CAeditome Logo

Home

Download

Statistics

Examples

Help

Contact

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: LIN28A (CAeditome ID:79727)

Gene summary for LIN28A

check button Gene summary
Gene informationGene symbol

LIN28A

Gene ID

79727

Gene namelin-28 homolog A
SynonymsCSDD1|LIN-28|LIN28|ZCCHC1|lin-28A
Cytomap

1p36.11

Type of geneprotein-coding
Descriptionprotein lin-28 homolog ARNA-binding protein LIN-28zinc finger CCHC domain-containing protein 1zinc finger, CCHC domain containing 1
Modification date20210518
UniProtAcc

Q9H9Z2

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
LIN28A

GO:0003723

Protein lin-28 homolog A

18951094

LIN28A

GO:0003723

Protein lin-28 homolog A

19703396

LIN28A

GO:1905538

Protein lin-28 homolog A

21247876

LIN28A

GO:0000932

Protein lin-28 homolog A

17617744

LIN28A

GO:0005634

Protein lin-28 homolog A

17617744

LIN28A

GO:0005730

Protein lin-28 homolog A

0000052

LIN28A

GO:0005737

Protein lin-28 homolog A

18604195

LIN28A

GO:0005737

Protein lin-28 homolog A

20014101

LIN28A

GO:0005829

Protein lin-28 homolog A

0000052

LIN28A

GO:0010494

Protein lin-28 homolog A

17617744

LIN28A

GO:0005844

Protein lin-28 homolog A

21247876

LIN28A

GO:1990904

Protein lin-28 homolog A

21247876


Top

RNA A-to-I events for LIN28A

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: ENSG00000131914.9

check button RNA A-to-I editing events in Cancer.
CAediting_28878(26428615, +), CAediting_28879(26428620, +), CAediting_28880(26428640, +), CAediting_28881(26428641, +), CAediting_28882(26428645, +), CAediting_28883(26428718, +), CAediting_28884(26428785, +), CAediting_28885(26428800, +), CAediting_28886(26428812, +), CAediting_28887(26428818, +), CAediting_28888(26428821, +), CAediting_28889(26428911, +), CAediting_28890(26428912, +), CAediting_28891(26428928, +), CAediting_28892(26428950, +), CAediting_28893(26428964, +), CAediting_28894(26428965, +), CAediting_28895(26428966, +), CAediting_28896(26428978, +), CAediting_28897(26428989, +), CAediting_28898(26429000, +), CAediting_28899(26429005, +), CAediting_28900(26429011, +), CAediting_28901(26429012, +), CAediting_28902(26429015, +), CAediting_28903(26429045, +), CAediting_28904(26429072, +), CAediting_28905(26429078, +), CAediting_28906(26429094, +), CAediting_28907(26429149, +),

Top

RNA editing positional annotations for LIN28A 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_28878chr1_26428615_+UTR3
CAediting_28879chr1_26428620_+UTR3
CAediting_28880chr1_26428640_+UTR3
CAediting_28881chr1_26428641_+UTR3
CAediting_28882chr1_26428645_+UTR3
CAediting_28883chr1_26428718_+UTR3
CAediting_28884chr1_26428785_+UTR3
CAediting_28885chr1_26428800_+UTR3
CAediting_28886chr1_26428812_+UTR3
CAediting_28887chr1_26428818_+UTR3
CAediting_28888chr1_26428821_+UTR3
CAediting_28889chr1_26428911_+UTR3
CAediting_28890chr1_26428912_+UTR3
CAediting_28891chr1_26428928_+UTR3
CAediting_28892chr1_26428950_+UTR3
CAediting_28893chr1_26428964_+UTR3
CAediting_28894chr1_26428965_+UTR3
CAediting_28895chr1_26428966_+UTR3
CAediting_28896chr1_26428978_+UTR3
CAediting_28897chr1_26428989_+UTR3
CAediting_28898chr1_26429000_+UTR3
CAediting_28899chr1_26429005_+UTR3
CAediting_28900chr1_26429011_+UTR3
CAediting_28901chr1_26429012_+UTR3
CAediting_28902chr1_26429015_+UTR3
CAediting_28903chr1_26429045_+UTR3
CAediting_28904chr1_26429072_+UTR3
CAediting_28905chr1_26429078_+UTR3
CAediting_28906chr1_26429094_+splicing
CAediting_28907chr1_26429149_+UTR3

