAediting_83168ENST00000496843.1chr1_99684578_+-1335.17-1335.17-1362.57
CAediting_83169ENST00000496843.1chr1_99684584_+-1338.37-1335.17-1362.57
CAediting_83170ENST00000496843.1chr1_99684590_+-1335.57-1335.17-1362.57
CAediting_83171ENST00000496843.1chr1_99684597_+-1335.47-1335.17-1362.57
CAediting_83172ENST00000496843.1chr1_99684602_+-1338.87-1335.17-1362.57
CAediting_83173ENST00000496843.1chr1_99684603_+-1336.97-1335.17-1362.57
CAediting_83174ENST00000496843.1chr1_99684622_+-1335.17-1335.17-1362.57
CAediting_83175ENST00000496843.1chr1_99684623_+-1336.57-1335.17-1362.57
CAediting_83176ENST00000496843.1chr1_99684624_+-1337.97-1335.17-1362.57
CAediting_83177ENST00000496843.1chr1_99684626_+-1335.17-1335.17-1362.57
CAediting_83178ENST00000496843.1chr1_99684635_+-1336.07-1335.17-1362.57
CAediting_83179ENST00000496843.1chr1_99684640_+-1335.67-1335.17-1362.57
CAediting_83180ENST00000496843.1chr1_99684648_+-1335.17-1335.17-1362.57
CAediting_83181ENST00000496843.1chr1_99684652_+-1339.17-1335.17-1362.57
CAediting_83182ENST00000496843.1chr1_99684699_+-1340.37-1335.17-1362.57
CAediting_83183ENST00000496843.1chr1_99684707_+-1336.37-1335.17-1362.57
CAediting_83184ENST00000496843.1chr1_99684726_+-1335.57-1335.17-1362.57
CAediting_83185ENST00000496843.1chr1_99684738_+-1335.07-1335.17-1362.57
CAediting_83186ENST00000496843.1chr1_99684739_+-1338.97-1335.17-1362.57
CAediting_83187ENST00000496843.1chr1_99684752_+-1341.37-1335.17-1362.57
CAediting_83188ENST00000496843.1chr1_99684755_+-1335.07-1335.17-1362.57
CAediting_83189ENST00000496843.1chr1_99684769_+-1336.27-1335.17-1362.57
CAediting_83190ENST00000496843.1chr1_99684778_+-1338.17-1335.17-1362.57
CAediting_83191ENST00000496843.1chr1_99684779_+-1335.47-1335.17-1362.57

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Relation with ADAR for PALMD

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.)
ESCACAediting_83137chr1_99682778_+0.002245085355399310.4001558508317160.0237941037032850.301789615298644..

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Relation with cancer stages for PALMD

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

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Relation with survival for PALMD

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR
ESCACAediting_83162chr1_99682927_+0.01533739984754250.0086214850.4266

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RelatedDrugs for PALMD

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 PALMD

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource
PALMDC0023893Liver Cirrhosis, Experimental1CTD_human