|
||||||
|
 | |
| |
| |
| 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 PLXNB2 |
 Gene summary |
| Gene information | Gene symbol | PLXNB2 | Gene ID | 23654 |
| Gene name | plexin B2 | |
| Synonyms | MM1|Nbla00445|PLEXB2|dJ402G11.3 | |
| Cytomap | 22q13.33 | |
| Type of gene | protein-coding | |
| Description | plexin-B2 | |
| 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 |
| PLXNB2 | GO:0007156 | homophilic cell adhesion via plasma membrane adhesion molecules | 16122393 |
| PLXNB2 | GO:0010976 | positive regulation of neuron projection development | 16122393 |
Top |
Gene structures and expression levels for PLXNB2 |
| 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. |
 |
ENSG00000196576
| 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 |
| PCC | UP | ENST00000479818.5 | PLXNB2-210:retained_intron:PLXNB2 | 2.640406e+01 | 1.475901e+00 | 8.272678e-04 | 2.264109e-02 |
| CB | DOWN | ENST00000479818.5 | PLXNB2-210:retained_intron:PLXNB2 | 4.883457e+02 | -1.956510e+00 | 5.312878e-12 | 5.875530e-10 |
| CB | UP | ENST00000432455.5 | PLXNB2-205:protein_coding:PLXNB2 | 4.564655e+01 | 1.206072e+00 | 1.559973e-03 | 7.499042e-03 |
| CB | UP | ENST00000425954.1 | PLXNB2-203:protein_coding:PLXNB2 | 1.022603e+01 | 1.635737e+00 | 1.530292e-02 | 4.901980e-02 |
| TC | DOWN | ENST00000479818.5 | PLXNB2-210:retained_intron:PLXNB2 | 1.253268e+02 | -1.839528e+00 | 2.391452e-06 | 8.205503e-05 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PLXNB2 |
| 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_108276 | chr22 | 50290507:50290597:50294719:50294778:50307553:50307603 | 50294719:50294778 |
| exon_skip_108678 | chr22 | 50276629:50276704:50276842:50276906:50277591:50277738 | 50276842:50276906 |
| exon_skip_128386 | chr22 | 50286173:50286287:50287111:50287264:50287667:50287793 | 50287111:50287264 |
| exon_skip_145269 | chr22 | 50278266:50278271:50278435:50278519:50278596:50278665 | 50278435:50278519 |
| exon_skip_154353 | chr22 | 50290534:50290597:50294726:50294778:50307553:50307603 | 50294726:50294778 |
| exon_skip_166814 | chr22 | 50279643:50279776:50280005:50280071:50280489:50280670 | 50280005:50280071 |
| exon_skip_179958 | chr22 | 50287111:50287264:50287667:50287793:50287937:50288037 | 50287667:50287793 |
| exon_skip_189751 | chr22 | 50281854:50282081:50282184:50282313:50282711:50282880 | 50282184:50282313 |
| exon_skip_203320 | chr22 | 50283833:50283990:50284132:50284244:50284573:50284605 | 50284132:50284244 |
| exon_skip_231139 | chr22 | 50278883:50279011:50279630:50279776:50280005:50280071 | 50279630:50279776 |
| exon_skip_233961 | chr22 | 50281854:50282081:50282184:50282313:50282711:50282838 | 50282184:50282313 |
| exon_skip_239542 | chr22 | 50283833:50283990:50284132:50284213:50284573:50284605 | 50284132:50284213 |
| exon_skip_250196 | chr22 | 50284573:50284665:50284845:50284913:50285800:50285843 | 50284845:50284913 |
| exon_skip_286430 | chr22 | 50290507:50290597:50294726:50294778:50307553:50307603 | 50294726:50294778 |
| exon_skip_296154 | chr22 | 50284167:50284213:50284573:50284665:50285800:50285843 | 50284573:50284665 |
| exon_skip_296311 | chr22 | 50283833:50283990:50284132:50284244:50284573:50284665 | 50284132:50284244 |
| exon_skip_30052 | chr22 | 50290100:50290597:50294726:50294778:50307553:50307603 | 50294726:50294778 |
| exon_skip_313 | chr22 | 50290100:50290597:50294719:50294778:50301347:50301462 | 50294719:50294778 |
| exon_skip_56080 | chr22 | 50290534:50290597:50294719:50294778:50307553:50307603 | 50294719:50294778 |
| exon_skip_57562 | chr22 | 50283833:50283990:50284132:50284213:50284573:50284665 | 50284132:50284213 |