check button Repat-regional RNA editing(s).
CAeditome IDPositionRepeat familyRepeat sub familyRepeat name
CAediting_28878chr1_26428615_+SINEAluAluSx1
CAediting_28879chr1_26428620_+SINEAluAluSx1
CAediting_28880chr1_26428640_+SINEAluAluSx1
CAediting_28881chr1_26428641_+SINEAluAluSx1
CAediting_28882chr1_26428645_+SINEAluAluSx1
CAediting_28883chr1_26428718_+SINEAluAluSx1
CAediting_28884chr1_26428785_+SINEAluAluSx1
CAediting_28885chr1_26428800_+SINEAluAluSx1
CAediting_28886chr1_26428812_+SINEAluAluSx1
CAediting_28887chr1_26428818_+SINEAluAluSx1
CAediting_28888chr1_26428821_+SINEAluAluSx1
CAediting_28889chr1_26428911_+SINEAluAluSc
CAediting_28890chr1_26428912_+SINEAluAluSc
CAediting_28891chr1_26428928_+SINEAluAluSc
CAediting_28892chr1_26428950_+SINEAluAluSc
CAediting_28893chr1_26428964_+SINEAluAluSc
CAediting_28894chr1_26428965_+SINEAluAluSc
CAediting_28895chr1_26428966_+SINEAluAluSc
CAediting_28896chr1_26428978_+SINEAluAluSc
CAediting_28897chr1_26428989_+SINEAluAluSc
CAediting_28898chr1_26429000_+SINEAluAluSc
CAediting_28899chr1_26429005_+SINEAluAluSc
CAediting_28900chr1_26429011_+SINEAluAluSc
CAediting_28901chr1_26429012_+SINEAluAluSc
CAediting_28902chr1_26429015_+SINEAluAluSc
CAediting_28903chr1_26429045_+SINEAluAluSc
CAediting_28904chr1_26429072_+SINEAluAluSc
CAediting_28905chr1_26429078_+SINEAluAluSc
CAediting_28906chr1_26429094_+SINEAluAluSc
CAediting_28907chr1_26429149_+SINEAluAluSc

Top

RNA A-to-I editing events in the alternative splicing sites for LIN28A

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
IRCAediting_28905chr1_26429078_+26429075:264290973SS0+17iGGAATCGCTTGAACCCGAGAGGC-14.45GGAGTCGCTTGAACCCGAGAGGC-14.75
IRCAediting_28906chr1_26429094_+26429075:264290973SS0+1iGGAATCGCTTGAACCCGAGAGGC-14.45GGAATCGCTTGAACCCGAGGGGC-5.7

check button Differential percent of spliced in (PSI) between RNA A-to-I edited and non-edited samples for ENSG00000131914.9.LIN28A.
boxplot

check button Correlation between RNA A-to-I editing and PSI for ENSG00000131914.9.LIN28A.

Top

Differntial gene expression between RNA A-to-I edited versus non-edited samples for LIN28A

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.
TGCT.CAediting_28886.ENSG00000131914.LIN28A.png
Soverview
TGCT.CAediting_28887.ENSG00000131914.LIN28A.png
Soverview
TGCT.CAediting_28893.ENSG00000131914.LIN28A.png
Soverview
TGCT.CAediting_28894.ENSG00000131914.LIN28A.png
Soverview
TGCT.CAediting_28903.ENSG00000131914.LIN28A.png
Soverview

Top

Protein coding region RNA A-to-I editings for LIN28A

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


Top

The effects of the RNA editing to the miRNA binding sites for LIN28A

**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_28907chr1_26429149_+ENSG00000131914.9ENST00000254231hsa-miR-874-3p26429145264291528mer-1a2642913126429152148.00-20.60

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_28907chr1_26429149_+ENSG00000131914.9ENST00000254231hsa-miR-368626429142264291487mer-m82642912826429149140-8.32
CAediting_28907chr1_26429149_+ENSG00000131914.9ENST00000254231hsa-miR-569126429145264291528mer-1a2642913126429152143-17.38
CAediting_28907chr1_26429149_+ENSG00000131914.9ENST00000254231hsa-miR-6805-3p26429145264291528mer-1a2642913026429152145-17.19

