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| Differntial gene expression between RNA A-to-I edited versus non-edited samples |
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| The effects of the RNA editing to the stability of the RNA structures |
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Gene summary for ATP10D |
 Gene summary |
| Gene information | Gene symbol | ATP10D | Gene ID | 57205 |
| Gene name | ATPase phospholipid transporting 10D (putative) | |
| Synonyms | ATPVD | |
| Cytomap | 4p12 | |
| Type of gene | protein-coding | |
| Description | probable phospholipid-transporting ATPase VDATPase, class V, type 10DP4-ATPase flippase complex alpha subunit ATP10Dtype IV aminophospholipid transporting ATPase | |
| Modification date | 20200313 | |
| UniProtAcc | Q9P241, | |
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
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RNA A-to-I events for ATP10D |
| RNA 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). |
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| RNA editing frequencies across three data sets. |
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| The number of RNA A-to-I editing events in different types of transcripts (# event, percentage). |
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| RNA A-to-I editing events in AD. |
| ADediting_1138065(47487108, +), ADediting_1138066(47487109, +), ADediting_1138067(47487114, +), ADediting_1138068(47487135, +), ADediting_1138069(47487141, +), ADediting_1138070(47502284, +), ADediting_1138071(47502294, +), ADediting_1138072(47502324, +), ADediting_1138079(47522670, +), ADediting_1138080(47535031, +), ADediting_1138081(47535124, +), ADediting_1138082(47582888, +), ADediting_1138083(47582961, +), ADediting_1138084(47584603, +), ADediting_1577774(47487138, +), ADediting_1577775(47582934, +), ADediting_1652219(47487078, +), |
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RNA editing positional annotations for ATP10D using Annovar |
| Protein coding RNA editing(s). |
| ADeditome ID | Position | Variant type | ENST | NTchange | AAchange | SIFT_score | Polyphen2_HVAR_score | PROVEAN_pred |
| Gene structure information of RNA editing(s). |
| ADeditome ID | Position | Variant type |
| ADediting_1138065 | chr4_47487108_+ | intronic |
| ADediting_1138066 | chr4_47487109_+ | intronic |
| ADediting_1138067 | chr4_47487114_+ | intronic |
| ADediting_1138068 | chr4_47487135_+ | intronic |
| ADediting_1138069 | chr4_47487141_+ | intronic |
| ADediting_1138070 | chr4_47502284_+ | intronic |
| ADediting_1138071 | chr4_47502294_+ | intronic |
| ADediting_1138072 | chr4_47502324_+ | intronic |
| ADediting_1138079 | chr4_47522670_+ | intronic |
| ADediting_1138080 | chr4_47535031_+ | intronic |
| ADediting_1138081 | chr4_47535124_+ | intronic |
| ADediting_1138082 | chr4_47582888_+ | intronic |
| ADediting_1138083 | chr4_47582961_+ | intronic |
| ADediting_1138084 | chr4_47584603_+ | intronic |
| ADediting_1577774 | chr4_47487138_+ | intronic |
| ADediting_1577775 | chr4_47582934_+ | intronic |
| ADediting_1652219 | chr4_47487078_+ | intronic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_1138065 | chr4_47487108_+ | SINE | Alu | Name=AluSp |
| ADediting_1138066 | chr4_47487109_+ | SINE | Alu | Name=AluSp |
| ADediting_1138067 | chr4_47487114_+ | SINE | Alu | Name=AluSp |
| ADediting_1138068 | chr4_47487135_+ | SINE | Alu | Name=AluSp |
