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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 CSGALNACT2 |
 Gene summary |
| Gene information | Gene symbol | CSGALNACT2 | Gene ID | 55454 |
| Gene name | chondroitin sulfate N-acetylgalactosaminyltransferase 2 | |
| Synonyms | CHGN2|ChGn-2|GALNACT-2|GALNACT2|PRO0082|beta4GalNAcT | |
| Cytomap | 10q11.21 | |
| Type of gene | protein-coding | |
| Description | chondroitin sulfate N-acetylgalactosaminyltransferase 2beta 4 GalNAcT-2chondroitin beta1,4 N-acetylgalactosaminyltransferase 2glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase 2 | |
| Modification date | 20180522 | |
| UniProtAcc | Q8N6G5 | |
| Context | PubMed: CSGALNACT2 [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 |
| CSGALNACT2 | GO:0030166 | proteoglycan biosynthetic process | 11788602 |
| CSGALNACT2 | GO:0050650 | chondroitin sulfate proteoglycan biosynthetic process | 11788602 |
| CSGALNACT2 | GO:0050651 | dermatan sulfate proteoglycan biosynthetic process | 11788602 |
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Exon skipping events across known transcript of Ensembl for CSGALNACT2 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 CSGALNACT2 |
| 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 CSGALNACT2 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40961 | 10 | 43633933:43634015:43650344:43651258:43654162:43654379 | 43650344:43651258 | ENSG00000169826.6 | ENST00000374464.1 |
| exon_skip_40968 | 10 | 43650344:43651258:43654162:43654379:43655941:43656043 | 43654162:43654379 | ENSG00000169826.6 | ENST00000374464.1,ENST00000374466.3 |
| exon_skip_40985 | 10 | 43655941:43656043:43659313:43659492:43662451:43662546 | 43659313:43659492 | ENSG00000169826.6 | ENST00000374466.3 |
| exon_skip_40989 | 10 | 43659313:43659492:43662451:43662546:43671398:43671480 | 43662451:43662546 | ENSG00000169826.6 | ENST00000374466.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for CSGALNACT2 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_40961 | 10 | 43633933:43634015:43650344:43651258:43654162:43654379 | 43650344:43651258 | ENSG00000169826.6 | ENST00000374464.1 |
| exon_skip_40968 | 10 | 43650344:43651258:43654162:43654379:43655941:43656043 | 43654162:43654379 | ENSG00000169826.6 | ENST00000374466.3,ENST00000374464.1 |
| exon_skip_40985 | 10 | 43655941:43656043:43659313:43659492:43662451:43662546 | 43659313:43659492 | ENSG00000169826.6 | ENST00000374466.3 |
| exon_skip_40989 | 10 | 43659313:43659492:43662451:43662546:43671398:43671480 | 43662451:43662546 | ENSG00000169826.6 | ENST00000374466.3 |
| 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 CSGALNACT2 |
| 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 |
| ENST00000374466 | 43654162 | 43654379 | Frame-shift |
| ENST00000374466 | 43659313 | 43659492 | Frame-shift |
| ENST00000374466 | 43662451 | 43662546 | 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 |
| ENST00000374466 | 43654162 | 43654379 | Frame-shift |
| ENST00000374466 | 43659313 | 43659492 | Frame-shift |
| ENST00000374466 | 43662451 | 43662546 | Frame-shift |
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Infer the effects of exon skipping event on protein functional features for CSGALNACT2 |
| 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 CSGALNACT2 |
| - 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 |
| STAD | TCGA-D7-A4YY-01 | exon_skip_40961 | 43650345 | 43651258 | 43650701 | 43650701 | Frame_Shift_Del | C | - | p.A35fs |
| COAD | TCGA-G4-6588-01 | exon_skip_40968 | 43654163 | 43654379 | 43654207 | 43654207 | Frame_Shift_Del | T | - | p.L235fs |
