|
||||||
|
 | |
| |
| |
| |
| 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 CLEC2D |
 Gene summary |
| Gene information | Gene symbol | CLEC2D | Gene ID | 29121 |
| Gene name | C-type lectin domain family 2 member D | |
| Synonyms | CLAX|LLT1|OCIL | |
| Cytomap | 12p13.31 | |
| Type of gene | protein-coding | |
| Description | C-type lectin domain family 2 member DC-type lectin related fC-type lectin superfamily 2, member DLLT-1lectin-like NK cell receptorlectin-like transcript 1osteoclast inhibitory lectin | |
| Modification date | 20180519 | |
| UniProtAcc | Q9UHP7 | |
| Context | PubMed: CLEC2D [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 |
Top |
Exon skipping events across known transcript of Ensembl for CLEC2D 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 CLEC2D |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for CLEC2D |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_80130 | 12 | 9822348:9822391:9832785:9832847:9833518:9833629 | 9832785:9832847 | ENSG00000069493.10 | ENST00000492359.2 |
| exon_skip_80133 | 12 | 9822348:9822391:9833518:9833629:9840497:9840682 | 9833518:9833629 | ENSG00000069493.10 | ENST00000479877.1,ENST00000444971.2,ENST00000261340.7,ENST00000325960.7,ENST00000290855.6,ENST00000543300.1 |
| exon_skip_80137 | 12 | 9840497:9840682:9845423:9845527:9847355:9847397 | 9845423:9845527 | ENSG00000069493.10 | ENST00000261339.6,ENST00000290855.6 |
| exon_skip_80140 | 12 | 9840497:9840682:9845423:9846544:9847355:9847397 | 9845423:9846544 | ENSG00000069493.10 | ENST00000479877.1 |
| exon_skip_80157 | 12 | 9845423:9845527:9845629:9845711:9847355:9847397 | 9845629:9845711 | ENSG00000069493.10 | ENST00000261340.7,ENST00000430909.1 |
| exon_skip_80163 | 12 | 9845423:9845527:9846420:9846544:9847355:9847397 | 9846420:9846544 | ENSG00000069493.10 | ENST00000460309.1 |
| exon_skip_80167 | 12 | 9845629:9845711:9846011:9846544:9847355:9847397 | 9846011:9846544 | ENSG00000069493.10 | ENST00000325960.7 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for CLEC2D |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_80130 | 12 | 9822348:9822391:9832785:9832847:9833518:9833629 | 9832785:9832847 | ENSG00000069493.10 | ENST00000492359.2 |
| exon_skip_80133 | 12 | 9822348:9822391:9833518:9833629:9840497:9840682 | 9833518:9833629 | ENSG00000069493.10 | ENST00000261340.7,ENST00000290855.6,ENST00000325960.7,ENST00000444971.2,ENST00000479877.1,ENST00000543300.1 |
| exon_skip_80137 | 12 | 9840497:9840682:9845423:9845527:9847355:9847397 | 9845423:9845527 | ENSG00000069493.10 | ENST00000290855.6,ENST00000261339.6 |
| exon_skip_80140 | 12 | 9840497:9840682:9845423:9846544:9847355:9847397 | 9845423:9846544 | ENSG00000069493.10 | ENST00000479877.1 |
| exon_skip_80157 | 12 | 9845423:9845527:9845629:9845711:9847355:9847397 | 9845629:9845711 | ENSG00000069493.10 | ENST00000261340.7,ENST00000430909.1 |
| exon_skip_80163 | 12 | 9845423:9845527:9846420:9846544:9847355:9847397 | 9846420:9846544 | ENSG00000069493.10 | ENST00000460309.1 |
| exon_skip_80167 | 12 | 9845629:9845711:9846011:9846544:9847355:9847397 | 9846011:9846544 | ENSG00000069493.10 | ENST00000325960.7 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for CLEC2D |
| 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 |
| ENST00000290855 | 9845423 | 9845527 | Frame-shift |
| ENST00000290855 | 9833518 | 9833629 | 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 |
| ENST00000290855 | 9845423 | 9845527 | Frame-shift |
| ENST00000290855 | 9833518 | 9833629 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for CLEC2D |
| 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 |
| ENST00000290855 | 876 | 191 | 9833518 | 9833629 | 84 | 194 | 20 | 57 |
| 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 |
| ENST00000290855 | 876 | 191 | 9833518 | 9833629 | 84 | 194 | 20 | 57 |
