|
||||||
|
 | |
| |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
| |
|
Gene summary for PGLYRP4 |
 Gene summary |
| Gene information | Gene symbol | PGLYRP4 | Gene ID | 57115 |
| Gene name | peptidoglycan recognition protein 4 | |
| Synonyms | PGLYRPIbeta|PGRP-Ibeta|PGRPIB|SBBI67 | |
| Cytomap | 1q21.3 | |
| Type of gene | protein-coding | |
| Description | peptidoglycan recognition protein 4PGRP-I-betapeptidoglycan recognition protein I-betapeptidoglycan recognition protein intermediate beta | |
| Modification date | 20180523 | |
| UniProtAcc | Q96LB8 | |
| Context | PubMed: PGLYRP4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| PGLYRP4 | GO:0016045 | detection of bacterium | 11461926 |
| PGLYRP4 | GO:0031640 | killing of cells of other organism | 16354652 |
| PGLYRP4 | GO:0050830 | defense response to Gram-positive bacterium | 11461926|16354652 |
| PGLYRP4 | GO:0051714 | positive regulation of cytolysis in other organism | 16354652 |
| PGLYRP4 | GO:0061844 | antimicrobial humoral immune response mediated by antimicrobial peptide | 16354652 |
Top |
Exon skipping events across known transcript of Ensembl for PGLYRP4 from UCSC genome browser |
| Skipped exons in TCGA and GTEx 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. |
 |
Top |
Gene isoform structures and expression levels for PGLYRP4 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for PGLYRP4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_30988 | 1 | 153303230:153303421:153309656:153309775:153312856:153313055 | 153309656:153309775 | ENSG00000163218.10 | ENST00000359650.5,ENST00000368739.3 |
| exon_skip_30989 | 1 | 153309656:153309775:153312856:153313055:153314102:153314255 | 153312856:153313055 | ENSG00000163218.10 | ENST00000359650.5,ENST00000368739.3 |
| exon_skip_30997 | 1 | 153315565:153315684:153317644:153317846:153318577:153318667 | 153317644:153317846 | ENSG00000163218.10 | ENST00000368739.3 |
| exon_skip_30998 | 1 | 153315565:153315684:153317644:153317858:153318577:153318667 | 153317644:153317858 | ENSG00000163218.10 | ENST00000359650.5 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for PGLYRP4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_30988 | 1 | 153303230:153303421:153309656:153309775:153312856:153313055 | 153309656:153309775 | ENSG00000163218.10 | ENST00000359650.5,ENST00000368739.3 |
| exon_skip_30989 | 1 | 153309656:153309775:153312856:153313055:153314102:153314255 | 153312856:153313055 | ENSG00000163218.10 | ENST00000359650.5,ENST00000368739.3 |
| exon_skip_30997 | 1 | 153315565:153315684:153317644:153317846:153318577:153318667 | 153317644:153317846 | ENSG00000163218.10 | ENST00000368739.3 |
| exon_skip_30998 | 1 | 153315565:153315684:153317644:153317858:153318577:153318667 | 153317644:153317858 | ENSG00000163218.10 | ENST00000359650.5 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PGLYRP4 |
| Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000359650 | 153309656 | 153309775 | Frame-shift |
| ENST00000359650 | 153312856 | 153313055 | Frame-shift |
| ENST00000359650 | 153317644 | 153317858 | Frame-shift |
| Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000359650 | 153309656 | 153309775 | Frame-shift |
| ENST00000359650 | 153312856 | 153313055 | Frame-shift |
| ENST00000359650 | 153317644 | 153317858 | Frame-shift |
Top |
Infer the effects of exon skipping event on protein functional features for PGLYRP4 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
 |
| Loci of skipped exons in TCGA 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 GTEx 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 TCGA. |
| 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 GTEx. |
| 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 |
Top |
SNVs in the skipped exons for PGLYRP4 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
 |
| - Differential PSIs between mutated versus non-mutated samples. |
PGLYRP4_LUAD_exon_skip_30989_psi_boxplot.png |