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_+ENSG00000131914.9ENST00000254231hsa-miR-605-3p26428366264283727mer-m82642835026428373148-18.91
CAediting_980496chr14_31014685_-ENSG00000131914.9ENST00000254231hsa-miR-624-3p26427737264277437mer-1a2642772226427743141-19.46
CAediting_1229414chr17_67471546_+ENSG00000131914.9ENST00000254231hsa-miR-548aa26428131264281377mer-m82642811226428138169-19.44
CAediting_1229415chr17_67471547_+ENSG00000131914.9ENST00000254231hsa-miR-548aa26427387264273937mer-m82642737126427394154-11.9
CAediting_524911chr7_5495852_-ENSG00000131914.9ENST00000254231hsa-miR-589-3p26426644264266507mer-m82642662726426651147-18.59

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_573000chr7_92204081_-ENSG00000131914.9ENST00000254231hsa-miR-1285-5p26427937264279437mer-m82642792426427944145-16.3
CAediting_573001chr7_92204086_-ENSG00000131914.9ENST00000254231hsa-miR-1285-5p26427937264279437mer-m82642792426427944145-16.3
CAediting_1306323chr19_13836462_-ENSG00000131914.9ENST00000254231hsa-miR-27a-3p26427935264279406mer2642792126427941140-16.38
CAediting_1368054chr19_46709310_-ENSG00000131914.9ENST00000254231hsa-miR-320e26426739264267457mer-m82642672926426746141-14.1
CAediting_688081chr9_63819627_+ENSG00000131914.9ENST00000254231hsa-miR-4477b26427790264277967mer-m82642777426427797144-9.82
CAediting_688081chr9_63819627_+ENSG00000131914.9ENST00000254231hsa-miR-4477b26427167264271737mer-m82642715326427174142-7.8
CAediting_1054808chr15_66496985_-ENSG00000131914.9ENST00000254231hsa-miR-451226427215264272217mer-m82642720126427222143-12.76
CAediting_1524209chrX_134546392_-ENSG00000131914.9ENST00000254231hsa-miR-503-5p26427016264270216mer2642699826427022140-26.75
CAediting_748296chr10_51299626_+ENSG00000131914.9ENST00000254231hsa-miR-605-3p26427482264274887mer-m82642746926427489145-13.12
CAediting_468389chr6_31355314_-ENSG00000131914.9ENST00000254231hsa-miR-6891-5p26429216264292238mer-1a2642920526429223140-16.61

check button Differentially expressed gene-miRNA network
boxplot

Top

The effects of the RNA editing to the stability of the RNA structures for LIN28A

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.
ENST00000254231.4protein_codingSoverviewSoverview
ENST00000326279.9protein_codingSoverviewSoverview