| 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 |
| Q9UHP7 | 20 | 57 | 21 | 57 | Alternative sequence | ID=VSP_039676;Note=In isoform 5 and isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:20843815;Dbxref=PMID:20843815 |
| Q9UHP7 | 20 | 57 | 1 | 191 | Chain | ID=PRO_0000315285;Note=C-type lectin domain family 2 member D |
| Q9UHP7 | 20 | 57 | 23 | 23 | Natural variant | ID=VAR_038173;Note=L->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:20843815;Dbxref=dbSNP:rs3764022,PMID:15489334,PMID:20843815 |
| Q9UHP7 | 20 | 57 | 1 | 38 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UHP7 | 20 | 57 | 39 | 59 | Transmembrane | Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| 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 |
| Q9UHP7 | 20 | 57 | 21 | 57 | Alternative sequence | ID=VSP_039676;Note=In isoform 5 and isoform 6. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:20843815;Dbxref=PMID:20843815 |
| Q9UHP7 | 20 | 57 | 1 | 191 | Chain | ID=PRO_0000315285;Note=C-type lectin domain family 2 member D |
| Q9UHP7 | 20 | 57 | 23 | 23 | Natural variant | ID=VAR_038173;Note=L->V;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:15489334,ECO:0000269|PubMed:20843815;Dbxref=dbSNP:rs3764022,PMID:15489334,PMID:20843815 |
| Q9UHP7 | 20 | 57 | 1 | 38 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q9UHP7 | 20 | 57 | 39 | 59 | Transmembrane | Note=Helical%3B Signal-anchor for type II membrane protein;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for CLEC2D |
| - 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 |
| HNSC | TCGA-T2-A6X2-01 | exon_skip_80140 | 9845424 | 9846544 | 9845688 | 9845688 | Nonsense_Mutation | C | T | p.R174* |
| HNSC | TCGA-T2-A6X2-01 | exon_skip_80157 | 9845630 | 9845711 | 9845688 | 9845688 | Nonsense_Mutation | C | T | p.R174* |
| - 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 |
| HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 9833519 | 9833629 | 9833537 | 9833537 | Missense_Mutation | A | G | p.E27G |
| 786O_KIDNEY | 9833519 | 9833629 | 9833567 | 9833567 | Missense_Mutation | G | A | p.R37H |
| FARAGE_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 9833519 | 9833629 | 9833627 | 9833627 | Missense_Mutation | G | A | p.S57N |
| D341MED_CENTRAL_NERVOUS_SYSTEM | 9845424 | 9845527 | 9845485 | 9845485 | Missense_Mutation | G | A | p.G140D |
| D341MED_CENTRAL_NERVOUS_SYSTEM | 9845424 | 9846544 | 9845485 | 9845485 | Missense_Mutation | G | A | p.G140D |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for CLEC2D |
| 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 |
| exon_skip_80133 | 12 | 9822348:9822391:9833518:9833629:9840497:9840682 | 9833518:9833629 | ENST00000479877.1,ENST00000444971.2,ENST00000261340.7,ENST00000325960.7,ENST00000290855.6,ENST00000543300.1 | THYM | rs3764022 | chr12:9833524 | C/G | 8.85e-05 |
| exon_skip_80133 | 12 | 9822348:9822391:9833518:9833629:9840497:9840682 | 9833518:9833629 | ENST00000479877.1,ENST00000444971.2,ENST00000261340.7,ENST00000325960.7,ENST00000290855.6,ENST00000543300.1 | THYM | rs3764021 | chr12:9833628 | C/T | 1.15e-04 |
| exon_skip_80140 | 12 | 9840497:9840682:9845423:9846544:9847355:9847397 | 9845423:9846544 | ENST00000479877.1 | THYM | rs7968401 | chr12:9846521 | C/G | 3.74e-04 |
| exon_skip_80163 | 12 | 9845423:9845527:9846420:9846544:9847355:9847397 | 9846420:9846544 | ENST00000460309.1 | THYM | rs7968401 | chr12:9846521 | C/G | 3.74e-04 |
| exon_skip_80167 | 12 | 9845629:9845711:9846011:9846544:9847355:9847397 | 9846011:9846544 | ENST00000325960.7 | THYM | rs7968401 | chr12:9846521 | C/G | 3.74e-04 |
Top |
Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLEC2D |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for CLEC2D |
Top |
RelatedDrugs for CLEC2D |
| 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 CLEC2D |
| 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)
|