|
||||||
|
 | |
| |
| |
| |
| 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 CCDC62 |
 Gene summary |
| Gene information | Gene symbol | CCDC62 | Gene ID | 84660 |
| Gene name | coiled-coil domain containing 62 | |
| Synonyms | CT109|ERAP75|TSP-NY | |
| Cytomap | 12q24.31 | |
| Type of gene | protein-coding | |
| Description | coiled-coil domain-containing protein 62aaa-proteincancer/testis antigen 109coiled-coil domain-containing protein 60testis-specific protein TSP-NY | |
| Modification date | 20180402 | |
| UniProtAcc | Q6P9F0 | |
| Context | PubMed: CCDC62 [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 |
| CCDC62 | GO:0045944 | positive regulation of transcription by RNA polymerase II | 19126643 |
| CCDC62 | GO:0071392 | cellular response to estradiol stimulus | 18563714|19126643 |
Top |
Exon skipping events across known transcript of Ensembl for CCDC62 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 CCDC62 |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CCDC62 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_88138 | 12 | 123262037:123262230:123265710:123265877:123270265:123270367 | 123265710:123265877 | ENSG00000130783.9 | ENST00000392441.4,ENST00000341952.4,ENST00000253079.6 |
| exon_skip_88139 | 12 | 123265710:123265877:123270265:123270367:123273304:123273358 | 123270265:123270367 | ENSG00000130783.9 | ENST00000392441.4,ENST00000341952.4,ENST00000253079.6 |
| exon_skip_88141 | 12 | 123281853:123281942:123282631:123282747:123285670:123286399 | 123282631:123282747 | ENSG00000130783.9 | ENST00000392441.4,ENST00000341952.4,ENST00000392440.2,ENST00000537566.1,ENST00000253079.6 |
| exon_skip_88142 | 12 | 123290697:123290842:123297816:123297966:123310968:123311164 | 123297816:123297966 | ENSG00000130783.9 | ENST00000392441.4,ENST00000341952.4 |
| exon_skip_88144 | 12 | 123297816:123297966:123307912:123308006:123310968:123311164 | 123307912:123308006 | ENSG00000130783.9 | ENST00000392440.2,ENST00000537566.1,ENST00000253079.6 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CCDC62 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_88138 | 12 | 123262037:123262230:123265710:123265877:123270265:123270367 | 123265710:123265877 | ENSG00000130783.9 | ENST00000253079.6,ENST00000392441.4,ENST00000341952.4 |
| exon_skip_88139 | 12 | 123265710:123265877:123270265:123270367:123273304:123273358 | 123270265:123270367 | ENSG00000130783.9 | ENST00000253079.6,ENST00000392441.4,ENST00000341952.4 |
| exon_skip_88141 | 12 | 123281853:123281942:123282631:123282747:123285670:123286399 | 123282631:123282747 | ENSG00000130783.9 | ENST00000253079.6,ENST00000392441.4,ENST00000341952.4,ENST00000537566.1,ENST00000392440.2 |
| exon_skip_88142 | 12 | 123290697:123290842:123297816:123297966:123310968:123311164 | 123297816:123297966 | ENSG00000130783.9 | ENST00000392441.4,ENST00000341952.4 |
| exon_skip_88144 | 12 | 123297816:123297966:123307912:123308006:123310968:123311164 | 123307912:123308006 | ENSG00000130783.9 | ENST00000253079.6,ENST00000537566.1,ENST00000392440.2 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CCDC62 |
| 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 |
| ENST00000253079 | 123307912 | 123308006 | 3UTR-3CDS |
| ENST00000253079 | 123265710 | 123265877 | Frame-shift |
| ENST00000253079 | 123282631 | 123282747 | Frame-shift |
| ENST00000253079 | 123270265 | 123270367 | 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 |
| ENST00000253079 | 123307912 | 123308006 | 3UTR-3CDS |
| ENST00000253079 | 123265710 | 123265877 | Frame-shift |
| ENST00000253079 | 123282631 | 123282747 | Frame-shift |
| ENST00000253079 | 123270265 | 123270367 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CCDC62 |
| 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 |
| ENST00000253079 | 3563 | 684 | 123270265 | 123270367 | 741 | 842 | 132 | 166 |
| 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 |
| ENST00000253079 | 3563 | 684 | 123270265 | 123270367 | 741 | 842 | 132 | 166 |
| 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 |