| LIHC | TCGA-DD-A39Y-01 | exon_skip_40985 | 43659314 | 43659492 | 43659386 | 43659386 | Frame_Shift_Del | G | - | p.V351fs |
| UCEC | TCGA-BG-A0M3-01 | exon_skip_40961 | 43650345 | 43651258 | 43650700 | 43650701 | Frame_Shift_Ins | - | C | p.A35fs |
| UCEC | TCGA-BG-A0M9-01 | exon_skip_40961 | 43650345 | 43651258 | 43650700 | 43650701 | Frame_Shift_Ins | - | C | p.A35fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_40961 | 43650345 | 43651258 | 43650835 | 43650836 | Frame_Shift_Ins | - | C | p.P80fs |
| LIHC | TCGA-BC-A112-01 | exon_skip_40961 | 43650345 | 43651258 | 43650889 | 43650890 | Frame_Shift_Ins | - | A | p.K98fs |
| KIRC | TCGA-CZ-5984-01 | exon_skip_40968 | 43654163 | 43654379 | 43654206 | 43654207 | Frame_Shift_Ins | - | T | p.L235fs |
| KIRC | TCGA-CZ-5984-01 | exon_skip_40968 | 43654163 | 43654379 | 43654206 | 43654207 | Frame_Shift_Ins | - | T | p.LF235fs |
| LUAD | TCGA-44-7670-01 | exon_skip_40961 | 43650345 | 43651258 | 43651075 | 43651075 | Nonsense_Mutation | G | T | p.E160* |
| COAD | TCGA-AD-6964-01 | exon_skip_40961 | 43650345 | 43651258 | 43651126 | 43651126 | Nonsense_Mutation | C | T | p.R177X |
| CHOL | TCGA-W5-AA2X-01 | exon_skip_40985 | 43659314 | 43659492 | 43659315 | 43659315 | Nonsense_Mutation | G | T | p.E328X |
| CHOL | TCGA-W5-AA38-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| CHOL | TCGA-W5-AA39-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| LGG | TCGA-HT-8104-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| PCPG | TCGA-QR-A6GX-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| PCPG | TCGA-QR-A70V-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| TGCT | TCGA-2G-AAKG-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| TGCT | TCGA-2G-AALO-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| TGCT | TCGA-2G-AALT-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| UVM | TCGA-VD-A8KE-01 | exon_skip_40985 | 43659314 | 43659492 | 43659372 | 43659372 | Nonsense_Mutation | C | T | p.R347X |
| STAD | TCGA-HU-A4G8-01 | exon_skip_40985 | 43659314 | 43659492 | 43659393 | 43659393 | Nonsense_Mutation | C | T | p.R354* |
| STAD | TCGA-HU-A4G8-01 | exon_skip_40985 | 43659314 | 43659492 | 43659393 | 43659393 | Nonsense_Mutation | C | T | p.R354X |
| BLCA | TCGA-SY-A9G5-01 | exon_skip_40985 | 43659314 | 43659492 | 43659401 | 43659401 | Nonsense_Mutation | G | A | p.W356* |
| - 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 |
| SKUT1_SOFT_TISSUE | 43654163 | 43654379 | 43654207 | 43654207 | Frame_Shift_Del | T | - | p.F237fs |
| NCIH1563_LUNG | 43650345 | 43651258 | 43650605 | 43650605 | Missense_Mutation | G | T | p.R3I |
| CAL72_BONE | 43650345 | 43651258 | 43650639 | 43650639 | Missense_Mutation | G | T | p.W14C |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43650345 | 43651258 | 43650665 | 43650665 | Missense_Mutation | G | T | p.C23F |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 43650345 | 43651258 | 43650665 | 43650665 | Missense_Mutation | G | T | p.C23F |
| MFE319_ENDOMETRIUM | 43650345 | 43651258 | 43650698 | 43650698 | Missense_Mutation | G | A | p.C34Y |
| AU565_BREAST | 43650345 | 43651258 | 43650746 | 43650746 | Missense_Mutation | A | G | p.E50G |
| LS180_LARGE_INTESTINE | 43650345 | 43651258 | 43650746 | 43650746 | Missense_Mutation | A | G | p.E50G |
| HCT15_LARGE_INTESTINE | 43650345 | 43651258 | 43650770 | 43650770 | Missense_Mutation | A | G | p.Q58R |
| MDAMB361_BREAST | 43650345 | 43651258 | 43650790 | 43650790 | Missense_Mutation | G | A | p.E65K |
| EN_ENDOMETRIUM | 43650345 | 43651258 | 43650797 | 43650797 | Missense_Mutation | A | G | p.H67R |
| HEC251_ENDOMETRIUM | 43650345 | 43651258 | 43650799 | 43650799 | Missense_Mutation | T | G | p.Y68D |
| DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43650345 | 43651258 | 43650826 | 43650826 | Missense_Mutation | C | T | p.R77C |
| CGTHW1_THYROID | 43650345 | 43651258 | 43650862 | 43650862 | Missense_Mutation | A | T | p.M89L |
| RKO_LARGE_INTESTINE | 43650345 | 43651258 | 43650877 | 43650877 | Missense_Mutation | C | T | p.R94W |
| KYSE220_OESOPHAGUS | 43650345 | 43651258 | 43650892 | 43650892 | Missense_Mutation | A | G | p.R99G |
| HCC2814_LUNG | 43650345 | 43651258 | 43650911 | 43650911 | Missense_Mutation | A | C | p.N105T |
| TYKNU_OVARY | 43650345 | 43651258 | 43650954 | 43650954 | Missense_Mutation | T | A | p.D119E |
| HEC50B_ENDOMETRIUM | 43650345 | 43651258 | 43651021 | 43651022 | Missense_Mutation | GA | AG | p.E142R |
| HEC50B_ENDOMETRIUM | 43650345 | 43651258 | 43651021 | 43651021 | Missense_Mutation | G | A | p.E142K |
| HEC50B_ENDOMETRIUM | 43650345 | 43651258 | 43651022 | 43651022 | Missense_Mutation | A | G | p.E142G |
| HCT15_LARGE_INTESTINE | 43650345 | 43651258 | 43651024 | 43651024 | Missense_Mutation | T | C | p.Y143H |
| M980513_SKIN | 43650345 | 43651258 | 43651036 | 43651036 | Missense_Mutation | C | T | p.P147S |
| MFE319_ENDOMETRIUM | 43650345 | 43651258 | 43651163 | 43651163 | Missense_Mutation | A | G | p.E189G |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 43650345 | 43651258 | 43651193 | 43651193 | Missense_Mutation | A | C | p.E199A |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43650345 | 43651258 | 43651193 | 43651193 | Missense_Mutation | A | C | p.E199A |
| SNU1040_LARGE_INTESTINE | 43654163 | 43654379 | 43654172 | 43654172 | Missense_Mutation | G | A | p.R224H |
| SBC1_LUNG | 43654163 | 43654379 | 43654188 | 43654188 | Missense_Mutation | G | T | p.K229N |
| SNU1040_LARGE_INTESTINE | 43654163 | 43654379 | 43654337 | 43654337 | Missense_Mutation | C | A | p.A279D |
| SNU81_LARGE_INTESTINE | 43654163 | 43654379 | 43654364 | 43654364 | Missense_Mutation | T | G | p.F288C |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 43659314 | 43659492 | 43659321 | 43659321 | Missense_Mutation | A | G | p.N330D |
| DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 43659314 | 43659492 | 43659351 | 43659351 | Missense_Mutation | A | G | p.N340D |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 43659314 | 43659492 | 43659351 | 43659351 | Missense_Mutation | A | G | p.N340D |
| SNU175_LARGE_INTESTINE | 43659314 | 43659492 | 43659367 | 43659367 | Missense_Mutation | G | A | p.R345H |
| HT115_LARGE_INTESTINE | 43659314 | 43659492 | 43659449 | 43659449 | Missense_Mutation | C | A | p.F372L |
| NCIH630_LARGE_INTESTINE | 43659314 | 43659492 | 43659469 | 43659469 | Missense_Mutation | G | T | p.S379I |
| MFE296_ENDOMETRIUM | 43662452 | 43662546 | 43662463 | 43662463 | Missense_Mutation | T | G | p.F391V |
| SNU1040_LARGE_INTESTINE | 43662452 | 43662546 | 43662497 | 43662497 | Missense_Mutation | C | T | p.A402V |
| RKO_LARGE_INTESTINE | 43662452 | 43662546 | 43662542 | 43662542 | Missense_Mutation | A | G | p.Q417R |
| LS411N_LARGE_INTESTINE | 43650345 | 43651258 | 43651126 | 43651126 | Nonsense_Mutation | C | T | p.R177* |
| BICR18_UPPER_AERODIGESTIVE_TRACT | 43654163 | 43654379 | 43654164 | 43654164 | Splice_Site | T | C | p.G221G |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CSGALNACT2 |
| 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 CSGALNACT2 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CSGALNACT2 |
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RelatedDrugs for CSGALNACT2 |
| 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 CSGALNACT2 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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