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| Open reading frame (ORF) annotation in the exon skipping event |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| Splicing Quantitative Trait Methylation (sQTM) in the skipped exon |
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Gene summary for PRIM2 |
 Gene summary |
| Gene information | Gene symbol | PRIM2 | Gene ID | 5558 |
| Gene name | DNA primase subunit 2 | |
| Synonyms | PRIM2A|p58 | |
| Cytomap | 6p11.2 | |
| Type of gene | protein-coding | |
| Description | DNA primase large subunitDNA primase 58 kDa subunitprimase (DNA) subunit 2primase, DNA, polypeptide 2 (58kDa) | |
| Modification date | 20180523 | |
| UniProtAcc | P49643 | |
| Context | PubMed: PRIM2 [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 |
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Exon skipping events across known transcript of Ensembl for PRIM2 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. |
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Gene isoform structures and expression levels for PRIM2 |
| Expression levels of gene isoforms across TCGA. |
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| Expression levels of gene isoforms across GTEx. |
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Exon skipping events with PSIs in TCGA for PRIM2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_452842 | 6 | 57246828:57246966:57372287:57372355:57393111:57393184 | 57372287:57372355 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1 |
| exon_skip_452860 | 6 | 57372287:57372355:57393111:57393184:57398131:57398317 | 57393111:57393184 | ENSG00000146143.13 | ENST00000470638.1,ENST00000389488.2,ENST00000607273.1 |
| exon_skip_452865 | 6 | 57467079:57467206:57472358:57472441:57498966:57499035 | 57472358:57472441 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1 |
| exon_skip_452867 | 6 | 57472358:57472441:57498966:57499035:57512471:57513375 | 57498966:57499035 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for PRIM2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_452842 | 6 | 57246828:57246966:57372287:57372355:57393111:57393184 | 57372287:57372355 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1 |
| exon_skip_452860 | 6 | 57372287:57372355:57393111:57393184:57398131:57398317 | 57393111:57393184 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1,ENST00000470638.1 |
| exon_skip_452867 | 6 | 57472358:57472441:57498966:57499035:57512471:57513375 | 57498966:57499035 | ENSG00000146143.13 | ENST00000389488.2,ENST00000607273.1 |
| PSI values of skipped exons in GTEx. |
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| * Skipped exon sequences. |
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Open reading frame (ORF) annotation in the exon skipping event for PRIM2 |
| 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 |
| 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 |
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Infer the effects of exon skipping event on protein functional features for PRIM2 |
| Exon skipping at the protein sequence level and followed lost functional features. * Click on the image to enlarge it in a new window. |
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| 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 |
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SNVs in the skipped exons for PRIM2 |
| - Lollipop plot for presenting exon skipping associated SNVs. * Click on the image to enlarge it in a new window. |
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| - 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 |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_452860 | 57393112 | 57393184 | 57393166 | 57393166 | Frame_Shift_Del | T | - | p.S272fs |
| HNSC | TCGA-BA-4076-01 | exon_skip_452865 | 57472359 | 57472441 | 57472415 | 57472415 | Nonsense_Mutation | A | T | p.K402* |
| HNSC | TCGA-BA-6872-01 | exon_skip_452865 | 57472359 | 57472441 | 57472427 | 57472427 | Nonsense_Mutation | G | T | p.G406* |
| LUSC | TCGA-22-5480-01 | exon_skip_452865 | 57472359 | 57472441 | 57472357 | 57472357 | Splice_Site | A | T | p.G382_splice |
| - 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 |
| BFTC905_URINARY_TRACT | 57393112 | 57393184 | 57393151 | 57393153 | In_Frame_Del | TGT | - | p.V268del |
| L540_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 57372288 | 57372355 | 57372306 | 57372306 | Missense_Mutation | C | T | p.P238S |
| NCIH1651_LUNG | 57372288 | 57372355 | 57372309 | 57372309 | Missense_Mutation | G | A | p.A239T |
| HT115_LARGE_INTESTINE | 57372288 | 57372355 | 57372328 | 57372328 | Missense_Mutation | G | A | p.R245K |
| U698M_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 57372288 | 57372355 | 57372342 | 57372342 | Missense_Mutation | C | A | p.L250I |
| NCIH2172_LUNG | 57393112 | 57393184 | 57393120 | 57393120 | Missense_Mutation | A | G | p.Y257C |
| MFE296_ENDOMETRIUM | 57393112 | 57393184 | 57393138 | 57393138 | Missense_Mutation | G | A | p.S263N |
| CAL12T_LUNG | 57393112 | 57393184 | 57393153 | 57393153 | Missense_Mutation | T | A | p.V268D |
| LU165_LUNG | 57393112 | 57393184 | 57393175 | 57393175 | Missense_Mutation | G | C | p.Q275H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PRIM2 |
| 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 |
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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRIM2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PRIM2 |
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RelatedDrugs for PRIM2 |
| 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 |
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RelatedDiseases for PRIM2 |
| 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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