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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 PSD2 |
 Gene summary |
| Gene information | Gene symbol | PSD2 | Gene ID | 84249 |
| Gene name | pleckstrin and Sec7 domain containing 2 | |
| Synonyms | EFA6C | |
| Cytomap | 5q31.2 | |
| Type of gene | protein-coding | |
| Description | PH and SEC7 domain-containing protein 2exchange factor for ADP-ribosylation factor guanine nucleotide factor 6 Cexchange factor for ARF6 Cpleckstrin homology and SEC7 domain-containing protein 2 | |
| Modification date | 20200313 | |
| UniProtAcc | Q9BQI7, | |
| 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 PSD2 |
| 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_1173962(139800483, +), ADediting_1173963(139800484, +), ADediting_1173964(139800497, +), ADediting_1173965(139800555, +), ADediting_1173966(139800557, +), ADediting_1173967(139800943, +), ADediting_1173968(139807987, +), ADediting_1173969(139813570, +), ADediting_1173970(139818283, +), ADediting_1173971(139818319, +), ADediting_1173972(139818349, +), ADediting_1173973(139818363, +), ADediting_1173974(139818387, +), ADediting_1173975(139818399, +), ADediting_1173976(139818407, +), ADediting_1173977(139818425, +), ADediting_1173978(139818461, +), ADediting_1173979(139818466, +), ADediting_1173980(139818485, +), ADediting_1173981(139818490, +), ADediting_1173982(139821012, +), ADediting_1173983(139821013, +), ADediting_1173984(139821033, +), ADediting_1173985(139821072, +), ADediting_1579424(139818380, +), |
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RNA editing positional annotations for PSD2 using Annovar |
| Protein coding RNA editing(s). |
| ADeditome ID | Position | Variant type | ENST | NTchange | AAchange | SIFT_score | Polyphen2_HVAR_score | PROVEAN_pred |
| ADediting_1173969 | chr5_139813570_+ | synonymous SNV | ENST00000274710.4 | c.A633G | p.A211A | . | . | . |
| Gene structure information of RNA editing(s). |
| ADeditome ID | Position | Variant type |
| ADediting_1173962 | chr5_139800483_+ | intronic |
| ADediting_1173963 | chr5_139800484_+ | intronic |
| ADediting_1173964 | chr5_139800497_+ | intronic |
| ADediting_1173965 | chr5_139800555_+ | intronic |
| ADediting_1173966 | chr5_139800557_+ | intronic |
| ADediting_1173967 | chr5_139800943_+ | intronic |
| ADediting_1173968 | chr5_139807987_+ | intronic |
| ADediting_1173969 | chr5_139813570_+ | exonic |
| ADediting_1173970 | chr5_139818283_+ | intronic |
| ADediting_1173971 | chr5_139818319_+ | intronic |
| ADediting_1173972 | chr5_139818349_+ | intronic |
| ADediting_1173973 | chr5_139818363_+ | intronic |
| ADediting_1173974 | chr5_139818387_+ | intronic |
| ADediting_1173975 | chr5_139818399_+ | intronic |
| ADediting_1173976 | chr5_139818407_+ | intronic |
| ADediting_1173977 | chr5_139818425_+ | intronic |
| ADediting_1173978 | chr5_139818461_+ | intronic |
| ADediting_1173979 | chr5_139818466_+ | intronic |
| ADediting_1173980 | chr5_139818485_+ | intronic |
| ADediting_1173981 | chr5_139818490_+ | intronic |
| ADediting_1173982 | chr5_139821012_+ | intronic |
| ADediting_1173983 | chr5_139821013_+ | intronic |
| ADediting_1173984 | chr5_139821033_+ | intronic |
| ADediting_1173985 | chr5_139821072_+ | intronic |
| ADediting_1579424 | chr5_139818380_+ | intronic |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_1173962 | chr5_139800483_+ | SINE | Alu | Name=AluSz |
| ADediting_1173963 | chr5_139800484_+ | SINE | Alu | Name=AluSz |
| ADediting_1173964 | chr5_139800497_+ | SINE | Alu | Name=AluSz |
| ADediting_1173965 | chr5_139800555_+ | SINE | Alu | Name=AluSz |
| ADediting_1173966 | chr5_139800557_+ | SINE | Alu | Name=AluSz |
| ADediting_1173967 | chr5_139800943_+ | SINE | Alu | Name=AluSx1 |
| ADediting_1173970 | chr5_139818283_+ | SINE | Alu | Name=AluJb |
| ADediting_1173971 | chr5_139818319_+ | SINE | Alu | Name=AluJb |
| ADediting_1173972 | chr5_139818349_+ | SINE | Alu | Name=AluJb |
| ADediting_1173973 | chr5_139818363_+ | SINE | Alu | Name=AluJb |
| ADediting_1173974 | chr5_139818387_+ | SINE | Alu | Name=AluJb |
| ADediting_1173975 | chr5_139818399_+ | SINE | Alu | Name=AluJb |
