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Open reading frame (ORF) annotation in the exon skipping event | |
3'-UTR located exon skipping events lost miRNA binding sites | |
Splicing Quantitative Trait Loci (sQTLs) in the skipped exons | |
Gene summary for LINC00639 |
Gene summary |
Gene information | Gene symbol | LINC00639 | Gene ID | 283547 |
Gene name | long intergenic non-protein coding RNA 639 | |
Synonyms | - | |
Cytomap | 14q21.1 | |
Type of gene | ncRNA | |
Description | - | |
Modification date | 20200313 | |
UniProtAcc | ||
Context | - 31280115(Identification of age- and gender-associated long noncoding RNAs in the human brain with Alzheimer's disease) |
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 LINC00639 |
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. |
Differentially expressed gene analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
PG | UP | ENST00000668589.1 | LINC00639-211:lncRNA:LINC00639 | 2.171063e+00 | 1.226240e+00 | 4.836002e-03 | 4.462015e-02 |
CB | DOWN | ENST00000668589.1 | LINC00639-211:lncRNA:LINC00639 | 9.653240e-01 | -1.628582e+00 | 4.896077e-04 | 2.829709e-03 |
CB | DOWN | ENST00000670844.1 | LINC00639-214:lncRNA:LINC00639 | 2.536250e+00 | -1.230127e+00 | 3.608246e-03 | 1.502005e-02 |
CB | DOWN | ENST00000669541.1 | LINC00639-212:lncRNA:LINC00639 | 5.306757e-01 | -1.202303e+00 | 8.500024e-03 | 3.042645e-02 |
TC | DOWN | ENST00000669541.1 | LINC00639-212:lncRNA:LINC00639 | 2.802457e+00 | -1.011210e+00 | 2.622338e-04 | 3.461938e-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 LINC00639 |
Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
All exon skipping events in AD cohorts. |
Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
exon_skip_106613 | chr14 | 38838894:38839204:38890741:38890798:38941520:38941695 | 38890741:38890798 |
exon_skip_117102 | chr14 | 38760182:38760248:38761110:38761253:38762102:38762174 | 38761110:38761253 |
exon_skip_134255 | chr14 | 38748243:38749654:38762924:38763045:38835231:38835398 | 38762924:38763045 |
exon_skip_134494 | chr14 | 38838889:38839204:38941520:38941695:38948178:38948200 | 38941520:38941695 |
exon_skip_148426 | chr14 | 38838889:38839204:38941354:38941373:38941520:38941695 | 38941354:38941373 |
exon_skip_164906 | chr14 | 38835542:38839204:38941354:38941373:38941520:38941695 | 38941354:38941373 |
exon_skip_171251 | chr14 | 38838889:38839204:38890741:38890798:38941520:38941695 | 38890741:38890798 |
exon_skip_174669 | chr14 | 38749354:38749654:38760182:38760248:38762102:38762174 | 38760182:38760248 |
exon_skip_184951 | chr14 | 38941520:38941695:38946692:38946882:38948178:38948200 | 38946692:38946882 |
exon_skip_198843 | chr14 | 38890741:38890798:38941520:38941695:38946692:38946882 | 38941520:38941695 |
exon_skip_20012 | chr14 | 38838894:38839204:38941354:38941373:38941520:38941695 | 38941354:38941373 |
exon_skip_206539 | chr14 | 38890741:38890798:38941520:38941695:38948178:38948200 | 38941520:38941695 |
exon_skip_217873 | chr14 | 38749592:38749654:38760182:38760248:38762102:38762174 | 38760182:38760248 |
exon_skip_219439 | chr14 | 38838894:38839204:38941520:38941695:38948178:38948200 | 38941520:38941695 |
exon_skip_227788 | chr14 | 38748243:38749654:38762102:38762174:38762924:38763045 | 38762102:38762174 |
exon_skip_249442 | chr14 | 38838889:38839204:38890741:38890798:38916782:38916882 | 38890741:38890798 |
exon_skip_259671 | chr14 | 38749592:38749654:38762924:38763045:38835231:38835398 | 38762924:38763045 |
exon_skip_48416 | chr14 | 38890741:38890798:38916782:38916882:38948178:38948200 | 38916782:38916882 |
exon_skip_66240 | chr14 | 38749592:38749654:38762102:38762174:38762924:38763045 | 38762102:38762174 |
exon_skip_75979 | chr14 | 38838894:38839204:38890741:38890798:38948178:38948200 | 38890741:38890798 |
exon_skip_9805 | chr14 | 38838889:38839204:38890741:38890798:38948178:38948200 | 38890741:38890798 |
Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for LINC00639 |
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 LINC00639 |
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 LINC00639 |
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 LINC00639 |
- 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 LINC00639 |
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 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LINC00639 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for LINC00639 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for LINC00639 |
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 LINC00639 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |