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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 P4HA2 |
Gene summary |
Gene information | Gene symbol | P4HA2 | Gene ID | 8974 |
Gene name | prolyl 4-hydroxylase subunit alpha 2 | |
Synonyms | MYP25 | |
Cytomap | 5q31.1 | |
Type of gene | protein-coding | |
Description | prolyl 4-hydroxylase subunit alpha-24-PH alpha 2C-P4Halpha(II)collagen prolyl 4-hydroxylase alpha(II)procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide IIprocollagen-proline,2-oxoglutarate-4-dioxygenase subun | |
Modification date | 20200315 | |
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 |
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Gene structures and expression levels for P4HA2 |
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. |
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 | ENST00000467587.1 | P4HA2-216:retained_intron:P4HA2 | 1.521848e+00 | 1.068126e+00 | 5.376976e-04 | 1.726846e-02 |
PCC | UP | ENST00000379086.5 | P4HA2-203:protein_coding:P4HA2 | 5.206173e+01 | 8.978672e-01 | 2.053371e-03 | 3.980943e-02 |
HCC | UP | ENST00000379086.5 | P4HA2-203:protein_coding:P4HA2 | 4.617586e+01 | 9.775022e-01 | 9.483878e-04 | 3.263976e-02 |
CB | UP | ENST00000166534.8 | P4HA2-201:protein_coding:P4HA2 | 4.529996e+01 | 9.807051e-01 | 3.658704e-05 | 3.157061e-04 |
CB | UP | ENST00000428369.5 | P4HA2-211:protein_coding:P4HA2 | 4.599572e+00 | 1.083743e+00 | 3.118454e-04 | 1.934973e-03 |
CB | UP | ENST00000417528.5 | P4HA2-209:protein_coding:P4HA2 | 2.779742e+00 | 1.241824e+00 | 3.429922e-04 | 2.097660e-03 |
CB | UP | ENST00000418055.5 | P4HA2-210:protein_coding:P4HA2 | 8.460995e-01 | 1.818886e+00 | 4.098448e-03 | 1.670314e-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 P4HA2 |
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_122809 | chr5 | 132218545:132218644:132227086:132227221:132227539:132227794 | 132227086:132227221 |
exon_skip_16252 | chr5 | 132195412:132195480:132198206:132198271:132198879:132198932 | 132198206:132198271 |
exon_skip_188120 | chr5 | 132218545:132218644:132226932:132227221:132227790:132227815 | 132226932:132227221 |
exon_skip_212075 | chr5 | 132218545:132218644:132227086:132227258:132227790:132227815 | 132227086:132227258 |
exon_skip_220299 | chr5 | 132198879:132198932:132203748:132203847:132204082:132204152 | 132203748:132203847 |
exon_skip_221531 | chr5 | 132218545:132218644:132227086:132227221:132227790:132227815 | 132227086:132227221 |
exon_skip_252706 | chr5 | 132204082:132204152:132207708:132207884:132209138:132209331 | 132207708:132207884 |
exon_skip_256628 | chr5 | 132218545:132218644:132227086:132227258:132227790:132227819 | 132227086:132227258 |
exon_skip_8030 | chr5 | 132195412:132195480:132198321:132198380:132198879:132198932 | 132198321:132198380 |
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_197008 | Mayo_CB | 2.171951e-01 | 1.067797e-01 | 1.104155e-01 | 2.643231e-02 |
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Open reading frame (ORF) annotation in the exon skipping event for P4HA2 |
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 |
ENST00000166534 | 132227086 | 132227221 | 3UTR-3UTR |
ENST00000166534 | 132203748 | 132203847 | Frame-shift |
ENST00000379104 | 132203748 | 132203847 | Frame-shift |
ENST00000401867 | 132203748 | 132203847 | Frame-shift |
ENST00000166534 | 132207708 | 132207884 | In-frame |
ENST00000379104 | 132207708 | 132207884 | In-frame |
ENST00000401867 | 132207708 | 132207884 | 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 |
ENST00000166534 | 132227086 | 132227221 | 3UTR-3UTR |
ENST00000166534 | 132203748 | 132203847 | Frame-shift |
ENST00000379104 | 132203748 | 132203847 | Frame-shift |
ENST00000401867 | 132203748 | 132203847 | 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 |
ENST00000166534 | 132227086 | 132227221 | 3UTR-3UTR |
ENST00000166534 | 132203748 | 132203847 | Frame-shift |
ENST00000379104 | 132203748 | 132203847 | Frame-shift |
ENST00000401867 | 132203748 | 132203847 | Frame-shift |
ENST00000166534 | 132198206 | 132198271 | In-frame |
ENST00000379104 | 132198206 | 132198271 | In-frame |
ENST00000401867 | 132198206 | 132198271 | In-frame |
ENST00000166534 | 132207708 | 132207884 | In-frame |
ENST00000379104 | 132207708 | 132207884 | In-frame |
ENST00000401867 | 132207708 | 132207884 | In-frame |
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Infer the effects of exon skipping event on protein functional features for P4HA2 |
p-ENSG00000072682_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 |
ENST00000166534 | 2247 | 535 | 132207708 | 132207884 | 1126 | 1301 | 301 | 359 |
ENST00000379104 | 2586 | 535 | 132207708 | 132207884 | 1468 | 1643 | 301 | 359 |
ENST00000401867 | 3366 | 535 | 132207708 | 132207884 | 1473 | 1648 | 301 | 359 |
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 |
ENST00000166534 | 2247 | 535 | 132207708 | 132207884 | 1126 | 1301 | 301 | 359 |
ENST00000379104 | 2586 | 535 | 132207708 | 132207884 | 1468 | 1643 | 301 | 359 |
ENST00000401867 | 3366 | 535 | 132207708 | 132207884 | 1473 | 1648 | 301 | 359 |
ENST00000166534 | 2247 | 535 | 132198206 | 132198271 | 1528 | 1592 | 435 | 456 |
ENST00000379104 | 2586 | 535 | 132198206 | 132198271 | 1870 | 1934 | 435 | 456 |
ENST00000401867 | 3366 | 535 | 132198206 | 132198271 | 1875 | 1939 | 435 | 456 |
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 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
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 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 301 | 359 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 435 | 456 | 436 | 451 | Alternative sequence | ID=VSP_004506;Note=In isoform IIa. NDERDTFKHLGTGNRV->RPFDSGLKTEGNRL;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12975309,ECO:0000303|PubMed:15489334;Dbxref=PMID:12975309,PMID:15489334 |
O15460 | 435 | 456 | 436 | 451 | Alternative sequence | ID=VSP_004506;Note=In isoform IIa. NDERDTFKHLGTGNRV->RPFDSGLKTEGNRL;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12975309,ECO:0000303|PubMed:15489334;Dbxref=PMID:12975309,PMID:15489334 |
O15460 | 435 | 456 | 436 | 451 | Alternative sequence | ID=VSP_004506;Note=In isoform IIa. NDERDTFKHLGTGNRV->RPFDSGLKTEGNRL;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:12975309,ECO:0000303|PubMed:15489334;Dbxref=PMID:12975309,PMID:15489334 |
O15460 | 435 | 456 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 435 | 456 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 435 | 456 | 22 | 535 | Chain | ID=PRO_0000022726;Note=Prolyl 4-hydroxylase subunit alpha-2 |
O15460 | 435 | 456 | 412 | 520 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
O15460 | 435 | 456 | 412 | 520 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
O15460 | 435 | 456 | 412 | 520 | Domain | Note=Fe2OG dioxygenase;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00805 |
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3'-UTR located exon skipping events that lost miRNA binding sites in P4HA2 |
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 | ENST00000166534 | 132227086 | 132227221 | hsa-miR-6077 | chr5:132227114-132227121 | 8mer-1a | chr5:132227113-132227136 | 170.00 | -31.20 |
Mayo | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3065-5p | chr5:132227182-132227189 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
Mayo | ENST00000166534 | 132227086 | 132227221 | hsa-miR-5583-5p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
Mayo | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3129-3p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
Mayo | ENST00000166534 | 132227086 | 132227221 | hsa-miR-7159-5p | chr5:132227183-132227190 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
MSBB | ENST00000166534 | 132227086 | 132227221 | hsa-miR-6077 | chr5:132227114-132227121 | 8mer-1a | chr5:132227113-132227136 | 170.00 | -31.20 |
MSBB | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3065-5p | chr5:132227182-132227189 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
MSBB | ENST00000166534 | 132227086 | 132227221 | hsa-miR-5583-5p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
MSBB | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3129-3p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
MSBB | ENST00000166534 | 132227086 | 132227221 | hsa-miR-7159-5p | chr5:132227183-132227190 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
ROSMAP | ENST00000166534 | 132227086 | 132227221 | hsa-miR-6077 | chr5:132227114-132227121 | 8mer-1a | chr5:132227113-132227136 | 170.00 | -31.20 |