| ADediting_1173976 | chr5_139818407_+ | SINE | Alu | Name=AluJb |
| ADediting_1173977 | chr5_139818425_+ | SINE | Alu | Name=AluJb |
| ADediting_1173978 | chr5_139818461_+ | SINE | Alu | Name=AluJb |
| ADediting_1173979 | chr5_139818466_+ | SINE | Alu | Name=AluJb |
| ADediting_1173980 | chr5_139818485_+ | SINE | Alu | Name=AluJb |
| ADediting_1173981 | chr5_139818490_+ | SINE | Alu | Name=AluJb |
| ADediting_1173982 | chr5_139821012_+ | SINE | Alu | Name=AluSx |
| ADediting_1173983 | chr5_139821013_+ | SINE | Alu | Name=AluSx |
| ADediting_1173984 | chr5_139821033_+ | SINE | Alu | Name=AluSx |
| ADediting_1173985 | chr5_139821072_+ | SINE | Alu | Name=AluSx |
| ADediting_1579424 | chr5_139818380_+ | SINE | Alu | Name=AluJb |
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RNA A-to-I editing events in the alternative splicing sites for PSD2 |
| 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 |
| 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 PSD2 |
| 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. |
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| - 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 PSD2 |
| - 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 PSD2 |
| 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 |
| 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 |
| 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_1097295 | chr3_85385762_+ | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-5688 | chr5 | 139843398 | 139843404 | 7mer-m8 | 139843384 | 139843405 | 140 | -9.81 |
| ADediting_1556067 | chr19_40282625_- | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-641 | chr5 | 139842507 | 139842513 | 7mer-m8 | 139842491 | 139842514 | 140 | -18.84 |
| ADediting_286380 | chr11_79422188_- | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-5579-3p | chr5 | 139843922 | 139843928 | 7mer-m8 | 139843908 | 139843929 | 140 | -11.55 |
| 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_1471003 | chr9_63819626_+ | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-4477b | chr5 | 139844328 | 139844334 | 7mer-m8 | 139844314 | 139844335 | 140 | -11.98 |
| ADediting_1471004 | chr9_63819627_+ | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-4477b | chr5 | 139844328 | 139844334 | 7mer-m8 | 139844314 | 139844335 | 140 | -11.98 |
| ADediting_1535951 | chr14_100874558_+ | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-337-3p | chr5 | 139843524 | 139843531 | 8mer-1a | 139843509 | 139843531 | 143 | -10.45 |
| ADediting_291761 | chr11_93733708_- | ENSG00000146005.4 | ENST00000274710.4 | PSD2-201 | hsa-miR-1304-3p | chr5 | 139842523 | 139842529 | 7mer-m8 | 139842511 | 139842530 | 145 | -19.14 |
| Differentially expressed gene-miRNA network |
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The effects of the RNA editing to the stability of the RNA structures for PSD2 |
| - 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. |
| ENST00000274710.4 | protein_coding |  |  |
| 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 |
| ADediting_1173969 | ENST00000274710.4 | chr5_139813570_+ | 851 | -1746.00 | -1739.80 | -1746.00 |
| RNA A-to-I editing in lncRNA. |
| ADeditom_ID | ENST | Editing_Information | Editing_Position | MFE_withoneAI | MFE_withoutAI | MFE_withmultipleAI |
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Relation with ADAR for PSD2 |
| 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.) |
| CER | ADediting_1173970 | chr5_139818283_+ | 6.90904076367052e-08 | 0.423061104939543 | 2.62713798226854e-07 | 0.405551968312865 | 0.00677470177665758 | 0.220206009404697 |
| CER | ADediting_1173973 | chr5_139818363_+ | 6.56802809878751e-06 | 0.358692436929413 | 2.21574756061282e-06 | 0.375338187918079 | 0.0185801529009721 | 0.192005419931252 |
| CER | ADediting_1173975 | chr5_139818399_+ | 0.000106570938026966 | 0.31111612922704 | 2.50012108110085e-05 | 0.336842303476237 | 0.0140667711026162 | 0.200136559226302 |
| CER | ADediting_1173976 | chr5_139818407_+ | 2.1519343516139e-05 | 0.339376599433369 | 2.17674056665026e-05 | 0.339183696095293 | 0.0212437990952186 | 0.187982561500956 |
