|
||||||
|
 | |
| |
| |
| |
| 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 PADI2 |
 Gene summary |
| Gene information | Gene symbol | PADI2 | Gene ID | 11240 |
| Gene name | peptidyl arginine deiminase 2 | |
| Synonyms | PAD-H19|PAD2|PDI2 | |
| Cytomap | 1p36.13 | |
| Type of gene | protein-coding | |
| Description | protein-arginine deiminase type-2peptidyl arginine deiminase, type IIprotein-arginine deiminase type II | |
| Modification date | 20180523 | |
| UniProtAcc | Q9Y2J8 | |
| Context | PubMed: PADI2 [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 |
| PADI2 | GO:0010848 | regulation of chromatin disassembly | 22853951 |
| PADI2 | GO:0018101 | protein citrullination | 12392711|15629448 |
| PADI2 | GO:0036413 | histone H3-R26 citrullination | 22853951 |
| PADI2 | GO:0070100 | negative regulation of chemokine-mediated signaling pathway | 18645041 |
| PADI2 | GO:1901624 | negative regulation of lymphocyte chemotaxis | 18645041 |
Top |
Exon skipping events across known transcript of Ensembl for PADI2 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 PADI2 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for PADI2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_22182 | 1 | 17396582:17396711:17397900:17397986:17401350:17401444 | 17397900:17397986 | ENSG00000117115.8 | ENST00000375486.4,ENST00000466151.1,ENST00000479534.1,ENST00000444885.2 |
| exon_skip_22185 | 1 | 17402173:17402318:17405758:17405910:17409039:17409147 | 17405758:17405910 | ENSG00000117115.8 | ENST00000375486.4,ENST00000466151.1,ENST00000444885.2 |
| exon_skip_22187 | 1 | 17410220:17410332:17411093:17411197:17413015:17413194 | 17411093:17411197 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22190 | 1 | 17411093:17411197:17413015:17413194:17418902:17419028 | 17413015:17413194 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22192 | 1 | 17413015:17413194:17418902:17419028:17420061:17420179 | 17418902:17419028 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22194 | 1 | 17413015:17413194:17422403:17422465:17429481:17429554 | 17422403:17422465 | ENSG00000117115.8 | ENST00000444885.2 |
| exon_skip_22195 | 1 | 17422403:17422465:17429481:17429554:17431372:17431556 | 17429481:17429554 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1,ENST00000444885.2 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for PADI2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_22182 | 1 | 17396582:17396711:17397900:17397986:17401350:17401444 | 17397900:17397986 | ENSG00000117115.8 | ENST00000375486.4,ENST00000479534.1,ENST00000466151.1,ENST00000444885.2 |
| exon_skip_22185 | 1 | 17402173:17402318:17405758:17405910:17409039:17409147 | 17405758:17405910 | ENSG00000117115.8 | ENST00000375486.4,ENST00000466151.1,ENST00000444885.2 |
| exon_skip_22187 | 1 | 17410220:17410332:17411093:17411197:17413015:17413194 | 17411093:17411197 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22190 | 1 | 17411093:17411197:17413015:17413194:17418902:17419028 | 17413015:17413194 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22192 | 1 | 17413015:17413194:17418902:17419028:17420061:17420179 | 17418902:17419028 | ENSG00000117115.8 | ENST00000375486.4,ENST00000375481.1 |
| exon_skip_22194 | 1 | 17413015:17413194:17422403:17422465:17429481:17429554 | 17422403:17422465 | ENSG00000117115.8 | ENST00000444885.2 |
| exon_skip_22195 | 1 | 17422403:17422465:17429481:17429554:17431372:17431556 | 17429481:17429554 | ENSG00000117115.8 | ENST00000375486.4,ENST00000444885.2,ENST00000375481.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for PADI2 |
| 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 |
| ENST00000375486 | 17397900 | 17397986 | Frame-shift |
| ENST00000375486 | 17405758 | 17405910 | Frame-shift |
| ENST00000375486 | 17411093 | 17411197 | Frame-shift |
| ENST00000375486 | 17413015 | 17413194 | Frame-shift |
| ENST00000375486 | 17429481 | 17429554 | Frame-shift |
| ENST00000375486 | 17418902 | 17419028 | In-frame |
| 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 |
| ENST00000375486 | 17397900 | 17397986 | Frame-shift |
| ENST00000375486 | 17405758 | 17405910 | Frame-shift |
| ENST00000375486 | 17411093 | 17411197 | Frame-shift |
| ENST00000375486 | 17413015 | 17413194 | Frame-shift |
| ENST00000375486 | 17429481 | 17429554 | Frame-shift |
| ENST00000375486 | 17418902 | 17419028 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for PADI2 |
| 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 |
| ENST00000375486 | 4362 | 665 | 17418902 | 17419028 | 594 | 719 | 176 | 218 |
| 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 |
| ENST00000375486 | 4362 | 665 | 17418902 | 17419028 | 594 | 719 | 176 | 218 |
| 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 |
| Q9Y2J8 | 176 | 218 | 181 | 193 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 198 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 212 | 216 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 1 | 665 | Chain | ID=PRO_0000220026;Note=Protein-arginine deiminase type-2 |
| Q9Y2J8 | 176 | 218 | 175 | 178 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 207 | 210 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 177 | 177 | Metal binding | Note=Calcium 2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:0000244|PDB:4N2A,ECO:0000244|PDB:4N2B,ECO: |