| exon_skip_63565 | chr22 | 50290100:50290597:50294719:50294778:50307553:50307603 | 50294719:50294778 |
| exon_skip_81080 | chr22 | 50284573:50284665:50285800:50285901:50285990:50286098 | 50285800:50285901 |
| exon_skip_90508 | chr22 | 50282711:50282881:50283050:50283186:50283337:50283445 | 50283050:50283186 |
| 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 |
| exon_skip_239542 | Mayo_CB | 7.236585e-01 | 8.735065e-01 | -1.498480e-01 | 3.804605e-09 |
| exon_skip_203320 | Mayo_CB | 2.106098e-01 | 3.302817e-01 | -1.196719e-01 | 2.288452e-08 |
| exon_skip_128386 | Mayo_CB | 7.660976e-01 | 8.800000e-01 | -1.139024e-01 | 3.806784e-06 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PLXNB2 |
| 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 |
| ENST00000359337 | 50294719 | 50294778 | 3UTR-3UTR |
| ENST00000449103 | 50294726 | 50294778 | 3UTR-3UTR |
| ENST00000359337 | 50282184 | 50282313 | Frame-shift |
| ENST00000449103 | 50282184 | 50282313 | Frame-shift |
| ENST00000359337 | 50283050 | 50283186 | Frame-shift |
| ENST00000449103 | 50283050 | 50283186 | Frame-shift |
| ENST00000359337 | 50284132 | 50284213 | Frame-shift |
| ENST00000449103 | 50284132 | 50284213 | Frame-shift |
| ENST00000359337 | 50287111 | 50287264 | Frame-shift |
| ENST00000449103 | 50287111 | 50287264 | Frame-shift |
| 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 |
| ENST00000359337 | 50294719 | 50294778 | 3UTR-3UTR |
| ENST00000449103 | 50294726 | 50294778 | 3UTR-3UTR |
| ENST00000359337 | 50287111 | 50287264 | Frame-shift |
| ENST00000449103 | 50287111 | 50287264 | Frame-shift |
| 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 |
| ENST00000359337 | 50294719 | 50294778 | 3UTR-3UTR |
| ENST00000449103 | 50294726 | 50294778 | 3UTR-3UTR |
| ENST00000359337 | 50276842 | 50276906 | Frame-shift |
| ENST00000449103 | 50276842 | 50276906 | Frame-shift |
| ENST00000359337 | 50278435 | 50278519 | Frame-shift |
| ENST00000449103 | 50278435 | 50278519 | Frame-shift |
| ENST00000359337 | 50280005 | 50280071 | Frame-shift |
| ENST00000449103 | 50280005 | 50280071 | Frame-shift |
| ENST00000359337 | 50282184 | 50282313 | Frame-shift |
| ENST00000449103 | 50282184 | 50282313 | Frame-shift |
| ENST00000359337 | 50283050 | 50283186 | Frame-shift |
| ENST00000449103 | 50283050 | 50283186 | Frame-shift |
| ENST00000359337 | 50284132 | 50284213 | Frame-shift |
| ENST00000449103 | 50284132 | 50284213 | Frame-shift |
| ENST00000359337 | 50287111 | 50287264 | Frame-shift |
| ENST00000449103 | 50287111 | 50287264 | Frame-shift |
| ENST00000359337 | 50287667 | 50287793 | Frame-shift |
| ENST00000449103 | 50287667 | 50287793 | Frame-shift |
| ENST00000359337 | 50279630 | 50279776 | In-frame |
| ENST00000449103 | 50279630 | 50279776 | In-frame |
| ENST00000359337 | 50284573 | 50284665 | In-frame |
| ENST00000449103 | 50284573 | 50284665 | In-frame |
| ENST00000359337 | 50285800 | 50285901 | In-frame |
| ENST00000449103 | 50285800 | 50285901 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PLXNB2 |
p-ENSG00000196576_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 |
| 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 |
| ENST00000359337 | 6352 | 1838 | 50285800 | 50285901 | 2080 | 2180 | 662 | 695 |
| ENST00000449103 | 6400 | 1838 | 50285800 | 50285901 | 2128 | 2228 | 662 | 695 |
| ENST00000359337 | 6352 | 1838 | 50284573 | 50284665 | 2182 | 2273 | 696 | 726 |
| ENST00000449103 | 6400 | 1838 | 50284573 | 50284665 | 2230 | 2321 | 696 | 726 |
| ENST00000359337 | 6352 | 1838 | 50279630 | 50279776 | 4336 | 4481 | 1414 | 1462 |
| ENST00000449103 | 6400 | 1838 | 50279630 | 50279776 | 4384 | 4529 | 1414 | 1462 |
| 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 |
