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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 LRFN3 |
 Gene summary |
| Gene information | Gene symbol | LRFN3 | Gene ID | 79414 |
| Gene name | leucine rich repeat and fibronectin type III domain containing 3 | |
| Synonyms | FIGLER1|SALM4 | |
| Cytomap | 19q13.12 | |
| Type of gene | protein-coding | |
| Description | leucine-rich repeat and fibronectin type-III domain-containing protein 3fibronectin type III, immunoglobulin and leucine rich repeat domains 1synaptic adhesion-like molecule 4 | |
| Modification date | 20180519 | |
| UniProtAcc | Q9BTN0 | |
| Context | PubMed: LRFN3 [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 LRFN3 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 LRFN3 |
| 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 LRFN3 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_306038 | 19 | 36428021:36428457:36430311:36431742:36435449:36436095 | 36430311:36431742 | ENSG00000126243.4 | ENST00000246529.3,ENST00000588831.1 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LRFN3 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_306038 | 19 | 36428021:36428457:36430311:36431742:36435449:36436095 | 36430311:36431742 | ENSG00000126243.4 | ENST00000588831.1,ENST00000246529.3 |
| 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 LRFN3 |
| 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 |
| ENST00000246529 | 36430311 | 36431742 | 5CDS-5UTR |
| ENST00000588831 | 36430311 | 36431742 | 5CDS-5UTR |
| 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 |
| ENST00000246529 | 36430311 | 36431742 | 5CDS-5UTR |
| ENST00000588831 | 36430311 | 36431742 | 5CDS-5UTR |
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Infer the effects of exon skipping event on protein functional features for LRFN3 |
| 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 LRFN3 |
| - 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-BR-6852-01 | exon_skip_306038 | 36430312 | 36431742 | 36431074 | 36431074 | Frame_Shift_Del | C | - | p.N249fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_306038 | 36430312 | 36431742 | 36431480 | 36431480 | Frame_Shift_Del | C | - | p.P389fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_306038 | 36430312 | 36431742 | 36431480 | 36431480 | Frame_Shift_Del | C | - | p.P389fs |
| BLCA | TCGA-BL-A0C8-01 | exon_skip_306038 | 36430312 | 36431742 | 36431511 | 36431517 | Frame_Shift_Del | CCAGCTG | - | p.T395fs |
| BLCA | TCGA-BL-A0C8-01 | exon_skip_306038 | 36430312 | 36431742 | 36431511 | 36431517 | Frame_Shift_Del | CCAGCTG | - | p.TSC395fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_306038 | 36430312 | 36431742 | 36431521 | 36431521 | Frame_Shift_Del | C | - | p.D398fs |
| UCEC | TCGA-A5-A0VQ-01 | exon_skip_306038 | 36430312 | 36431742 | 36431521 | 36431521 | Frame_Shift_Del | C | - | p.D398fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_306038 | 36430312 | 36431742 | 36431584 | 36431584 | Frame_Shift_Del | G | - | p.K419fs |
| STAD | TCGA-BR-4363-01 | exon_skip_306038 | 36430312 | 36431742 | 36431600 | 36431600 | Frame_Shift_Del | C | - | p.G424fs |
| LIHC | TCGA-DD-A1EG-01 | exon_skip_306038 | 36430312 | 36431742 | 36431683 | 36431683 | Frame_Shift_Del | G | - | p.P452fs |
| KICH | TCGA-KL-8342-01 | exon_skip_306038 | 36430312 | 36431742 | 36430411 | 36430412 | Frame_Shift_Ins | - | C | p.C28fs |
| STAD | TCGA-BR-8361-01 | exon_skip_306038 | 36430312 | 36431742 | 36431520 | 36431521 | Frame_Shift_Ins | - | C | p.D398fs |
| STAD | TCGA-BR-8361-01 | exon_skip_306038 | 36430312 | 36431742 | 36431521 | 36431522 | Frame_Shift_Ins | - | C | p.D398fs |
| LUAD | TCGA-J2-8194-01 | exon_skip_306038 | 36430312 | 36431742 | 36430423 | 36430423 | Nonsense_Mutation | C | A | p.C32* |
| BLCA | TCGA-UY-A9PB-01 | exon_skip_306038 | 36430312 | 36431742 | 36431143 | 36431143 | Nonsense_Mutation | C | A | p.C272* |
| - 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 |
| GP5D_LARGE_INTESTINE | 36430312 | 36431742 | 36430924 | 36430924 | Frame_Shift_Del | T | - | p.A199fs |
| SISO_CERVIX | 36430312 | 36431742 | 36431480 | 36431480 | Frame_Shift_Del | C | - | p.P389fs |
| GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431480 | 36431480 | Frame_Shift_Del | C | - | p.P389fs |
| REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431521 | 36431521 | Frame_Shift_Del | C | - | p.D398fs |
