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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 PTN |
 Gene summary |
| Gene information | Gene symbol | PTN | Gene ID | 5764 |
| Gene name | pleiotrophin | |
| Synonyms | HARP|HB-GAM|HBBM|HBGF-8|HBGF8|HBNF|HBNF-1|NEGF1|OSF-1 | |
| Cytomap | 7q33 | |
| Type of gene | protein-coding | |
| Description | pleiotrophinheparin affin regulatory proteinheparin-binding brain mitogenheparin-binding growth factor 8heparin-binding growth-associated moleculeheparin-binding neurite outgrowth promoting factorheparin-binding neurite outgrowth-promoting factor 1 | |
| Modification date | 20200313 | |
| UniProtAcc | ||
| Context | - 26046300(Chronic Cocaine Use Causes Changes in the Striatal Proteome Depending on the Endogenous Expression of Pleiotrophin) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PTN | GO:0007229 | integrin-mediated signaling pathway | 19141530 |
| PTN | GO:0008284 | positive regulation of cell proliferation | 1733956 |
| PTN | GO:0043113 | receptor clustering | 27445335 |
| PTN | GO:0043932 | ossification involved in bone remodeling | 19442624 |
| PTN | GO:0048714 | positive regulation of oligodendrocyte differentiation | 27445335 |
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Gene structures and expression levels for PTN |
| 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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ENSG00000105894
| 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 |
| CB | UP | ENST00000263036.9 | OPTN-201:protein_coding:OPTN | 2.054713e+02 | 8.669637e-01 | 1.359228e-14 | 4.483964e-12 |
| CB | UP | ENST00000482140.5 | OPTN-210:nonsense_mediated_decay:OPTN | 1.084331e+01 | 9.506610e-01 | 1.264476e-07 | 2.592935e-06 |
| CB | DOWN | ENST00000600551.1 | KPTN-208:lncRNA:KPTN | 6.237849e+01 | -8.861893e-01 | 2.841875e-07 | 5.142548e-06 |
| CB | UP | ENST00000565325.5 | NPTN-209:protein_coding:NPTN | 6.593351e+01 | 1.109568e+00 | 1.656982e-06 | 2.304897e-05 |
| CB | UP | ENST00000378764.6 | OPTN-206:protein_coding:OPTN | 2.484351e+02 | 1.050183e+00 | 1.417989e-03 | 6.928552e-03 |
| CB | DOWN | ENST00000469025.1 | OPTN-209:lncRNA:OPTN | 5.857417e+00 | -8.697325e-01 | 1.820188e-03 | 8.526139e-03 |
| CB | UP | ENST00000378748.7 | OPTN-203:protein_coding:OPTN | 2.045269e+01 | 1.192742e+00 | 8.103665e-03 | 2.925606e-02 |
| 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 PTN |
| 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_184125 | chr7 | 137227364:137228075:137251230:137251391:137253464:137253637 | 137251230:137251391 |
| exon_skip_264198 | chr7 | 137251230:137251391:137253464:137253637:137254859:137254974 | 137253464:137253637 |
| 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 PTN |
| 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 |
| ENST00000348225 | 137251230 | 137251391 | 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 |
| 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 |
| ENST00000348225 | 137253464 | 137253637 | In-frame |
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Infer the effects of exon skipping event on protein functional features for PTN |
p-ENSG00000105894_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 |
| ENST00000348225 | 1631 | 168 | 137251230 | 137251391 | 718 | 878 | 96 | 150 |
| 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 |
| ENST00000348225 | 1631 | 168 | 137253464 | 137253637 | 544 | 716 | 38 | 96 |
| 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 |
| P21246 | 96 | 150 | 97 | 104 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 96 | 150 | 115 | 124 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 96 | 150 | 133 | 142 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 96 | 150 | 33 | 168 | Chain | ID=PRO_0000024659;Note=Pleiotrophin |
| P21246 | 96 | 150 | 99 | 131 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:2N6F,ECO:0000269|PubMed:26896299,ECO:0000269|PubMed:8484780;Dbxref=PMID:26896299,PMID:8484780 |
| P21246 | 96 | 150 | 109 | 141 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:2N6F,ECO:0000269|PubMed:26896299,ECO:0000269|PubMed:8484780;Dbxref=PMID:26896299,PMID:8484780 |
| P21246 | 96 | 150 | 92 | 99 | Region | Note=Chondroitin sulfate binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26896299;Dbxref=PMID:26896299 |
| P21246 | 96 | 150 | 123 | 131 | Region | Note=Chondroitin sulfate binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26896299;Dbxref=PMID:26896299 |
| P21246 | 96 | 150 | 147 | 168 | Region | Note=Chondroitin sulfate A binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26896299;Dbxref=PMID:26896299 |
| P21246 | 96 | 150 | 111 | 114 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| 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 |
| P21246 | 38 | 96 | 48 | 52 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 38 | 96 | 60 | 62 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 38 | 96 | 66 | 72 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 38 | 96 | 78 | 84 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2N6F |
| P21246 | 38 | 96 | 33 | 168 | Chain | ID=PRO_0000024659;Note=Pleiotrophin |
| P21246 | 38 | 96 | 47 | 76 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:2N6F,ECO:0000269|PubMed:26896299,ECO:0000269|PubMed:8484780;Dbxref=PMID:26896299,PMID:8484780 |
| P21246 | 38 | 96 | 55 | 85 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:2N6F,ECO:0000269|PubMed:26896299,ECO:0000269|PubMed:8484780;Dbxref=PMID:26896299,PMID:8484780 |
| P21246 | 38 | 96 | 62 | 89 | Disulfide bond | Ontology_term=ECO:0000244,ECO:0000269,ECO:0000269;evidence=ECO:0000244|PDB:2N6F,ECO:0000269|PubMed:26896299,ECO:0000269|PubMed:8484780;Dbxref=PMID:26896299,PMID:8484780 |
| P21246 | 38 | 96 | 92 | 99 | Region | Note=Chondroitin sulfate binding;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:26896299;Dbxref=PMID:26896299 |
| P21246 | 38 | 96 | 42 | 42 | Sequence conflict | Note=V->K;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P21246 | 38 | 96 | 47 | 47 | Sequence conflict | Note=C->D;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P21246 | 38 | 96 | 75 | 75 | Sequence conflict | Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
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3'-UTR located exon skipping events that lost miRNA binding sites in PTN |
| 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 PTN |
| - 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 PTN |
| 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 PTN |
| 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 PTN |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for PTN |
| 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 PTN |
| 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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