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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 SVIP |
 Gene summary |
| Gene information | Gene symbol | SVIP | Gene ID | 258010 |
| Gene name | small VCP interacting protein | |
| Synonyms | - | |
| Cytomap | 11p14.3 | |
| Type of gene | protein-coding | |
| Description | small VCP/p97-interacting protein | |
| Modification date | 20200313 | |
| UniProtAcc | Q8NHG7, | |
| 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 SVIP |
| 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_247125(22816307, -), ADediting_247126(22816416, -), ADediting_247127(22816487, -), ADediting_247128(22816488, -), ADediting_247129(22816504, -), ADediting_247130(22819515, -), ADediting_247131(22819624, -), ADediting_247132(22819660, -), ADediting_247133(22819689, -), ADediting_247134(22819690, -), ADediting_247135(22819696, -), ADediting_247136(22819720, -), ADediting_1526609(22819623, -), |
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RNA editing positional annotations for SVIP 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_247125 | chr11_22816307_- | intergenic |
| ADediting_247126 | chr11_22816416_- | intergenic |
| ADediting_247127 | chr11_22816487_- | intergenic |
| ADediting_247128 | chr11_22816488_- | intergenic |
| ADediting_247129 | chr11_22816504_- | intergenic |
| ADediting_247130 | chr11_22819515_- | UTR3 |
| ADediting_247131 | chr11_22819624_- | UTR3 |
| ADediting_247132 | chr11_22819660_- | UTR3 |
| ADediting_247133 | chr11_22819689_- | UTR3 |
| ADediting_247134 | chr11_22819690_- | UTR3 |
| ADediting_247135 | chr11_22819696_- | UTR3 |
| ADediting_247136 | chr11_22819720_- | UTR3 |
| ADediting_1526609 | chr11_22819623_- | UTR3 |
| Repat-regional RNA editing(s). |
| ADeditome ID | Position | Repeat family | Repeat sub family | Repeat name |
| ADediting_247125 | chr11_22816307_- | SINE | Alu | Name=AluSz |
| ADediting_247126 | chr11_22816416_- | SINE | Alu | Name=AluSz |
| ADediting_247127 | chr11_22816487_- | SINE | Alu | Name=AluSz |
| ADediting_247128 | chr11_22816488_- | SINE | Alu | Name=AluSz |
| ADediting_247129 | chr11_22816504_- | SINE | Alu | Name=AluSz |
| ADediting_247130 | chr11_22819515_- | SINE | Alu | Name=AluSp |
| ADediting_247131 | chr11_22819624_- | SINE | Alu | Name=AluSp |
| ADediting_247132 | chr11_22819660_- | SINE | Alu | Name=AluSp |
| ADediting_247133 | chr11_22819689_- | SINE | Alu | Name=AluSp |
| ADediting_247134 | chr11_22819690_- | SINE | Alu | Name=AluSp |
| ADediting_247135 | chr11_22819696_- | SINE | Alu | Name=AluSp |
| ADediting_247136 | chr11_22819720_- | SINE | Alu | Name=AluSp |
| ADediting_1526609 | chr11_22819623_- | SINE | Alu | Name=AluSp |
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RNA A-to-I editing events in the alternative splicing sites for SVIP |
| 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 SVIP |
| 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 SVIP |
| - 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 SVIP |
| 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 |
| ADediting_1526609 | chr11_22819623_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-1323 | chr11 | 22819618 | 22819624 | 7mer-m8 | 22819617 | 22819639 | 148 | -13.65 |
| ADediting_1526609 | chr11_22819623_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-548o-3p | chr11 | 22819618 | 22819624 | 7mer-m8 | 22819617 | 22819636 | 148 | -9.29 |
| ADediting_1526609 | chr11_22819623_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-7844-5p | chr11 | 22819620 | 22819626 | 7mer-m8 | 22819619 | 22819640 | 164 | -23.61 |
| ADediting_247132 | chr11_22819660_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4691-3p | chr11 | 22819656 | 22819662 | 7mer-m8 | 22819655 | 22819682 | 150 | -26.36 |
| ADediting_247133 | chr11_22819689_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3622a-3p | chr11 | 22819685 | 22819692 | 8mer-1a | 22819685 | 22819707 | 149 | -18.21 |
| ADediting_247133 | chr11_22819689_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3622b-3p | chr11 | 22819685 | 22819692 | 8mer-1a | 22819685 | 22819705 | 147 | -18.77 |
| ADediting_247135 | chr11_22819696_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-1247-3p | chr11 | 22819694 | 22819700 | 7mer-m8 | 22819693 | 22819715 | 150 | -22.21 |