| - Non-synonymous mutations located in the skipped exons in TCGA. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_30988 | 153309657 | 153309775 | 153309707 | 153309707 | Frame_Shift_Del | G | - | p.P294fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_30997 | 153317645 | 153317846 | 153317788 | 153317788 | Frame_Shift_Del | A | - | p.I66fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_30998 | 153317645 | 153317858 | 153317788 | 153317788 | Frame_Shift_Del | A | - | p.I66fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_30997 | 153317645 | 153317846 | 153317811 | 153317811 | Frame_Shift_Del | C | - | p.A59fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_30998 | 153317645 | 153317858 | 153317811 | 153317811 | Frame_Shift_Del | C | - | p.A59fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_30997 | 153317645 | 153317846 | 153317811 | 153317811 | Frame_Shift_Del | C | - | p.A59fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_30998 | 153317645 | 153317858 | 153317811 | 153317811 | Frame_Shift_Del | C | - | p.A59fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_30998 | 153317645 | 153317858 | 153317851 | 153317851 | Frame_Shift_Del | G | - | p.P49fs |
| BLCA | TCGA-CF-A3MG-01 | exon_skip_30988 | 153309657 | 153309775 | 153309655 | 153309655 | Splice_Site | A | G | p.G315_splice |
| LUAD | TCGA-05-4398-01 | exon_skip_30989 | 153312857 | 153313055 | 153312856 | 153312856 | Splice_Site | C | A | p.N275_splice |
| LUAD | TCGA-44-2659-01 | exon_skip_30989 | 153312857 | 153313055 | 153312856 | 153312856 | Splice_Site | C | A | p.N275_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-05-4398-01 |
| Cancer type: LUAD | |
| ESID: exon_skip_30989 | |
| Skipped exon start: 153312857 | |
| Skipped exon end: 153313055 | |
| Mutation start: 153312856 | |
| Mutation end: 153312856 | |
| Mutation type: Splice_Site | |
| Reference seq: C | |
| Mutation seq: A | |
| AAchange: p.N275_splice | |
exon_skip_291997_LUAD_TCGA-05-4398-01.png | |
exon_skip_30989_LUAD_TCGA-05-4398-01.png | |
exon_skip_332646_LUAD_TCGA-05-4398-01.png | |
exon_skip_436294_LUAD_TCGA-05-4398-01.png | |
exon_skip_436296_LUAD_TCGA-05-4398-01.png | |
exon_skip_489149_LUAD_TCGA-05-4398-01.png | |
| - 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 |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153309657 | 153309775 | 153309749 | 153309749 | Missense_Mutation | A | T | p.I284N |
| CCK81_LARGE_INTESTINE | 153312857 | 153313055 | 153312945 | 153312945 | Missense_Mutation | A | G | p.C246R |
| MM383_SKIN | 153312857 | 153313055 | 153312956 | 153312956 | Missense_Mutation | G | A | p.A242V |
| EVSAT_BREAST | 153312857 | 153313055 | 153312990 | 153312990 | Missense_Mutation | G | A | p.L231F |
| HT115_LARGE_INTESTINE | 153312857 | 153313055 | 153313040 | 153313040 | Missense_Mutation | A | G | p.V214A |
| TE11_OESOPHAGUS | 153317645 | 153317858 | 153317676 | 153317676 | Missense_Mutation | G | A | p.H108Y |
| TE11_OESOPHAGUS | 153317645 | 153317846 | 153317676 | 153317676 | Missense_Mutation | G | A | p.H108Y |
| P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153317645 | 153317858 | 153317676 | 153317676 | Missense_Mutation | G | A | p.H108Y |
| P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 153317645 | 153317846 | 153317676 | 153317676 | Missense_Mutation | G | A | p.H108Y |
| CAPAN2_PANCREAS | 153312857 | 153313055 | 153312871 | 153312871 | Nonsense_Mutation | G | T | p.C270* |
| LN229_CENTRAL_NERVOUS_SYSTEM | 153317645 | 153317858 | 153317857 | 153317857 | Splice_Site | G | A | p.G47G |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PGLYRP4 |
| sQTL information located at the skipped exons. |
| Exon skip ID | Chromosome | Three exons | Skippped exon | ENST | Cancer type | SNP id | Location | DNA change (ref/var) | P-value |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PGLYRP4 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PGLYRP4 |
Top |
RelatedDrugs for PGLYRP4 |
| 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 |
Top |
RelatedDiseases for PGLYRP4 |
| 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)
|