ROSMAP | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3065-5p | chr5:132227182-132227189 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
ROSMAP | ENST00000166534 | 132227086 | 132227221 | hsa-miR-5583-5p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
ROSMAP | ENST00000166534 | 132227086 | 132227221 | hsa-miR-3129-3p | chr5:132227190-132227197 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
ROSMAP | ENST00000166534 | 132227086 | 132227221 | hsa-miR-7159-5p | chr5:132227183-132227190 | 8mer-1a | chr5:132227177-132227197 | 153.00 | -7.52 |
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SNVs in the skipped exons for P4HA2 |
- 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 P4HA2 |
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 P4HA2 |
sQTL information located at the skipped exons. |
Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
CB | exon_skip_221531 | rs2089855 | chr5:132237836 | 1.399059e-09 | 1.123120e-06 |
CB | exon_skip_212075 | rs2089855 | chr5:132237836 | 2.318321e-05 | 5.208043e-03 |
CB | exon_skip_221531 | rs162907 | chr5:132244459 | 2.797316e-05 | 6.100026e-03 |
CB | exon_skip_221531 | rs6871350 | chr5:132244527 | 4.378896e-05 | 8.788122e-03 |
CB | exon_skip_221531 | rs272842 | chr5:132320824 | 9.672811e-05 | 1.676990e-02 |
CB | exon_skip_221531 | rs273913 | chr5:132325463 | 9.672811e-05 | 1.676990e-02 |
CB | exon_skip_221531 | rs156029 | chr5:132196941 | 1.814230e-04 | 2.765991e-02 |
TC | exon_skip_221531 | rs2089855 | chr5:132237836 | 3.507584e-08 | 1.749355e-05 |
TC | exon_skip_221531 | rs6871350 | chr5:132244527 | 5.544302e-06 | 1.513071e-03 |
TC | exon_skip_221531 | rs162907 | chr5:132244459 | 1.384849e-05 | 3.239458e-03 |
TC | exon_skip_212075 | rs2089855 | chr5:132237836 | 1.676225e-04 | 2.453845e-02 |
TC | exon_skip_221531 | rs272842 | chr5:132320824 | 3.721169e-04 | 4.651322e-02 |
TC | exon_skip_221531 | rs273913 | chr5:132325463 | 3.721169e-04 | 4.651322e-02 |
HCC | exon_skip_221531 | rs4705928 | chr5:132242944 | 1.264257e-05 | 1.543843e-03 |
HCC | exon_skip_221531 | rs272842 | chr5:132320824 | 1.648676e-04 | 1.386973e-02 |
HCC | exon_skip_221531 | rs10076701 | chr5:132260726 | 3.474572e-04 | 2.539771e-02 |
HCC | exon_skip_221531 | rs2136188 | chr5:132241821 | 4.234526e-04 | 2.964160e-02 |
HCC | exon_skip_221531 | rs6890009 | chr5:132244340 | 6.608157e-04 | 4.222668e-02 |
HCC | exon_skip_221531 | rs6871350 | chr5:132244527 | 6.608157e-04 | 4.222668e-02 |
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Correlation with RNA binding proteins (RBPs) for P4HA2 |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
CB | DAZAP1 | exon_skip_8030 | -4.804655e-01 | 4.283398e-10 |
CB | HNRNPA2B1 | exon_skip_8030 | -4.105358e-01 | 1.645388e-07 |
CB | RBM4 | exon_skip_8030 | -5.694435e-01 | 2.353236e-14 |
CB | CNOT4 | exon_skip_220299 | -4.584742e-01 | 1.222969e-09 |
CB | TRA2A | exon_skip_220299 | -5.657203e-01 | 7.853187e-15 |
CB | DAZAP1 | exon_skip_197008 | 4.140738e-01 | 3.324056e-07 |
CB | TARDBP | exon_skip_197008 | 5.299270e-01 | 1.405974e-11 |
CB | SAMD4A | exon_skip_197008 | 5.720454e-01 | 1.266380e-13 |
CB | CNOT4 | exon_skip_197008 | 5.747221e-01 | 9.174674e-14 |
CB | MBNL1 | exon_skip_197008 | 4.045464e-01 | 6.513846e-07 |
CB | PCBP1 | exon_skip_197008 | 4.344669e-01 | 7.330828e-08 |
CB | PCBP4 | exon_skip_197008 | -4.701185e-01 | 4.060681e-09 |
CB | RC3H1 | exon_skip_197008 | 4.152439e-01 | 3.056043e-07 |
CB | FUBP1 | exon_skip_197008 | 5.206477e-01 | 3.644852e-11 |
CB | KHSRP | exon_skip_197008 | 4.243573e-01 | 1.570429e-07 |
CB | SRSF1 | exon_skip_197008 | 4.099055e-01 | 4.473087e-07 |
CB | SRSF4 | exon_skip_197008 | 4.817770e-01 | 1.463744e-09 |
CB | HNRNPF | exon_skip_197008 | 4.187670e-01 | 2.368052e-07 |
CB | RBM4 | exon_skip_197008 | 6.226859e-01 | 1.670318e-16 |
CB | RBM4B | exon_skip_197008 | 4.135081e-01 | 3.461525e-07 |
CB | TARDBP | exon_skip_221531 | 4.553725e-01 | 9.773323e-09 |
CB | RBM4B | exon_skip_221531 | 4.201721e-01 | 1.581106e-07 |
CB | U2AF2 | exon_skip_212075 | 4.988346e-01 | 4.108559e-10 |
CB | SRSF4 | exon_skip_212075 | 4.024187e-01 | 9.068238e-07 |
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RelatedDrugs for P4HA2 |
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 P4HA2 |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |