|
||||||
|
 | |
| |
| |
| |
| 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 LRRC37B |
 Gene summary |
| Gene information | Gene symbol | LRRC37B | Gene ID | 114659 |
| Gene name | leucine rich repeat containing 37B | |
| Synonyms | LRRC37 | |
| Cytomap | 17q11.2 | |
| Type of gene | protein-coding | |
| Description | leucine-rich repeat-containing protein 37BC66 SLIT-like testicular protein | |
| Modification date | 20180519 | |
| UniProtAcc | Q96QE4 | |
| Context | PubMed: LRRC37B [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 LRRC37B 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 LRRC37B |
| Expression levels of gene isoforms across TCGA. |
 |
| Expression levels of gene isoforms across GTEx. |
 |
Top |
Exon skipping events with PSIs in TCGA for LRRC37B |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_150735 | 17 | 30335054:30335151:30344990:30345073:30347715:30347822 | 30344990:30345073 | ENSG00000185158.8 | ENST00000543378.2 |
| exon_skip_150737 | 17 | 30335054:30335151:30347715:30347822:30348411:30348875 | 30347715:30347822 | ENSG00000185158.8 | ENST00000579206.1 |
| exon_skip_150740 | 17 | 30351754:30351801:30354787:30354859:30357674:30357746 | 30354787:30354859 | ENSG00000185158.8 | ENST00000327564.7,ENST00000580871.1,ENST00000341671.7,ENST00000543378.2,ENST00000578674.1,ENST00000583204.1 |
| exon_skip_150741 | 17 | 30351754:30351801:30354787:30354859:30361928:30362000 | 30354787:30354859 | ENSG00000185158.8 | ENST00000394713.3,ENST00000584368.1 |
| exon_skip_150743 | 17 | 30361928:30362000:30362583:30362658:30372718:30372837 | 30362583:30362658 | ENSG00000185158.8 | ENST00000583758.1,ENST00000327564.7,ENST00000341671.7,ENST00000582815.1,ENST00000543378.2,ENST00000394713.3,ENST00000584368.1 |
| exon_skip_150747 | 17 | 30362585:30362658:30372718:30372837:30374779:30374920 | 30372718:30372837 | ENSG00000185158.8 | ENST00000583758.1,ENST00000327564.7,ENST00000341671.7,ENST00000582815.1,ENST00000543378.2,ENST00000394713.3,ENST00000584368.1 |
| exon_skip_150748 | 17 | 30376120:30376413:30377021:30377126:30380284:30380370 | 30377021:30377126 | ENSG00000185158.8 | ENST00000327564.7,ENST00000341671.7,ENST00000543378.2,ENST00000579094.1,ENST00000578674.1,ENST00000394713.3,ENST00000584368.1 |
| PSI values of skipped exons in TCGA. |
 |
Top |
Exon skipping events with PSIs in GTEx for LRRC37B |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_150735 | 17 | 30335054:30335151:30344990:30345073:30347715:30347822 | 30344990:30345073 | ENSG00000185158.8 | ENST00000543378.2 |
| exon_skip_150737 | 17 | 30335054:30335151:30347715:30347822:30348411:30348875 | 30347715:30347822 | ENSG00000185158.8 | ENST00000579206.1 |
| exon_skip_150740 | 17 | 30351754:30351801:30354787:30354859:30357674:30357746 | 30354787:30354859 | ENSG00000185158.8 | ENST00000543378.2,ENST00000327564.7,ENST00000578674.1,ENST00000583204.1,ENST00000341671.7,ENST00000580871.1 |
| exon_skip_150741 | 17 | 30351754:30351801:30354787:30354859:30361928:30362000 | 30354787:30354859 | ENSG00000185158.8 | ENST00000584368.1,ENST00000394713.3 |
| exon_skip_150742 | 17 | 30358396:30358477:30360995:30361084:30361928:30362000 | 30360995:30361084 | ENSG00000185158.8 | ENST00000583204.1 |
| exon_skip_150747 | 17 | 30362585:30362658:30372718:30372837:30374779:30374920 | 30372718:30372837 | ENSG00000185158.8 | ENST00000543378.2,ENST00000327564.7,ENST00000584368.1,ENST00000394713.3,ENST00000341671.7,ENST00000582815.1,ENST00000583758.1 |
| exon_skip_150748 | 17 | 30376120:30376413:30377021:30377126:30380284:30380370 | 30377021:30377126 | ENSG00000185158.8 | ENST00000543378.2,ENST00000327564.7,ENST00000584368.1,ENST00000578674.1,ENST00000394713.3,ENST00000341671.7,ENST00000579094.1 |
| PSI values of skipped exons in GTEx. |
 |
| * Skipped exon sequences. |
Top |
Open reading frame (ORF) annotation in the exon skipping event for LRRC37B |
| 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 |
| ENST00000341671 | 30372718 | 30372837 | Frame-shift |
| ENST00000394713 | 30372718 | 30372837 | Frame-shift |
| ENST00000341671 | 30354787 | 30354859 | In-frame |
| ENST00000394713 | 30354787 | 30354859 | In-frame |
| ENST00000341671 | 30362583 | 30362658 | In-frame |
| ENST00000394713 | 30362583 | 30362658 | In-frame |
| ENST00000341671 | 30377021 | 30377126 | In-frame |
| ENST00000394713 | 30377021 | 30377126 | 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 |
| ENST00000341671 | 30372718 | 30372837 | Frame-shift |
| ENST00000394713 | 30372718 | 30372837 | Frame-shift |
| ENST00000341671 | 30354787 | 30354859 | In-frame |
| ENST00000394713 | 30354787 | 30354859 | In-frame |
| ENST00000341671 | 30377021 | 30377126 | In-frame |
| ENST00000394713 | 30377021 | 30377126 | In-frame |
Top |
Infer the effects of exon skipping event on protein functional features for LRRC37B |
| 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 |
| ENST00000341671 | 3042 | 947 | 30354787 | 30354859 | 1757 | 1828 | 584 | 607 |
| ENST00000394713 | 2781 | 947 | 30354787 | 30354859 | 1802 | 1873 | 584 | 607 |
| ENST00000394713 | 2781 | 947 | 30362583 | 30362658 | 1946 | 2020 | 632 | 656 |
| ENST00000341671 | 3042 | 947 | 30362583 | 30362658 | 2054 | 2128 | 683 | 707 |
| ENST00000394713 | 2781 | 947 | 30377021 | 30377126 | 2574 | 2678 | 841 | 876 |
| ENST00000341671 | 3042 | 947 | 30377021 | 30377126 | 2682 | 2786 | 892 | 927 |
| 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 |
| ENST00000341671 | 3042 | 947 | 30354787 | 30354859 | 1757 | 1828 | 584 | 607 |
| ENST00000394713 | 2781 | 947 | 30354787 | 30354859 | 1802 | 1873 | 584 | 607 |
| ENST00000394713 | 2781 | 947 | 30377021 | 30377126 | 2574 | 2678 | 841 | 876 |
| ENST00000341671 | 3042 | 947 | 30377021 | 30377126 | 2682 | 2786 | 892 | 927 |
| 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 |
| Q96QE4 | 584 | 607 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 584 | 607 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 584 | 607 | 580 | 601 | Repeat | Note=LRR 2 |
| Q96QE4 | 584 | 607 | 580 | 601 | Repeat | Note=LRR 2 |
| Q96QE4 | 584 | 607 | 604 | 625 | Repeat | Note=LRR 3 |
| Q96QE4 | 584 | 607 | 604 | 625 | Repeat | Note=LRR 3 |
| Q96QE4 | 584 | 607 | 604 | 604 | Sequence conflict | Note=Y->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 584 | 607 | 604 | 604 | Sequence conflict | Note=Y->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 584 | 607 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 584 | 607 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 632 | 656 | 608 | 658 | Alternative sequence | ID=VSP_054513;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15489334;Dbxref=PMID:15489334 |
| Q96QE4 | 632 | 656 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 632 | 656 | 628 | 649 | Repeat | Note=LRR 4 |
| Q96QE4 | 632 | 656 | 655 | 676 | Repeat | Note=LRR 5 |
| Q96QE4 | 632 | 656 | 641 | 641 | Sequence conflict | Note=K->E;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 632 | 656 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 683 | 707 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 683 | 707 | 679 | 699 | Repeat | Note=LRR 6 |
| Q96QE4 | 683 | 707 | 702 | 702 | Sequence conflict | Note=T->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 683 | 707 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 841 | 876 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 841 | 876 | 867 | 897 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 841 | 876 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 892 | 927 | 867 | 897 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 927 | 947 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 906 | 926 | Transmembrane | Note=Helical;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 |