| ADediting_247136 | chr11_22819720_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4537 | chr11 | 22819715 | 22819722 | 8mer-1a | 22819715 | 22819738 | 154 | -23.74 |
| 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 |
| ADediting_247132 | chr11_22819660_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-5690 | chr11 | 22819656 | 22819662 | 7mer-m8 | 22819655 | 22819675 | 150 | -16.63 |
| ADediting_247133 | chr11_22819689_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3614-5p | chr11 | 22819685 | 22819691 | 7mer-1a | 22819685 | 22819708 | 155 | -25.83 |
| ADediting_247134 | chr11_22819690_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3614-5p | chr11 | 22819685 | 22819691 | 7mer-1a | 22819685 | 22819708 | 155 | -25.83 |
| ADediting_247135 | chr11_22819696_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3689a-3p | chr11 | 22819696 | 22819702 | 7mer-m8 | 22819695 | 22819715 | 150 | -24.43 |
| ADediting_247135 | chr11_22819696_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-490-3p | chr11 | 22819692 | 22819698 | 7mer-m8 | 22819691 | 22819713 | 146 | -17.12 |
| ADediting_247135 | chr11_22819696_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-6779-5p | chr11 | 22819696 | 22819702 | 7mer-m8 | 22819695 | 22819713 | 152 | -23.44 |
| ADediting_247135 | chr11_22819696_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-6780a-5p | chr11 | 22819696 | 22819702 | 7mer-m8 | 22819695 | 22819719 | 147 | -23.46 |
| ADediting_247136 | chr11_22819720_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-3160-3p | chr11 | 22819715 | 22819722 | 8mer-1a | 22819715 | 22819736 | 152 | -17.18 |
| 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_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22822636 | 22822642 | 7mer-m8 | 22822635 | 22822656 | 150 | -8.44 |
| 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_1097295 | chr3_85385762_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-5688 | chr11 | 22820714 | 22820720 | 7mer-m8 | 22820713 | 22820731 | 152 | -11.28 |
| ADediting_1556067 | chr19_40282625_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-641 | chr11 | 22819435 | 22819441 | 7mer-m8 | 22819434 | 22819459 | 153 | -11.15 |
| ADediting_1556067 | chr19_40282625_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-641 | chr11 | 22821210 | 22821217 | 8mer-1a | 22821210 | 22821233 | 140 | -15.7 |
| ADediting_1631458 | chr19_40282624_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-641 | chr11 | 22819435 | 22819441 | 7mer-m8 | 22819434 | 22819459 | 153 | -11.15 |
| ADediting_1631458 | chr19_40282624_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-641 | chr11 | 22821210 | 22821217 | 8mer-1a | 22821210 | 22821233 | 140 | -15.7 |
| ADediting_286380 | chr11_79422188_- | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-5579-3p | chr11 | 22820084 | 22820091 | 8mer-1a | 22820084 | 22820103 | 148 | -12.83 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22820603 | 22820609 | 7mer-m8 | 22820602 | 22820623 | 145 | -4.67 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22820937 | 22820943 | 7mer-m8 | 22820936 | 22820956 | 150 | -5.87 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22821800 | 22821806 | 7mer-m8 | 22821799 | 22821822 | 151 | -6.83 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22821889 | 22821895 | 7mer-m8 | 22821888 | 22821908 | 151 | -6.2 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22822465 | 22822471 | 7mer-m8 | 22822464 | 22822484 | 150 | -8.4 |
| ADediting_843620 | chr2_207754818_+ | ENSG00000198168.9 | ENST00000354193.5 | SVIP-201 | hsa-miR-4775 | chr11 | 22822520 | 22822527 | 8mer-1a | 22822520 | 22822541 | 143 | -6.37 |
| Differentially expressed gene-miRNA network |
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The effects of the RNA editing to the stability of the RNA structures for SVIP |
| - 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. |
| ENST00000354193.5 | 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_247130 | ENST00000354193.5 | chr11_22819515_- | 3891 | -1031.40 | -1032.40 | -1036.30 |
| ADediting_1526609 | ENST00000354193.5 | chr11_22819623_- | 3783 | -1031.60 | -1032.40 | -1036.30 |