| ADediting_1138069 | chr4_47487141_+ | SINE | Alu | Name=AluSp |
| ADediting_1138070 | chr4_47502284_+ | SINE | Alu | Name=AluYj4 |
| ADediting_1138071 | chr4_47502294_+ | SINE | Alu | Name=AluYj4 |
| ADediting_1138072 | chr4_47502324_+ | SINE | Alu | Name=AluYj4 |
| ADediting_1138079 | chr4_47522670_+ | SINE | Alu | Name=AluSx |
| ADediting_1138080 | chr4_47535031_+ | LINE | L1 | Name=L1PA15 |
| ADediting_1138081 | chr4_47535124_+ | LINE | L1 | Name=L1PA15 |
| ADediting_1138082 | chr4_47582888_+ | SINE | Alu | Name=AluJr |
| ADediting_1138083 | chr4_47582961_+ | SINE | Alu | Name=AluJr |
| ADediting_1138084 | chr4_47584603_+ | SINE | Alu | Name=AluY |
| ADediting_1577774 | chr4_47487138_+ | SINE | Alu | Name=AluSp |
| ADediting_1577775 | chr4_47582934_+ | SINE | Alu | Name=AluJr |
| ADediting_1652219 | chr4_47487078_+ | SINE | Alu | Name=AluSp |
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RNA A-to-I editing events in the alternative splicing sites for ATP10D |
| RNA A-to-I editing(s) in the alternative splicing sites. |
| AStype | ADeditomID | Editing position | AS position | AS direction | Exonic location | Wildtype sequence | Wildtype splicing strength | RNA edited sequence | RNA edited splicing strength |
| ES | ADediting_1138083 | chr4_47582961_+ | 47582959:47582967 | 5ss | 1e | ATAGTGAGA | 1.69 | ATGGTGAGA | 7.23 |
| 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 ATP10D |
| 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. |
| Distribution of the averaged gene isoform expression in AD and control with or without RNA A-to-I editing event. |
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| - 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. |
| - 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 ID | Chr | Positoing | Skipped exon | ENSG | ENSTs |
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Protein coding region RNA A-to-I editings for ATP10D |
| - 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 ATP10D |
| RNA A-to-I editings in the ROSMAP, MSBB, and Mayo data sets based on Ensembl gene isoform structure. |
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| RNA A-to-I editing in the 3'-UTR regions of mRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in the 3'-UTR regions of mRNA lost miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in lncRNA gained miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_1138083 | chr4_47582961_+ | ENSG00000145246.14 | ENST00000505277.1 | ATP10D-204 | hsa-miR-224-5p | chr4 | 47582960 | 47587023 | 7mer-m8 | 47582945 | 47587024 | 151 | -15.34 |
| ADediting_1138083 | chr4_47582961_+ | ENSG00000145246.14 | ENST00000512393.1 | ATP10D-207 | hsa-miR-4716-5p | chr4 | 47582956 | 47582962 | 7mer-m8 | 47582942 | 47582963 | 148 | -14.09 |
| ADediting_1138083 | chr4_47582961_+ | ENSG00000145246.14 | ENST00000512393.1 | ATP10D-207 | hsa-miR-6511a-3p | chr4 | 47582960 | 47582967 | 8mer-1a | 47582946 | 47582967 | 145 | -18.84 |
| ADediting_1138083 | chr4_47582961_+ | ENSG00000145246.14 | ENST00000512393.1 | ATP10D-207 | hsa-miR-6511b-3p | chr4 | 47582960 | 47582967 | 8mer-1a | 47582945 | 47582967 | 140 | -17.97 |
| RNA A-to-I editing in lncRNA lost miRNA binding sites. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_1138082 | chr4_47582888_+ | ENSG00000145246.14 | ENST00000505277.1 | ATP10D-204 | hsa-miR-3665 | chr4 | 47582887 | 47582894 | 8mer-1a | 47582877 | 47582894 | 151 | -18.14 |
