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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 COL25A1 |
 Gene summary |
| Gene information | Gene symbol | COL25A1 | Gene ID | 84570 |
| Gene name | collagen type XXV alpha 1 chain | |
| Synonyms | AMY|CFEOM5|CLAC|CLAC-P|CLACP | |
| Cytomap | 4q25 | |
| Type of gene | protein-coding | |
| Description | collagen alpha-1(XXV) chainalzheimer disease amyloid-associated proteincollagen-like Alzheimer amyloid plaque componentcollagenous Alzheimer amyloid plaque component | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 19548013(COL25A1 triggers and promotes Alzheimer's disease-like pathology in vivo) |
| 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 COL25A1 |
| 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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ENSG00000188517
| 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 |
| 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 COL25A1 |
| 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_156052 | chr4 | 108832380:108832433:108834355:108834390:108838098:108838178 | 108834355:108834390 |
| exon_skip_183682 | chr4 | 108824174:108824227:108825196:108825222:108827135:108827188 | 108825196:108825222 |
| exon_skip_188053 | chr4 | 108859656:108859733:108860927:108860971:108862501:108862545 | 108860927:108860971 |
| exon_skip_196166 | chr4 | 108889701:108889733:108896667:108896711:108899154:108899180 | 108896667:108896711 |
| exon_skip_204308 | chr4 | 108859656:108859733:108860927:108860971:108863319:108863387 | 108860927:108860971 |
| exon_skip_220774 | chr4 | 108860927:108860971:108862501:108862545:108863319:108863387 | 108862501:108862545 |
| exon_skip_266838 | chr4 | 108834355:108834390:108838098:108838178:108841695:108841721 | 108838098:108838178 |
| exon_skip_274735 | chr4 | 108832380:108832433:108834355:108834390:108841695:108841721 | 108834355:108834390 |
| exon_skip_289494 | chr4 | 108852236:108852280:108852902:108852925:108859656:108859733 | 108852902:108852925 |
| exon_skip_293106 | chr4 | 108823876:108824227:108825196:108825222:108827135:108827188 | 108825196:108825222 |
| exon_skip_293735 | chr4 | 108918172:108918216:108920578:108920604:108937808:108937843 | 108920578:108920604 |
| exon_skip_46014 | chr4 | 108824174:108824227:108827135:108827188:108832380:108832433 | 108827135:108827188 |
| exon_skip_94431 | chr4 | 108869088:108869150:108884178:108884222:108889221:108889256 | 108884178:108884222 |
| 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 COL25A1 |
| 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 |
| ENST00000399132 | 108825196 | 108825222 | In-frame |
| ENST00000399132 | 108852902 | 108852925 | In-frame |
| ENST00000399132 | 108860927 | 108860971 | In-frame |
| ENST00000399132 | 108862501 | 108862545 | In-frame |
| ENST00000399132 | 108884178 | 108884222 | In-frame |
| ENST00000399132 | 108896667 | 108896711 | In-frame |
| ENST00000399132 | 108920578 | 108920604 | In-frame |
| 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 |
| ENST00000399132 | 108825196 | 108825222 | In-frame |
| ENST00000399132 | 108852902 | 108852925 | In-frame |
| 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 |
| ENST00000399132 | 108825196 | 108825222 | In-frame |
| ENST00000399132 | 108852902 | 108852925 | In-frame |
| ENST00000399132 | 108862501 | 108862545 | In-frame |
| ENST00000399132 | 108884178 | 108884222 | In-frame |
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Infer the effects of exon skipping event on protein functional features for COL25A1 |
p-ENSG00000188517_img4.png |
| 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 |
| ENST00000399132 | 2741 | 654 | 108896667 | 108896711 | 1393 | 1436 | 287 | 301 |
| ENST00000399132 | 2741 | 654 | 108884178 | 108884222 | 1507 | 1550 | 325 | 339 |
| ENST00000399132 | 2741 | 654 | 108862501 | 108862545 | 1684 | 1727 | 384 | 398 |
| ENST00000399132 | 2741 | 654 | 108860927 | 108860971 | 1729 | 1772 | 399 | 413 |
| 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 |
| ENST00000399132 | 2741 | 654 | 108884178 | 108884222 | 1507 | 1550 | 325 | 339 |
| ENST00000399132 | 2741 | 654 | 108862501 | 108862545 | 1684 | 1727 | 384 | 398 |
| 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 |
| Q9BXS0 | 287 | 301 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 287 | 301 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 287 | 301 | 249 | 308 | Domain | Note=Collagen-like 3;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 287 | 301 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 325 | 339 | 326 | 340 | Alternative sequence | ID=VSP_052198;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14656069;Dbxref=PMID:14656069 |
| Q9BXS0 | 325 | 339 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 325 | 339 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 325 | 339 | 311 | 370 | Domain | Note=Collagen-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 325 | 339 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 384 | 398 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 384 | 398 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 384 | 398 | 372 | 425 | Domain | Note=Collagen-like 5;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 384 | 398 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 399 | 413 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 399 | 413 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 399 | 413 | 372 | 425 | Domain | Note=Collagen-like 5;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 399 | 413 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9BXS0 | 325 | 339 | 326 | 340 | Alternative sequence | ID=VSP_052198;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14656069;Dbxref=PMID:14656069 |
| Q9BXS0 | 325 | 339 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 325 | 339 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 325 | 339 | 311 | 370 | Domain | Note=Collagen-like 4;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 325 | 339 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 384 | 398 | 1 | 654 | Chain | ID=PRO_0000259611;Note=Collagen alpha-1(XXV) chain |
| Q9BXS0 | 384 | 398 | 113 | 654 | Chain | ID=PRO_0000259612;Note=Collagen-like Alzheimer amyloid plaque component;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:11927537,ECO:0000269|PubMed:15522881;Dbxref=PMID:11927537,PMID:15522881 |
| Q9BXS0 | 384 | 398 | 372 | 425 | Domain | Note=Collagen-like 5;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9BXS0 | 384 | 398 | 55 | 654 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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3'-UTR located exon skipping events that lost miRNA binding sites in COL25A1 |
| 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 COL25A1 |
| - 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 COL25A1 |
| 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 COL25A1 |
| 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 COL25A1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for COL25A1 |
| 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 COL25A1 |
| 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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