| Q96QE4 | 584 | 607 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 584 | 607 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 584 | 607 | 580 | 601 | Repeat | Note=LRR 2 |
| Q96QE4 | 584 | 607 | 580 | 601 | Repeat | Note=LRR 2 |
| Q96QE4 | 584 | 607 | 604 | 625 | Repeat | Note=LRR 3 |
| Q96QE4 | 584 | 607 | 604 | 625 | Repeat | Note=LRR 3 |
| Q96QE4 | 584 | 607 | 604 | 604 | Sequence conflict | Note=Y->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 584 | 607 | 604 | 604 | Sequence conflict | Note=Y->S;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| Q96QE4 | 584 | 607 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 584 | 607 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 841 | 876 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 841 | 876 | 867 | 897 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 841 | 876 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 28 | 947 | Chain | ID=PRO_0000232653;Note=Leucine-rich repeat-containing protein 37B |
| Q96QE4 | 892 | 927 | 867 | 897 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 28 | 905 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 927 | 947 | Topological domain | Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q96QE4 | 892 | 927 | 906 | 926 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
Top |
SNVs in the skipped exons for LRRC37B |
| - 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. |
LRRC37B_TGCT_exon_skip_150743_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 |
| TGCT | TCGA-YU-A912-01 | exon_skip_150743 | 30362584 | 30362658 | 30362658 | 30362659 | Frame_Shift_Del | TG | - | p.708_708del |
| UCEC | TCGA-AP-A0LI-01 | exon_skip_150743 | 30362584 | 30362658 | 30362658 | 30362659 | Frame_Shift_Del | TG | - | p.L708fs |
| UCEC | TCGA-AP-A056-01 | exon_skip_150740 exon_skip_150741 | 30354788 | 30354859 | 30354829 | 30354829 | Nonsense_Mutation | C | A | p.S598* |
| UCEC | TCGA-AP-A0LI-01 | exon_skip_150743 | 30362584 | 30362658 | 30362658 | 30362659 | Splice_Site | TG | - | p.L708_splice |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-YU-A912-01 |
| Cancer type: TGCT | |
| ESID: exon_skip_150743 | |
| Skipped exon start: 30362584 | |
| Skipped exon end: 30362658 | |
| Mutation start: 30362658 | |
| Mutation end: 30362659 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: TG | |
| Mutation seq: - | |
| AAchange: p.708_708del | |
exon_skip_150743_TGCT_TCGA-YU-A912-01.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 |
| HCC1569_BREAST | 30354788 | 30354859 | 30354832 | 30354832 | Missense_Mutation | T | C | p.F599S |
| A1207_CENTRAL_NERVOUS_SYSTEM | 30354788 | 30354859 | 30354847 | 30354847 | Missense_Mutation | A | C | p.Y604S |
| OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30354788 | 30354859 | 30354847 | 30354847 | Missense_Mutation | A | C | p.Y604S |
| NCIH630_LARGE_INTESTINE | 30372719 | 30372837 | 30372765 | 30372765 | Missense_Mutation | A | G | p.S724G |
| JJN3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 30372719 | 30372837 | 30372783 | 30372783 | Missense_Mutation | A | C | p.K730Q |
| RKO_LARGE_INTESTINE | 30377022 | 30377126 | 30377022 | 30377022 | Splice_Site | C | T | p.L893F |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRRC37B |
| 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 LRRC37B |
Top |
Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRRC37B |
Top |
RelatedDrugs for LRRC37B |
| 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 LRRC37B |
| 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)
|