| ADediting_1138082 | chr4_47582888_+ | ENSG00000145246.14 | ENST00000505277.1 | ATP10D-204 | hsa-miR-3934-5p | chr4 | 47582886 | 47582892 | 7mer-m8 | 47582871 | 47582893 | 155 | -22.77 |
| ADediting_1138082 | chr4_47582888_+ | ENSG00000145246.14 | ENST00000512393.1 | ATP10D-207 | hsa-miR-3665 | chr4 | 47582887 | 47582894 | 8mer-1a | 47582877 | 47582894 | 151 | -18.14 |
| ADediting_1138082 | chr4_47582888_+ | ENSG00000145246.14 | ENST00000512393.1 | ATP10D-207 | hsa-miR-3934-5p | chr4 | 47582886 | 47582892 | 7mer-m8 | 47582871 | 47582893 | 155 | -22.77 |
| RNA A-to-I editing in miRNAs gained binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs lost binding to lncRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| RNA A-to-I editing in miRNAs gained binding to the 3'-UTR region of mRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_1337757 | chr7_5495852_- | ENSG00000145246.14 | ENST00000504445.1 | ATP10D-203 | hsa-miR-589-3p | chr4 | 47547280 | 47547286 | 7mer-m8 | 47547263 | 47547287 | 149 | -17.14 |
| ADediting_1535954 | chr14_101045974_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-381-3p | chr4 | 47592137 | 47592143 | 7mer-1a | 47592123 | 47592143 | 157 | -24.69 |
| ADediting_1535954 | chr14_101045974_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-381-3p | chr4 | 47592218 | 47592224 | 7mer-m8 | 47592206 | 47592225 | 148 | -15.77 |
| ADediting_1535954 | chr14_101045974_+ | ENSG00000145246.14 | ENST00000504445.1 | ATP10D-203 | hsa-miR-381-3p | chr4 | 47547542 | 47547549 | 8mer-1a | 47547528 | 47547549 | 140 | -11.9 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-4775 | chr4 | 47592425 | 47592431 | 7mer-m8 | 47592411 | 47592432 | 140 | -6.75 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-4775 | chr4 | 47592539 | 47592545 | 7mer-m8 | 47592525 | 47592546 | 145 | -7.82 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-4775 | chr4 | 47593007 | 47593013 | 7mer-m8 | 47592993 | 47593014 | 153 | -5.99 |
| RNA A-to-I editing in miRNAs lost binding to the 3'-UTR mRNA. |
| ADeditom_ID | Position | ENSG | ENST | Transcript name | miRNA ID | Chromosome | Targt | Targetscan end | Targetscan score | Miranda start | Miranda end | Miranda score | Miranda energy |
| ADediting_1643790 | chr3_121049689_+ | ENSG00000145246.14 | ENST00000273859.8 | ATP10D-201 | hsa-miR-5682 | chr4 | 47592528 | 47592534 | 7mer-m8 | 47592514 | 47592535 | 152 | -18.85 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000145246.14 | ENST00000504445.1 | ATP10D-203 | hsa-miR-4775 | chr4 | 47547510 | 47547516 | 7mer-m8 | 47547496 | 47547517 | 150 | -13.21 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000145246.14 | ENST00000504445.1 | ATP10D-203 | hsa-miR-4775 | chr4 | 47547535 | 47547541 | 7mer-m8 | 47547522 | 47547542 | 142 | -5.95 |
| Differentially expressed gene-miRNA network |
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The effects of the RNA editing to the stability of the RNA structures for ATP10D |
| - RNA A-to-I editing in mRNA. * Click on the image to enlarge it in a new window. |
| ENST | ENST type | RNA structure without RNA A-to-I editing. | RNA structure with RNA A-to-I editing. |
| ENST00000512393.1 | lncRNA |  |  |
| ENST00000505277.1 | lncRNA |  |  |
| RNA A-to-I editing in miRNA. |
| ADeditom_ID | ENST | mir_ID | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in mRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| RNA A-to-I editing in lncRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