| HEC108_ENDOMETRIUM | 36430312 | 36431742 | 36430335 | 36430335 | Missense_Mutation | T | C | p.I3T |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36430400 | 36430400 | Missense_Mutation | C | T | p.P25S |
| HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36430455 | 36430455 | Missense_Mutation | T | G | p.V43G |
| BEN_LUNG | 36430312 | 36431742 | 36430569 | 36430569 | Missense_Mutation | A | G | p.N81S |
| HEC59_ENDOMETRIUM | 36430312 | 36431742 | 36430679 | 36430679 | Missense_Mutation | C | T | p.R118W |
| TGBC11TKB_STOMACH | 36430312 | 36431742 | 36430704 | 36430704 | Missense_Mutation | A | T | p.Q126L |
| SNU175_LARGE_INTESTINE | 36430312 | 36431742 | 36430709 | 36430709 | Missense_Mutation | C | T | p.R128C |
| SNU175_LARGE_INTESTINE | 36430312 | 36431742 | 36430727 | 36430727 | Missense_Mutation | C | T | p.R134C |
| CW2_LARGE_INTESTINE | 36430312 | 36431742 | 36430874 | 36430874 | Missense_Mutation | A | G | p.N183D |
| CCFSTTG1_CENTRAL_NERVOUS_SYSTEM | 36430312 | 36431742 | 36431030 | 36431030 | Missense_Mutation | C | G | p.R235G |
| DOK_UPPER_AERODIGESTIVE_TRACT | 36430312 | 36431742 | 36431030 | 36431030 | Missense_Mutation | C | G | p.R235G |
| NCIH2373_PLEURA | 36430312 | 36431742 | 36431030 | 36431030 | Missense_Mutation | C | G | p.R235G |
| CCRFCEM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431091 | 36431091 | Missense_Mutation | G | A | p.C255Y |
| SNU175_LARGE_INTESTINE | 36430312 | 36431742 | 36431108 | 36431108 | Missense_Mutation | C | T | p.R261C |
| JAR_PLACENTA | 36430312 | 36431742 | 36431121 | 36431121 | Missense_Mutation | G | A | p.R265Q |
| HEC265_ENDOMETRIUM | 36430312 | 36431742 | 36431165 | 36431165 | Missense_Mutation | G | A | p.G280S |
| MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431181 | 36431181 | Missense_Mutation | C | T | p.A285V |
| MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431196 | 36431196 | Missense_Mutation | A | G | p.E290G |
| ES2_OVARY | 36430312 | 36431742 | 36431227 | 36431227 | Missense_Mutation | C | G | p.H300Q |
| HEC59_ENDOMETRIUM | 36430312 | 36431742 | 36431229 | 36431229 | Missense_Mutation | G | A | p.R301H |
| LS411N_LARGE_INTESTINE | 36430312 | 36431742 | 36431244 | 36431244 | Missense_Mutation | C | T | p.A306V |
| MALME3M_SKIN | 36430312 | 36431742 | 36431258 | 36431258 | Missense_Mutation | C | T | p.R311W |
| HCC1954_BREAST | 36430312 | 36431742 | 36431280 | 36431280 | Missense_Mutation | G | C | p.R318P |
| HCC1954_MATCHED_NORMAL_TISSUE | 36430312 | 36431742 | 36431280 | 36431280 | Missense_Mutation | G | C | p.R318P |
| SUPB15_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431280 | 36431280 | Missense_Mutation | G | A | p.R318Q |
| JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431282 | 36431282 | Missense_Mutation | G | A | p.A319T |
| CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431283 | 36431283 | Missense_Mutation | C | T | p.A319V |
| SNU520_STOMACH | 36430312 | 36431742 | 36431303 | 36431303 | Missense_Mutation | C | T | p.R326C |
| EJM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 36430312 | 36431742 | 36431450 | 36431450 | Missense_Mutation | G | A | p.A375T |
| CCFSTTG1_CENTRAL_NERVOUS_SYSTEM | 36430312 | 36431742 | 36431513 | 36431513 | Missense_Mutation | A | G | p.S396G |
| SNU175_LARGE_INTESTINE | 36430312 | 36431742 | 36431513 | 36431513 | Missense_Mutation | A | T | p.S396C |
| FTC133_THYROID | 36430312 | 36431742 | 36431528 | 36431528 | Missense_Mutation | C | T | p.R401W |
| SNU1040_LARGE_INTESTINE | 36430312 | 36431742 | 36431529 | 36431529 | Missense_Mutation | G | A | p.R401Q |
| C32_SKIN | 36430312 | 36431742 | 36431540 | 36431540 | Missense_Mutation | C | T | p.P405S |
| HS618T_FIBROBLAST | 36430312 | 36431742 | 36431564 | 36431564 | Missense_Mutation | G | A | p.A413T |
| EFO27_OVARY | 36430312 | 36431742 | 36431643 | 36431643 | Missense_Mutation | C | T | p.T439I |
| PACADD137_PANCREAS | 36430312 | 36431742 | 36431682 | 36431682 | Missense_Mutation | C | T | p.P452L |
| HEC6_ENDOMETRIUM | 36430312 | 36431742 | 36431709 | 36431709 | Missense_Mutation | A | G | p.Y461C |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LRFN3 |
| 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 LRFN3 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LRFN3 |
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RelatedDrugs for LRFN3 |
| 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 LRFN3 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
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