| ADediting_247131 | ENST00000354193.5 | chr11_22819624_- | 3782 | -1031.60 | -1032.40 | -1036.30 |
| ADediting_247132 | ENST00000354193.5 | chr11_22819660_- | 3746 | -1036.30 | -1032.40 | -1036.30 |
| ADediting_247133 | ENST00000354193.5 | chr11_22819689_- | 3717 | -1033.40 | -1032.40 | -1036.30 |
| ADediting_247134 | ENST00000354193.5 | chr11_22819690_- | 3716 | -1036.00 | -1032.40 | -1036.30 |
| ADediting_247135 | ENST00000354193.5 | chr11_22819696_- | 3710 | -1033.50 | -1032.40 | -1036.30 |
| ADediting_247136 | ENST00000354193.5 | chr11_22819720_- | 3686 | -1032.50 | -1032.40 | -1036.30 |
| 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 SVIP |
| 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_247125 | chr11_22816307_- | 1.8896320251468e-05 | 0.341555428350084 | 8.83913389587258e-13 | 0.541025306731607 | 0.00743159259445034 | 0.217757023715432 |
| TCX | ADediting_247125 | chr11_22816307_- | 0.0511547566503312 | 0.159544648087046 | 0.096771017609682 | -0.136103519324547 | 4.07660524719532e-10 | 0.482407464133864 |
| CER | ADediting_247127 | chr11_22816487_- | 0.00212308275126653 | 0.24898455324972 | 1.41094033054318e-05 | 0.346393544915183 | 0.515733819273934 | 0.0534763840410708 |
| CER | ADediting_247129 | chr11_22816504_- | 0.00481643492946464 | 0.229023743192871 | 4.85999391396759e-05 | 0.325334632885997 | 0.251672213458078 | 0.0941744123381878 |
| CER | ADediting_247130 | chr11_22819515_- | 8.30501261920323e-05 | 0.31570949353408 | 1.8588518186458e-09 | 0.466013543282634 | 0.0253771283829659 | 0.182527700178819 |
| CER | ADediting_247131 | chr11_22819624_- | 0.0142935536874434 | 0.199677108361678 | 4.87268163267218e-05 | 0.325288575899758 | 0.0199715370753539 | 0.189846089042126 |
| CER | ADediting_247132 | chr11_22819660_- | 0.000213755656361532 | 0.297881769214052 | 1.8861210793938e-08 | 0.439178399601462 | 0.00444242318125839 | 0.231066734346155 |
| CER | ADediting_247135 | chr11_22819696_- | 0.0115278028282087 | 0.205778761227743 | 2.97201279677839e-06 | 0.370930412688516 | 0.0255272877576251 | 0.182344317453359 |
| CER | ADediting_247136 | chr11_22819720_- | 0.000513791662441724 | 0.280246409069483 | 1.15767101449502e-08 | 0.445027325476675 | 0.0036809590776238 | 0.23575394844142 |
| 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 | 6.66342697981261e-28 | 0.568213914184775 | 6.06488086670043e-28 | 0.568575433132625 | 0.0418429828194035 | 0.115663741011467 |
| AC | 1.31778711591593e-92 | 0.902311859712457 | 4.37427671036635e-67 | 0.837664007994088 | 8.42193991064812e-12 | 0.414526118729911 |
| PCC | 2.98623586940768e-43 | 0.796991242802896 | 7.81808507171525e-49 | 0.825511783019534 | 0.0560452372500245 | 0.138494357541332 |
| CER | 1.13419015174136e-23 | 0.703059818455001 | 1.31273487097353e-11 | 0.516605870784451 | 0.00079014556919799 | 0.27115053071199 |
| TCX | 1.58057975670901e-15 | 0.591533510817212 | 0.16720824519039 | 0.113361392578587 | 6.09360445715831e-16 | 0.598443267203011 |
| FP | 3.10725265031219e-11 | 0.471402894991216 | 1.36648117027194e-19 | 0.610905453230906 | 0.910547070747059 | 0.00848047361449467 |
| IFG | 0.00296620351422286 | 0.569458861079615 | 0.0326597952063442 | 0.428339453603437 | 0.922051713362797 | 0.020623763939649 |
| PG | 1.29786060261527e-45 | 0.815717424755965 | 8.06464225232992e-27 | 0.682245824938311 | 0.970030461629004 | -0.00277346362932378 |
| STG | 1.03682975752997e-13 | 0.701773392708306 | 3.19599433213294e-13 | 0.691760395843283 | 0.926457273442504 | 0.0102240214264495 |
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Relation with AD stages for SVIP |
| Correlation between AD stages and RNA editing frequency |
| Tissue | ADeditomID | position | P-val | Coeff. |
| CER | ADediting_247125 | chr11_22816307_- | 0.000246375000093237 | 0.345835272312357 |
| CER | ADediting_247136 | chr11_22819720_- | 0.000816524011824369 | 0.317400764171535 |
| Correlation between AD stages and this gene's expression |
| Tissue | P-val | Coeff. |
| CER | 0.000414853077507254 | 0.33380365630445 |
| TCX | 0.000974873390525138 | 0.315805188477204 |
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RelatedDrugs for SVIP |
| 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 SVIP |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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