| ADediting_1138082 | ENST00000512393.1 | chr4_47582888_+ | 205 | -184.70 | -183.80 | -185.60 |
| ADediting_1577775 | ENST00000512393.1 | chr4_47582934_+ | 251 | -183.80 | -183.80 | -185.60 |
| ADediting_1138083 | ENST00000512393.1 | chr4_47582961_+ | 278 | -184.60 | -183.80 | -185.60 |
| ADediting_1138082 | ENST00000505277.1 | chr4_47582888_+ | 54 | -171.50 | -170.30 | -171.50 |
| ADediting_1577775 | ENST00000505277.1 | chr4_47582934_+ | 100 | -170.20 | -170.30 | -171.50 |
| ADediting_1138083 | ENST00000505277.1 | chr4_47582961_+ | 127 | -170.40 | -170.30 | -171.50 |
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Relation with ADAR for ATP10D |
| Correlation between ADAR gene expression and RNA editing frequency |
| Tissue | ADeditomID | position | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| DLPFC | ADediting_1138065 | chr4_47487108_+ | 0.0767091139919033 | 0.10068651286246 | 0.277490082394879 | -0.0618700642624842 | 3.23362357549962e-28 | 0.570979772370346 |
| CER | ADediting_1138065 | chr4_47487108_+ | 0.0049962715419172 | 0.22809157164169 | 1.19098668008185e-05 | 0.349164140810582 | 0.948044481761892 | 0.00536535541313487 |
| DLPFC | ADediting_1138066 | chr4_47487109_+ | 0.164259723662606 | 0.0791928695923514 | 0.121637439385349 | -0.0881017948782164 | 1.24772468245851e-25 | 0.547385883980038 |
| CER | ADediting_1138066 | chr4_47487109_+ | 0.0304347622990239 | 0.176805735490304 | 2.82591650013096e-05 | 0.334755805108223 | 0.844882040991297 | 0.0161086929520699 |
| Correlation between ADAR gene expression and this gene's expression |
| Tissue | ADAR1 (p-val) | ADAR1 (coeff.) | ADAR2 (p-val) | ADAR2 (coeff.) | ADAR3 (p-val) | ADAR3 (coeff.) |
| DLPFC | 1.11156318525869e-22 | 0.517983299294023 | 2.90216837245413e-08 | 0.30858635777785 | 1.90862457598676e-07 | 0.290563547903178 |
| AC | 2.77687419883636e-44 | 0.738152712332561 | 5.79468883234289e-25 | 0.591276635937252 | 8.32940186123414e-26 | 0.599692920403512 |
| PCC | 4.04390475089425e-08 | 0.384327365487941 | 1.54607341332746e-05 | 0.307153383649812 | 1.03637097444411e-12 | 0.485919124637956 |
| CER | 3.15706516216583e-14 | 0.568694145044389 | 9.47121925740508e-06 | 0.352868638983712 | 5.10053986901621e-15 | 0.582808451713993 |
| TCX | 1.24885620439215e-08 | 0.444126022595801 | 0.935311938286976 | 0.00668280175501067 | 6.00362785196708e-10 | 0.478306449463318 |
| FP | 9.76148123172204e-16 | 0.554474147513587 | 2.81228147370463e-12 | 0.492749614245218 | 3.02687594516349e-08 | 0.400536752716457 |
| IFG | 0.0054969121124126 | 0.53838304241187 | 0.000394803852886669 | 0.653668326699389 | 0.0163347941742776 | 0.475329336028869 |
| PG | 1.5282910489803e-32 | 0.732418493030787 | 3.24649248443421e-17 | 0.567035259962062 | 0.060404806770677 | 0.137959873766362 |
| STG | 0.000145652165501725 | 0.40277235014749 | 0.0134132064264777 | 0.268825391479122 | 2.22760385802923e-05 | 0.444960952334116 |
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Relation with AD stages for ATP10D |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
| CER | 0.000178232606480947 | 0.353074796694629 |
| TCX | 6.02338183687226e-10 | 0.556192771343005 |
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RelatedDrugs for ATP10D |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for ATP10D |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ATP10D | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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