| Q9Y2J8 | 176 | 218 | 180 | 180 | Metal binding | Note=Calcium 2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:0000244|PDB:4N2A,ECO:0000244|P |
| Q9Y2J8 | 176 | 218 | 180 | 180 | Metal binding | Note=Calcium 3;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:000024 |
| Q9Y2J8 | 176 | 218 | 177 | 177 | Mutagenesis | Note=Reduced enzyme activity. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25621824;Dbxref=PMID:25621824 |
| 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 |
| Q9Y2J8 | 176 | 218 | 181 | 193 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 198 | 203 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 212 | 216 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 1 | 665 | Chain | ID=PRO_0000220026;Note=Protein-arginine deiminase type-2 |
| Q9Y2J8 | 176 | 218 | 175 | 178 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 207 | 210 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4N2K |
| Q9Y2J8 | 176 | 218 | 177 | 177 | Metal binding | Note=Calcium 2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:0000244|PDB:4N2A,ECO:0000244|PDB:4N2B,ECO: |
| Q9Y2J8 | 176 | 218 | 180 | 180 | Metal binding | Note=Calcium 2;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:0000244|PDB:4N2A,ECO:0000244|P |
| Q9Y2J8 | 176 | 218 | 180 | 180 | Metal binding | Note=Calcium 3;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000244,ECO:0000269;evidence=ECO:0000244|PDB:4N25,ECO:0000244|PDB:4N26,ECO:0000244|PDB:4N28,ECO:000024 |
| Q9Y2J8 | 176 | 218 | 177 | 177 | Mutagenesis | Note=Reduced enzyme activity. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:25621824;Dbxref=PMID:25621824 |
Top |
SNVs in the skipped exons for PADI2 |
| - 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. |
| - 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 |
| THCA | TCGA-DO-A1JZ-01 | exon_skip_22187 | 17411094 | 17411197 | 17411155 | 17411155 | Frame_Shift_Del | G | - | p.R293fs |
| HNSC | TCGA-CV-7411-01 | exon_skip_22190 | 17413016 | 17413194 | 17413121 | 17413121 | Frame_Shift_Del | A | - | p.G243fs |
| HNSC | TCGA-CV-7411-01 | exon_skip_22190 | 17413016 | 17413194 | 17413121 | 17413121 | Frame_Shift_Del | A | - | p.G244fs |
| BRCA | TCGA-AR-A1AH-01 | exon_skip_22192 | 17418903 | 17419028 | 17418927 | 17418930 | Frame_Shift_Del | TGTC | - | p.D210fs |
| ACC | TCGA-P6-A5OG-01 | exon_skip_22192 | 17418903 | 17419028 | 17418973 | 17418973 | Frame_Shift_Del | G | - | p.A196fs |
| ACC | TCGA-P6-A5OG-01 | exon_skip_22192 | 17418903 | 17419028 | 17418973 | 17418973 | Frame_Shift_Del | G | - | p.P195fs |
| BRCA | TCGA-AR-A1AH-01 | exon_skip_22192 | 17418903 | 17419028 | 17418927 | 17418928 | Frame_Shift_Ins | - | GA | p.K210fs |
| BLCA | TCGA-BT-A20J-01 | exon_skip_22190 | 17413016 | 17413194 | 17413062 | 17413062 | Nonsense_Mutation | G | C | p.S263* |
| CESC | TCGA-C5-A2LZ-01 | exon_skip_22194 | 17422404 | 17422465 | 17422424 | 17422424 | Nonsense_Mutation | C | A | p.E131* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
| - 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 |
| CAL51_BREAST | 17405759 | 17405910 | 17405807 | 17405807 | Missense_Mutation | C | T | p.G421D |
| RERFGC1B_STOMACH | 17405759 | 17405910 | 17405808 | 17405808 | Missense_Mutation | C | T | p.G421S |
| TT_THYROID | 17405759 | 17405910 | 17405843 | 17405843 | Missense_Mutation | C | T | p.G409E |
| NBSUSSR_AUTONOMIC_GANGLIA | 17405759 | 17405910 | 17405897 | 17405897 | Missense_Mutation | C | A | p.G391V |
| PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17411094 | 17411197 | 17411137 | 17411137 | Missense_Mutation | T | C | p.M299V |
| MDAMB231_BREAST | 17411094 | 17411197 | 17411141 | 17411141 | Missense_Mutation | C | G | p.W297C |
| PLCPRF5_LIVER | 17413016 | 17413194 | 17413116 | 17413116 | Missense_Mutation | G | T | p.S245Y |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17413016 | 17413194 | 17413143 | 17413143 | Missense_Mutation | T | C | p.Y236C |
| P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17413016 | 17413194 | 17413155 | 17413155 | Missense_Mutation | C | T | p.R232Q |
| MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 17418903 | 17419028 | 17418918 | 17418918 | Missense_Mutation | C | T | p.V214M |
| HCT15_LARGE_INTESTINE | 17418903 | 17419028 | 17418980 | 17418980 | Missense_Mutation | C | T | p.R193H |
| SKNSH_AUTONOMIC_GANGLIA | 17422404 | 17422465 | 17422422 | 17422422 | Missense_Mutation | C | A | p.E131D |
| NUGC3_STOMACH | 17429482 | 17429554 | 17429490 | 17429490 | Missense_Mutation | G | A | p.T114I |
| NCIH2023_LUNG | 17397901 | 17397986 | 17397901 | 17397901 | Splice_Site | C | A | p.Q545H |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PADI2 |
| 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 PADI2 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PADI2 |
Top |
RelatedDrugs for PADI2 |
| 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 PADI2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| PADI2 | C0036341 | Schizophrenia | 1 | PSYGENET |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|