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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 GCSAM |
 Gene summary |
| Gene information | Gene symbol | GCSAM | Gene ID | 257144 |
| Gene name | germinal center associated signaling and motility | |
| Synonyms | GCAT2|GCET2|HGAL | |
| Cytomap | 3q13.2 | |
| Type of gene | protein-coding | |
| Description | germinal center-associated signaling and motility proteingerminal center B-cell-expressed transcript 2 proteingerminal center expressed transcript 2germinal center-associated lymphoma proteinhuman germinal center-associated lymphoma | |
| Modification date | 20180519 | |
| UniProtAcc | Q8N6F7 | |
| Context | PubMed: GCSAM [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 GCSAM 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 GCSAM |
| 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 GCSAM |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_386471 | 3 | 111842453:111842619:111844072:111844101:111845833:111845880 | 111844072:111844101 | ENSG00000174500.8 | ENST00000487901.1,ENST00000460387.2,ENST00000470085.1,ENST00000488580.1,ENST00000484193.1,ENST00000308910.4 |
| exon_skip_386473 | 3 | 111845833:111845880:111846863:111846908:111849291:111849360 | 111846863:111846908 | ENSG00000174500.8 | ENST00000487901.1,ENST00000488580.1,ENST00000484193.1,ENST00000308910.4 |
| exon_skip_386475 | 3 | 111845833:111845880:111846863:111847075:111849291:111849360 | 111846863:111847075 | ENSG00000174500.8 | ENST00000470085.1,ENST00000495418.1 |
| exon_skip_386477 | 3 | 111846863:111846908:111849291:111849366:111851938:111852013 | 111849291:111849366 | ENSG00000174500.8 | ENST00000484193.1 |
| exon_skip_386479 | 3 | 111846863:111847075:111849291:111849360:111851938:111852013 | 111849291:111849360 | ENSG00000174500.8 | ENST00000470085.1,ENST00000495418.1 |
| exon_skip_386482 | 3 | 111849291:111849360:111851483:111851757:111851938:111852013 | 111851483:111851757 | ENSG00000174500.8 | ENST00000487901.1 |
| exon_skip_386483 | 3 | 111849291:111849366:111851483:111851757:111851938:111852013 | 111851483:111851757 | ENSG00000174500.8 | ENST00000488580.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for GCSAM |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_386471 | 3 | 111842453:111842619:111844072:111844101:111845833:111845880 | 111844072:111844101 | ENSG00000174500.8 | ENST00000308910.4,ENST00000484193.1,ENST00000470085.1,ENST00000460387.2,ENST00000488580.1,ENST00000487901.1 |
| exon_skip_386473 | 3 | 111845833:111845880:111846863:111846908:111849291:111849360 | 111846863:111846908 | ENSG00000174500.8 | ENST00000308910.4,ENST00000484193.1,ENST00000488580.1,ENST00000487901.1 |
| exon_skip_386475 | 3 | 111845833:111845880:111846863:111847075:111849291:111849360 | 111846863:111847075 | ENSG00000174500.8 | ENST00000470085.1,ENST00000495418.1 |
| exon_skip_386477 | 3 | 111846863:111846908:111849291:111849366:111851938:111852013 | 111849291:111849366 | ENSG00000174500.8 | ENST00000484193.1 |
| exon_skip_386479 | 3 | 111846863:111847075:111849291:111849360:111851938:111852013 | 111849291:111849360 | ENSG00000174500.8 | ENST00000470085.1,ENST00000495418.1 |
| exon_skip_386482 | 3 | 111849291:111849360:111851483:111851757:111851938:111852013 | 111851483:111851757 | ENSG00000174500.8 | ENST00000487901.1 |
| exon_skip_386483 | 3 | 111849291:111849366:111851483:111851757:111851938:111852013 | 111851483:111851757 | ENSG00000174500.8 | ENST00000488580.1 |
| 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 GCSAM |
| 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 GCSAM |
| 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 GCSAM |
| - 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. |
GCSAM_DLBC_exon_skip_386471_psi_boxplot.png |
| - 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 |
| KIRP | TCGA-Y8-A8RZ-01 | exon_skip_386479 | 111849292 | 111849360 | 111849299 | 111849306 | Frame_Shift_Del | TTCTCTGT | - | p.31_33del |
| KIRP | TCGA-Y8-A8RZ-01 | exon_skip_386477 | 111849292 | 111849366 | 111849299 | 111849306 | Frame_Shift_Del | TTCTCTGT | - | p.31_33del |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_386479 | 111849292 | 111849360 | 111849332 | 111849332 | Frame_Shift_Del | A | - | p.W20fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_386477 | 111849292 | 111849366 | 111849332 | 111849332 | Frame_Shift_Del | A | - | p.W20fs |
| DLBC | TCGA-G8-6909-01 | exon_skip_386471 | 111844073 | 111844101 | 111844089 | 111844089 | Nonsense_Mutation | G | T | p.S70X |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-G8-6909-01 |
| Cancer type: DLBC | |
| ESID: exon_skip_386471 | |
| Skipped exon start: 111844073 | |
| Skipped exon end: 111844101 | |
| Mutation start: 111844089 | |
| Mutation end: 111844089 | |
| Mutation type: Nonsense_Mutation | |
| Reference seq: G | |
| Mutation seq: T | |
| AAchange: p.S70X | |
exon_skip_386471_DLBC_TCGA-G8-6909-01.png | |
| - 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 |
| HCC2450_LUNG | 111844073 | 111844101 | 111844086 | 111844086 | Missense_Mutation | G | C | p.S69C |
| F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 111846864 | 111847075 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 111846864 | 111846908 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| T3M10_LUNG | 111846864 | 111847075 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| T3M10_LUNG | 111846864 | 111846908 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| LU134A_LUNG | 111846864 | 111847075 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| LU134A_LUNG | 111846864 | 111846908 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| HCET_UPPER_AERODIGESTIVE_TRACT | 111846864 | 111847075 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| HCET_UPPER_AERODIGESTIVE_TRACT | 111846864 | 111846908 | 111846879 | 111846879 | Missense_Mutation | C | T | p.C43Y |
| OC316_OVARY | 111846864 | 111847075 | 111846902 | 111846902 | Missense_Mutation | C | A | p.W35C |
| OC316_OVARY | 111846864 | 111846908 | 111846902 | 111846902 | Missense_Mutation | C | A | p.W35C |
| OC314_OVARY | 111846864 | 111847075 | 111846902 | 111846902 | Missense_Mutation | C | A | p.W35C |
| OC314_OVARY | 111846864 | 111846908 | 111846902 | 111846902 | Missense_Mutation | C | A | p.W35C |
| NCIH2126_LUNG | 111849292 | 111849360 | 111849303 | 111849303 | Missense_Mutation | C | A | p.Q29H |
| NCIH2126_LUNG | 111849292 | 111849366 | 111849303 | 111849303 | Missense_Mutation | C | A | p.Q29H |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for GCSAM |
| 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 GCSAM |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for GCSAM |
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RelatedDrugs for GCSAM |
| 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 GCSAM |
| 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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