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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for LINC00320 |
 Gene summary |
| Gene information | Gene symbol | LINC00320 | Gene ID | 387486 |
| Gene name | long intergenic non-protein coding RNA 320 | |
| Synonyms | C21orf131|NCRNA00320|PRED14 | |
| Cytomap | 21q21.1 | |
| Type of gene | ncRNA | |
| Description | - | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| 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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Gene structures and expression levels for LINC00320 |
| Skipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure. * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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ENSG00000224924
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| PCC | UP | 5.396964e+02 | 8.851381e-01 | 1.895182e-07 | 3.525732e-05 |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| DLPFC | UP | ENST00000663537.1 | LINC00320-244:lncRNA:LINC00320 | 1.034478e+01 | 9.626424e-01 | 1.115026e-03 | 3.611707e-02 |
| DLPFC | UP | ENST00000655551.1 | LINC00320-217:lncRNA:LINC00320 | 6.890350e+00 | 1.797217e+00 | 1.392069e-03 | 4.176714e-02 |
| PCC | UP | ENST00000665470.1 | LINC00320-250:lncRNA:LINC00320 | 5.564051e+01 | 1.428728e+00 | 3.734314e-06 | 6.462746e-04 |
| PCC | UP | ENST00000658406.1 | LINC00320-226:lncRNA:LINC00320 | 3.098521e+01 | 1.109371e+00 | 5.081685e-05 | 3.894200e-03 |
| PCC | UP | ENST00000663537.1 | LINC00320-244:lncRNA:LINC00320 | 6.830741e+00 | 1.713115e+00 | 6.132731e-04 | 1.874560e-02 |
| PCC | UP | ENST00000666665.1 | LINC00320-260:lncRNA:LINC00320 | 8.050382e+00 | 2.095612e+00 | 1.069282e-03 | 2.666105e-02 |
| PCC | UP | ENST00000435279.6 | LINC00320-203:lncRNA:LINC00320 | 3.990302e+01 | 1.004051e+00 | 2.264866e-03 | 4.218844e-02 |
| PG | UP | ENST00000666665.1 | LINC00320-260:lncRNA:LINC00320 | 3.472452e+01 | 1.069587e+00 | 1.924795e-04 | 4.432538e-03 |
| CB | DOWN | ENST00000653294.1 | LINC00320-207:lncRNA:LINC00320 | 8.135777e+01 | -1.111668e+00 | 2.740796e-05 | 2.471900e-04 |
| CB | DOWN | ENST00000656294.1 | LINC00320-222:lncRNA:LINC00320 | 8.087051e+00 | -1.293930e+00 | 2.115878e-03 | 9.656205e-03 |
| CB | DOWN | ENST00000665477.1 | LINC00320-251:lncRNA:LINC00320 | 4.549138e+01 | -9.499889e-01 | 2.442301e-03 | 1.087554e-02 |
| TC | DOWN | ENST00000665477.1 | LINC00320-251:lncRNA:LINC00320 | 1.721848e+02 | -1.168375e+00 | 1.797401e-06 | 6.492735e-05 |
| TC | UP | ENST00000666665.1 | LINC00320-260:lncRNA:LINC00320 | 1.101905e+02 | 1.004640e+00 | 5.784737e-04 | 6.456189e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for LINC00320 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_101069 | chr21 | 20778418:20778547:20778643:20778762:20781349:20781474 | 20778643:20778762 |
| exon_skip_103852 | chr21 | 20781570:20781661:20782250:20782446:20802995:20803094 | 20782250:20782446 |
| exon_skip_104749 | chr21 | 20778643:20778796:20780811:20780907:20781349:20781474 | 20780811:20780907 |
| exon_skip_105073 | chr21 | 20728965:20729000:20743616:20743833:20778418:20778466 | 20743616:20743833 |
| exon_skip_111769 | chr21 | 20778418:20778547:20778643:20778796:20781349:20781474 | 20778643:20778796 |
| exon_skip_119905 | chr21 | 20743801:20743833:20757311:20757417:20778418:20778466 | 20757311:20757417 |
| exon_skip_128598 | chr21 | 20743813:20743833:20757311:20757417:20778184:20778344 | 20757311:20757417 |
| exon_skip_132953 | chr21 | 20757311:20757417:20778184:20778344:20778418:20778466 | 20778184:20778344 |
| exon_skip_143550 | chr21 | 20743813:20743833:20757311:20757417:20778418:20778466 | 20757311:20757417 |
| exon_skip_145485 | chr21 | 20778643:20778762:20780811:20780907:20781349:20781472 | 20780811:20780907 |
| exon_skip_14777 | chr21 | 20782307:20782446:20786036:20786088:20802995:20803080 | 20786036:20786088 |