| CER | ADediting_1173977 | chr5_139818425_+ | 0.000118075598123701 | 0.309205847592267 | 1.19639114599445e-06 | 0.384384086418123 | 0.00911286252397549 | 0.212268788851748 |
| CER | ADediting_1173980 | chr5_139818485_+ | 8.12524599006531e-11 | 0.498933703052165 | 5.68553114273859e-10 | 0.478886476535685 | 0.000582113818712409 | 0.277639709679166 |
| TCX | ADediting_1173980 | chr5_139818485_+ | 0.0122722955230292 | 0.20401979815744 | 0.888020557696412 | 0.0115936351307813 | 0.000123899390795536 | 0.308304194769402 |
| CER | ADediting_1173981 | chr5_139818490_+ | 1.07316455213577e-09 | 0.472049539097683 | 1.30167689263466e-10 | 0.494195446195026 | 8.37599623820612e-05 | 0.315553949765123 |
| CER | ADediting_1173983 | chr5_139821013_+ | 1.88445917395904e-06 | 0.377741720225378 | 1.01044939635041e-06 | 0.386816890838082 | 0.000336574546229601 | 0.288895213545185 |
| CER | ADediting_1173984 | chr5_139821033_+ | 2.47786935012794e-06 | 0.373667515013834 | 3.14916855943606e-06 | 0.370053632679099 | 0.057176525650472 | 0.15564854668662 |
| 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 | 5.1303119756701e-16 | 0.438737511367345 | 7.43230036261865e-08 | 0.299741899784532 | 2.20901666944042e-13 | 0.400663352008595 |
| AC | 1.42094589791833e-35 | 0.682140040322003 | 4.49866555222835e-23 | 0.571451721761699 | 1.15944648316798e-16 | 0.492243155315951 |
| PCC | 4.13029596226474e-09 | 0.409287086760819 | 6.29781580642026e-08 | 0.379231015348237 | 3.66988896832962e-05 | 0.293948562900577 |
| CER | 3.43692291278764e-24 | 0.708755205729301 | 1.91039756263305e-10 | 0.490283705373355 | 0.000135216445840024 | 0.306659785668242 |
| TCX | 3.47165696699374e-05 | 0.331216084104107 | 0.100151013059245 | 0.134756260198186 | 0.0557228228439892 | 0.156556897891776 |
| FP | 0.00473343198299624 | 0.210815989461731 | 0.166331102352336 | 0.104193361074592 | 8.49421990230533e-15 | 0.538911036526455 |
| IFG | 0.000534681870117927 | 0.64243772365989 | 0.000133904181558694 | 0.690334656593205 | 0.0227545050422728 | 0.453621300524801 |
| PG | 4.6338954225044e-05 | 0.294026684980218 | 0.500473393584424 | 0.0497059204149495 | 6.42832272196204e-06 | 0.324034831122258 |
| STG | 0.0245071034905268 | 0.245308445320509 | 0.305779398769174 | 0.113075916686316 | 7.89749891717483e-08 | 0.545805510340222 |
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Relation with AD stages for PSD2 |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| CER | ADediting_1173977 | chr5_139818425_+ | 6.85192270127207e-05 | 0.373493629878981 |
| CER | ADediting_1173980 | chr5_139818485_+ | 0.00127970397511286 | 0.305984524552342 |
| CER | ADediting_1173981 | chr5_139818490_+ | 8.19833981406508e-07 | 0.453642613021546 |
| CER | ADediting_1173983 | chr5_139821013_+ | 0.0010048969257157 | 0.312182456408935 |
| TCX | ADediting_1173970 | chr5_139818283_+ | 0.000415766312678156 | 0.336772336980378 |
| TCX | ADediting_1173977 | chr5_139818425_+ | 0.00160611678189659 | 0.302784337809913 |
| TCX | ADediting_1173980 | chr5_139818485_+ | 9.2587538803236e-06 | 0.415903335314294 |
| TCX | ADediting_1173981 | chr5_139818490_+ | 4.33131342513539e-05 | 0.386219015476703 |
| TCX | ADediting_1173983 | chr5_139821013_+ | 3.77749912487263e-06 | 0.431939889492626 |
| TCX | ADediting_1173984 | chr5_139821033_+ | 0.000674781022045645 | 0.325040994094547 |
| TCX | ADediting_1173985 | chr5_139821072_+ | 0.00104659568519435 | 0.313989054566669 |
| IFG | ADediting_1173981 | chr5_139818490_+ | 0.0354713369979928 | 0.422303326441651 |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
| CER | 2.84284775908979e-05 | 0.391152209231005 |
| TCX | 1.49196442081422e-07 | 0.483782676780359 |
| IFG | 0.00516068056871542 | 0.541701077037008 |
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RelatedDrugs for PSD2 |
| 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 PSD2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PSD2 | C0032927 | Precancerous Conditions | 1 | CTD_human |
| PSD2 | C0282313 | Condition, Preneoplastic | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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