| O15031 | 662 | 695 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 662 | 695 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 662 | 695 | 20 | 1197 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15031 | 662 | 695 | 20 | 1197 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15031 | 696 | 726 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 696 | 726 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 696 | 726 | 20 | 1197 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15031 | 696 | 726 | 20 | 1197 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15031 | 1414 | 1462 | 1462 | 1469 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4E71 |
| O15031 | 1414 | 1462 | 1462 | 1469 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4E71 |
| O15031 | 1414 | 1462 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 1414 | 1462 | 20 | 1838 | Chain | ID=PRO_0000024673;Note=Plexin-B2 |
| O15031 | 1414 | 1462 | 1219 | 1838 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| O15031 | 1414 | 1462 | 1219 | 1838 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in PLXNB2 |
| 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 |
| Mayo | ENST00000359337 | 50294719 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| Mayo | ENST00000449103 | 50294726 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| Mayo | ENST00000359337 | 50294719 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
| Mayo | ENST00000449103 | 50294726 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
| MSBB | ENST00000359337 | 50294719 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| MSBB | ENST00000449103 | 50294726 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| MSBB | ENST00000359337 | 50294719 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
| MSBB | ENST00000449103 | 50294726 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
| ROSMAP | ENST00000359337 | 50294719 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| ROSMAP | ENST00000449103 | 50294726 | 50294778 | hsa-miR-4487 | chr22:50294741-50294748 | 8mer-1a | chr22:50294729-50294754 | 152.00 | -23.91 |
| ROSMAP | ENST00000359337 | 50294719 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
| ROSMAP | ENST00000449103 | 50294726 | 50294778 | hsa-miR-6081 | chr22:50294753-50294760 | 8mer-1a | chr22:50294749-50294767 | 153.00 | -22.30 |
Top |
SNVs in the skipped exons for PLXNB2 |
| - 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 |
Top |
AD stage-associated exon skippint events for PLXNB2 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PLXNB2 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
Top |
Correlation with RNA binding proteins (RBPs) for PLXNB2 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_239542 | -5.118853e-01 | 5.344931e-12 |
| CB | PCBP1 | exon_skip_239542 | -4.163632e-01 | 4.797971e-08 |
| CB | TRA2A | exon_skip_239542 | -6.276058e-01 | 8.547717e-19 |
| CB | TARDBP | exon_skip_203320 | -4.798392e-01 | 3.476941e-10 |
| CB | TRA2A | exon_skip_203320 | -4.921122e-01 | 1.043936e-10 |
| CB | RBM6 | exon_skip_128386 | -5.091601e-01 | 7.218734e-12 |
| CB | PCBP4 | exon_skip_128386 | 6.472233e-01 | 3.036305e-20 |
| CB | HNRNPA2B1 | exon_skip_128386 | -4.863498e-01 | 8.069224e-11 |
| CB | NUP42 | exon_skip_128386 | 5.555567e-01 | 2.946266e-14 |
| CB | PTBP1 | exon_skip_128386 | -4.705358e-01 | 3.886707e-10 |
| CB | RBM4B | exon_skip_128386 | -4.857534e-01 | 8.574713e-11 |
| TC | PTBP1 | exon_skip_128386 | -4.063517e-01 | 1.552313e-07 |
Top |
RelatedDrugs for PLXNB2 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for PLXNB2 |
| 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)
|