| exon_skip_149951 | chr21 | 20781570:20781661:20782307:20782446:20802995:20803094 | 20782307:20782446 |
| exon_skip_153477 | chr21 | 20781570:20781661:20782307:20782446:20786036:20786088 | 20782307:20782446 |
| exon_skip_155982 | chr21 | 20778418:20778547:20780811:20780907:20781349:20781472 | 20780811:20780907 |
| exon_skip_168390 | chr21 | 20778497:20778547:20778643:20778762:20781349:20781474 | 20778643:20778762 |
| exon_skip_181772 | chr21 | 20742986:20743833:20778184:20778344:20778418:20778466 | 20778184:20778344 |
| exon_skip_182458 | chr21 | 20778418:20778547:20778643:20778796:20780811:20780907 | 20778643:20778796 |
| exon_skip_184448 | chr21 | 20781570:20781661:20782307:20782446:20802995:20803025 | 20782307:20782446 |
| exon_skip_18505 | chr21 | 20743616:20743833:20778184:20778344:20778418:20778466 | 20778184:20778344 |
| exon_skip_194549 | chr21 | 20781570:20781661:20782250:20782446:20802995:20803025 | 20782250:20782446 |
| exon_skip_213828 | chr21 | 20778497:20778547:20778643:20778796:20781349:20781474 | 20778643:20778796 |
| exon_skip_217403 | chr21 | 20778418:20778547:20781349:20781474:20781570:20781661 | 20781349:20781474 |
| exon_skip_227235 | chr21 | 20757311:20757417:20778418:20778547:20781349:20781474 | 20778418:20778547 |
| exon_skip_230914 | chr21 | 20743801:20743833:20778184:20778344:20778418:20778466 | 20778184:20778344 |
| exon_skip_2418 | chr21 | 20743813:20743833:20757219:20757417:20778418:20778466 | 20757219:20757417 |
| exon_skip_286396 | chr21 | 20782422:20782446:20783272:20783409:20786036:20786088 | 20783272:20783409 |
| exon_skip_292417 | chr21 | 20742921:20743833:20757219:20757417:20778418:20778466 | 20757219:20757417 |
| exon_skip_294919 | chr21 | 20782307:20782446:20786036:20786111:20802995:20803094 | 20786036:20786111 |
| exon_skip_29935 | chr21 | 20782307:20782446:20786036:20786088:20802995:20803025 | 20786036:20786088 |
| exon_skip_37608 | chr21 | 20739398:20739649:20743616:20743833:20778418:20778466 | 20743616:20743833 |
| exon_skip_45011 | chr21 | 20778643:20778762:20780811:20780907:20781349:20781474 | 20780811:20780907 |
| exon_skip_60427 | chr21 | 20743813:20743833:20778184:20778344:20778418:20778466 | 20778184:20778344 |
| exon_skip_72228 | chr21 | 20743616:20743833:20757311:20757417:20778418:20778466 | 20757311:20757417 |
| exon_skip_72440 | chr21 | 20778418:20778547:20780811:20780907:20781349:20781474 | 20780811:20780907 |
| exon_skip_77779 | chr21 | 20743616:20743833:20778418:20778547:20781349:20781474 | 20778418:20778547 |
| exon_skip_84021 | chr21 | 20781570:20781661:20782250:20782446:20786036:20786088 | 20782250:20782446 |
| exon_skip_86787 | chr21 | 20778418:20778547:20778643:20778762:20780811:20780907 | 20778643:20778762 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
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| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
| exon_skip_101069 | ROSMAP_HCC | 2.336364e-01 | 3.516304e-01 | -1.179941e-01 | 2.571068e-09 |
| exon_skip_101069 | Mayo_CB | 2.068293e-01 | 3.393151e-01 | -1.324858e-01 | 5.260273e-08 |
| exon_skip_168390 | Mayo_TC | 2.285366e-01 | 3.415385e-01 | -1.130019e-01 | 5.163831e-07 |
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Open reading frame (ORF) annotation in the exon skipping event for LINC00320 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
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Infer the effects of exon skipping event on protein functional features for LINC00320 |
| Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases. |
| ENST | Length of mRNA | Length of AA seq. | Genomic start | Genomic end | mRNA start | mRNA end | AA start | AA end |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in MSBB. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
| Lost protein functional features of individual exon skipping events in Mayo. |