check button RNA A-to-I editing in RNA structures for Minimum free energy (MFE).
CAeditom_IDENSTEditing_PositionMFE_withoneAIMFE_withoutAIMFE_withmultipleAI
CAediting_28907ENST00000254231.4chr1_26429149_+-1162.50-1162.50-1162.50
CAediting_28878ENST00000326279.9chr1_26428615_+-1589.40-1589.80-1592.40
CAediting_28879ENST00000326279.9chr1_26428620_+-1589.00-1589.80-1592.40
CAediting_28880ENST00000326279.9chr1_26428640_+-1589.50-1589.80-1592.40
CAediting_28881ENST00000326279.9chr1_26428641_+-1589.50-1589.80-1592.40
CAediting_28882ENST00000326279.9chr1_26428645_+-1589.20-1589.80-1592.40
CAediting_28883ENST00000326279.9chr1_26428718_+-1589.50-1589.80-1592.40
CAediting_28884ENST00000326279.9chr1_26428785_+-1595.20-1589.80-1592.40
CAediting_28885ENST00000326279.9chr1_26428800_+-1589.50-1589.80-1592.40
CAediting_28886ENST00000326279.9chr1_26428812_+-1589.80-1589.80-1592.40
CAediting_28887ENST00000326279.9chr1_26428818_+-1594.00-1589.80-1592.40
CAediting_28888ENST00000326279.9chr1_26428821_+-1588.90-1589.80-1592.40
CAediting_28889ENST00000326279.9chr1_26428911_+-1589.90-1589.80-1592.40
CAediting_28890ENST00000326279.9chr1_26428912_+-1589.80-1589.80-1592.40
CAediting_28891ENST00000326279.9chr1_26428928_+-1589.70-1589.80-1592.40
CAediting_28892ENST00000326279.9chr1_26428950_+-1589.80-1589.80-1592.40
CAediting_28893ENST00000326279.9chr1_26428964_+-1590.70-1589.80-1592.40
CAediting_28894ENST00000326279.9chr1_26428965_+-1595.00-1589.80-1592.40
CAediting_28895ENST00000326279.9chr1_26428966_+-1590.10-1589.80-1592.40
CAediting_28896ENST00000326279.9chr1_26428978_+-1589.50-1589.80-1592.40
CAediting_28897ENST00000326279.9chr1_26428989_+-1589.80-1589.80-1592.40
CAediting_28898ENST00000326279.9chr1_26429000_+-1589.80-1589.80-1592.40
CAediting_28899ENST00000326279.9chr1_26429005_+-1589.90-1589.80-1592.40
CAediting_28900ENST00000326279.9chr1_26429011_+-1589.90-1589.80-1592.40
CAediting_28901ENST00000326279.9chr1_26429012_+-1589.90-1589.80-1592.40
CAediting_28902ENST00000326279.9chr1_26429015_+-1590.20-1589.80-1592.40
CAediting_28903ENST00000326279.9chr1_26429045_+-1588.80-1589.80-1592.40
CAediting_28904ENST00000326279.9chr1_26429072_+-1589.10-1589.80-1592.40
CAediting_28905ENST00000326279.9chr1_26429078_+-1589.80-1589.80-1592.40
CAediting_28906ENST00000326279.9chr1_26429094_+-1588.90-1589.80-1592.40
CAediting_28907ENST00000326279.9chr1_26429149_+-1589.80-1589.80-1592.40

Top

Relation with ADAR for LIN28A

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.)
TGCTCAediting_28878chr1_26428615_+1.11587198905008e-080.53097848482046....
TGCTCAediting_28879chr1_26428620_+6.54209109152039e-090.476834900320474....
TGCTCAediting_28880chr1_26428640_+9.04042791929014e-050.336547040119571....
TGCTCAediting_28881chr1_26428641_+4.62368450254528e-060.381399485145983....
TGCTCAediting_28882chr1_26428645_+0.01935621177422550.21064342667123....
TGCTCAediting_28883chr1_26428718_+2.33121754565203e-140.6606691827726....
TGCTCAediting_28884chr1_26428785_+8.93287930324141e-060.463633044238556....
TGCTCAediting_28885chr1_26428800_+3.18585877172669e-100.575065227947468....
TGCTCAediting_28886chr1_26428812_+2.80410451553565e-060.551511920618118....
TGCTCAediting_28887chr1_26428818_+3.64781575722451e-080.584616059909602....
TGCTCAediting_28893chr1_26428964_+5.48565518506475e-060.510216789035833....
TGCTCAediting_28894chr1_26428965_+3.77330526390326e-050.505635668870597....
TGCTCAediting_28900chr1_26429011_+0.0001127144910410110.514393963437128....
TGCTCAediting_28903chr1_26429045_+0.0003939573302887260.446428607153418....

Top

Relation with cancer stages for LIN28A

check button Correlation between Cancer stages and RNA editing frequency
CancerStage_typeCAeditomIDpositionP-valCoeff.
TGCTclinical_stageCAediting_28883chr1_26428718_+0.018013410000302-0.317921467216725
TGCTpathologic_stageCAediting_28883chr1_26428718_+0.00765433548967299-0.352803880936388

Top

Relation with survival for LIN28A

check button Correlation between RNA editing and survival
CancerCAeditomIDpositionKMpvalueCoxpvalueCoxHR

Top

RelatedDrugs for LIN28A

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

Top

RelatedDiseases for LIN28A

check button Diseases associated with this gene.
(DisGeNet 7.0)
GeneDisease IDDisease name# pubmedsSource
LIN28AC0006826Malignant Neoplasms1CTD_human
LIN28AC0007621Neoplastic Cell Transformation1CTD_human
LIN28AC0027626Neoplasm Invasiveness1CTD_human
LIN28AC0027651Neoplasms1CTD_human
LIN28AC0086692Benign Neoplasm1CTD_human