| Q6P9F0 | 132 | 166 | 1 | 239 | Alternative sequence | ID=VSP_019327;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q6P9F0 | 132 | 166 | 1 | 684 | Chain | ID=PRO_0000240247;Note=Coiled-coil domain-containing protein 62 |
| Q6P9F0 | 132 | 166 | 11 | 160 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q6P9F0 | 132 | 166 | 141 | 141 | Natural variant | ID=VAR_061585;Note=T->M;Dbxref=dbSNP:rs58131754 |
| 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 |
| Q6P9F0 | 132 | 166 | 1 | 239 | Alternative sequence | ID=VSP_019327;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| Q6P9F0 | 132 | 166 | 1 | 684 | Chain | ID=PRO_0000240247;Note=Coiled-coil domain-containing protein 62 |
| Q6P9F0 | 132 | 166 | 11 | 160 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q6P9F0 | 132 | 166 | 141 | 141 | Natural variant | ID=VAR_061585;Note=T->M;Dbxref=dbSNP:rs58131754 |
Top |
SNVs in the skipped exons for CCDC62 |
| - 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 |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_88141 | 123282632 | 123282747 | 123282640 | 123282640 | Frame_Shift_Del | A | - | p.V290fs |
| STAD | TCGA-BR-4201-01 | exon_skip_88144 | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| STAD | TCGA-CG-5726-01 | exon_skip_88144 | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| UCEC | TCGA-A5-A0GB-01 | exon_skip_88144 | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| UCEC | TCGA-D1-A101-01 | exon_skip_88144 | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| BLCA | TCGA-GU-A42P-01 | exon_skip_88139 | 123270266 | 123270367 | 123270332 | 123270332 | Nonsense_Mutation | C | T | p.R155* |
| COAD | TCGA-D5-6534-01 | exon_skip_88138 | 123265711 | 123265877 | 123265710 | 123265710 | Splice_Site | G | C | . |
| SKCM | TCGA-FR-A3YO-06 | exon_skip_88138 | 123265711 | 123265877 | 123265710 | 123265710 | Splice_Site | G | A | . |
| ESCA | TCGA-LN-A4A5-01 | exon_skip_88141 | 123282632 | 123282747 | 123282748 | 123282748 | Splice_Site | G | T | . |
| ESCA | TCGA-LN-A4A5-01 | exon_skip_88141 | 123282632 | 123282747 | 123282748 | 123282748 | Splice_Site | G | T | e8+1 |
| - 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 |
| HEC6_ENDOMETRIUM | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| MDAPCA2B_PROSTATE | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| EFO27_OVARY | 123307913 | 123308006 | 123307941 | 123307941 | Frame_Shift_Del | A | - | p.Q677fs |
| JHUEM7_ENDOMETRIUM | 123265711 | 123265877 | 123265726 | 123265726 | Missense_Mutation | G | T | p.R82I |
| LS411N_LARGE_INTESTINE | 123265711 | 123265877 | 123265726 | 123265726 | Missense_Mutation | G | A | p.R82K |
| KMBC2_URINARY_TRACT | 123270266 | 123270367 | 123270281 | 123270281 | Missense_Mutation | C | G | p.L138V |
| DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 123282632 | 123282747 | 123282653 | 123282653 | Missense_Mutation | G | T | p.D295Y |
| NY_BONE | 123282632 | 123282747 | 123282681 | 123282681 | Missense_Mutation | A | C | p.E304A |
| HT115_LARGE_INTESTINE | 123282632 | 123282747 | 123282735 | 123282735 | Missense_Mutation | C | A | p.A322D |
| SISO_CERVIX | 123282632 | 123282747 | 123282744 | 123282744 | Missense_Mutation | C | A | p.S325Y |
| SKUT1_SOFT_TISSUE | 123297817 | 123297966 | 123297871 | 123297871 | Missense_Mutation | C | T | p.R636C |
| RERFGC1B_STOMACH | 123297817 | 123297966 | 123297881 | 123297881 | Missense_Mutation | C | T | p.A639V |
| HKA1_SKIN | 123307913 | 123308006 | 123307922 | 123307922 | Missense_Mutation | G | T | p.V671F |
| MZ2MEL_SKIN | 123307913 | 123308006 | 123307925 | 123307925 | Missense_Mutation | C | T | p.P672S |
| JHUEM7_ENDOMETRIUM | 123270266 | 123270367 | 123270335 | 123270335 | Nonsense_Mutation | G | T | p.E156* |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CCDC62 |
| 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 CCDC62 |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CCDC62 |
Top |
RelatedDrugs for CCDC62 |
| 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 CCDC62 |
| 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)
|