| UniProt acc. | Start of exon skipping (AA) | End of exon skipping (AA) | Protein feature start (AA) | Protein feature end (AA) | Category of protein feature | Description of feature |
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3'-UTR located exon skipping events that lost miRNA binding sites in LINC00320 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for LINC00320 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - Non-synonymous mutations located in the skipped exons in CCLE. |
| Sample | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
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AD stage-associated exon skippint events for LINC00320 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
| ADstage | MSBB | IFG | exon_skip_111769 | -4.353373e-01 | 2.059076e-02 | chr21 | - | 20778418 | 20778547 | 20778643 | 20778796 | 20781349 | 20781474 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LINC00320 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_72228 | rs7278126 | chr21:20767142 | 8.316128e-05 | 7.824546e-03 |
| HCC | exon_skip_72228 | rs2826510 | chr21:20772860 | 2.108872e-04 | 1.692921e-02 |
| HCC | exon_skip_72228 | rs2826500 | chr21:20761006 | 3.464902e-04 | 2.534197e-02 |
| DLPFC | exon_skip_72228 | rs2826509 | chr21:20772819 | 2.779431e-05 | 2.760312e-03 |
| DLPFC | exon_skip_72228 | rs6517997 | chr21:20778274 | 2.779431e-05 | 2.760312e-03 |
| DLPFC | exon_skip_72228 | rs7277729 | chr21:20781317 | 2.779431e-05 | 2.760312e-03 |
| DLPFC | exon_skip_72228 | rs2826500 | chr21:20761006 | 3.344562e-04 | 2.348565e-02 |
| DLPFC | exon_skip_72228 | rs2826510 | chr21:20772860 | 8.371907e-04 | 4.835645e-02 |
| DLPFC | exon_skip_72228 | rs7278126 | chr21:20767142 | 8.556096e-04 | 4.918224e-02 |
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Correlation with RNA binding proteins (RBPs) for LINC00320 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | ELAVL1 | exon_skip_101069 | -4.077428e-01 | 1.394753e-07 |
| CB | SAMD4A | exon_skip_101069 | -4.975869e-01 | 4.492955e-11 |
| CB | TRA2A | exon_skip_101069 | -4.987556e-01 | 3.982036e-11 |
| CB | NUP42 | exon_skip_101069 | 4.141161e-01 | 8.488428e-08 |
| IFG | RBFOX2 | exon_skip_72228 | -4.874394e-01 | 8.514010e-03 |
| IFG | HNRNPA0 | exon_skip_72228 | -4.281799e-01 | 2.301712e-02 |
| IFG | SAMD4A | exon_skip_101069 | -4.546587e-01 | 1.506839e-02 |
| IFG | IGF2BP3 | exon_skip_101069 | -4.374056e-01 | 1.993011e-02 |
| IFG | RBM47 | exon_skip_101069 | -4.185891e-01 | 2.662950e-02 |
| IFG | EIF4B | exon_skip_101069 | 4.704443e-01 | 1.152372e-02 |
| IFG | PABPN1L | exon_skip_111769 | 4.009210e-01 | 3.448391e-02 |
| TC | RBMS2 | exon_skip_168390 | -4.900344e-01 | 4.805417e-11 |
| TC | SAMD4A | exon_skip_168390 | -5.280573e-01 | 7.190625e-13 |
| TC | NOVA1 | exon_skip_168390 | 4.441432e-01 | 4.029568e-09 |
| TC | RBFOX2 | exon_skip_194549 | -5.938310e-01 | 1.975774e-16 |
| TC | ILF2 | exon_skip_194549 | -4.704656e-01 | 4.448265e-10 |
| TC | HNRNPK | exon_skip_194549 | -4.306359e-01 | 1.625280e-08 |
| TC | KHDRBS2 | exon_skip_194549 | -5.807699e-01 | 1.254523e-15 |
| TC | KHDRBS3 | exon_skip_194549 | -5.752928e-01 | 2.658098e-15 |
| TC | PUM1 | exon_skip_194549 | -5.445752e-01 | 1.399383e-13 |
| TC | NUP42 | exon_skip_194549 | -4.102076e-01 | 8.662052e-08 |
| TC | SRSF9 | exon_skip_194549 | -4.633295e-01 | 8.772927e-10 |
| TC | HNRNPH2 | exon_skip_194549 | -5.592682e-01 | 2.211289e-14 |
| TC | ESRP1 | exon_skip_194549 | -4.100820e-01 | 8.748647e-08 |
| TC | PCBP4 | exon_skip_29935 | 4.276081e-01 | 1.703672e-08 |
| TC | NOVA1 | exon_skip_29935 | 4.620993e-01 | 7.697424e-10 |
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RelatedDrugs for LINC00320 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for LINC00320 |
| 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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