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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 LAMP1 |
 Gene summary |
| Gene information | Gene symbol | LAMP1 | Gene ID | 3916 |
| Gene name | lysosomal associated membrane protein 1 | |
| Synonyms | CD107a|LAMPA|LGP120 | |
| Cytomap | 13q34 | |
| Type of gene | protein-coding | |
| Description | lysosome-associated membrane glycoprotein 1CD107 antigen-like family member ALAMP-1lysosome-associated membrane protein 1 | |
| Modification date | 20180519 | |
| UniProtAcc | P11279 | |
| Context | PubMed: LAMP1 [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 LAMP1 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 LAMP1 |
| 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 LAMP1 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_101590 | 13 | 113951699:113951810:113960799:113960921:113963957:113964020 | 113960799:113960921 | ENSG00000185896.9 | ENST00000397181.3 |
| exon_skip_101595 | 13 | 113960799:113960921:113963957:113964177:113965023:113965182 | 113963957:113964177 | ENSG00000185896.9 | ENST00000472564.1,ENST00000332556.4 |
| exon_skip_101596 | 13 | 113963957:113964177:113965023:113965182:113973783:113973810 | 113965023:113965182 | ENSG00000185896.9 | ENST00000472564.1,ENST00000332556.4 |
| exon_skip_101600 | 13 | 113975718:113975785:113975871:113976042:113976596:113976909 | 113975871:113976042 | ENSG00000185896.9 | ENST00000397181.3,ENST00000332556.4 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for LAMP1 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_101590 | 13 | 113951699:113951810:113960799:113960921:113963957:113964020 | 113960799:113960921 | ENSG00000185896.9 | ENST00000397181.3 |
| exon_skip_101595 | 13 | 113960799:113960921:113963957:113964177:113965023:113965182 | 113963957:113964177 | ENSG00000185896.9 | ENST00000332556.4,ENST00000472564.1 |
| exon_skip_101596 | 13 | 113963957:113964177:113965023:113965182:113973783:113973810 | 113965023:113965182 | ENSG00000185896.9 | ENST00000332556.4,ENST00000472564.1 |
| exon_skip_101600 | 13 | 113975718:113975785:113975871:113976042:113976596:113976909 | 113975871:113976042 | ENSG00000185896.9 | ENST00000332556.4,ENST00000397181.3 |
| 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 LAMP1 |
| 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 |
| ENST00000332556 | 113963957 | 113964177 | Frame-shift |
| ENST00000332556 | 113965023 | 113965182 | In-frame |
| ENST00000332556 | 113975871 | 113976042 | 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 |
| ENST00000332556 | 113963957 | 113964177 | Frame-shift |
| ENST00000332556 | 113965023 | 113965182 | In-frame |
| ENST00000332556 | 113975871 | 113976042 | In-frame |
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Infer the effects of exon skipping event on protein functional features for LAMP1 |
| 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 |
| ENST00000332556 | 2716 | 417 | 113965023 | 113965182 | 598 | 756 | 134 | 187 |
| ENST00000332556 | 2716 | 417 | 113975871 | 113976042 | 1138 | 1308 | 314 | 371 |
| 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 |
| ENST00000332556 | 2716 | 417 | 113965023 | 113965182 | 598 | 756 | 134 | 187 |
| ENST00000332556 | 2716 | 417 | 113975871 | 113976042 | 1138 | 1308 | 314 | 371 |
| 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 |
| P11279 | 134 | 187 | 135 | 187 | Alternative sequence | ID=VSP_056032;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P11279 | 134 | 187 | 29 | 417 | Chain | ID=PRO_0000017104;Note=Lysosome-associated membrane glycoprotein 1 |
| P11279 | 134 | 187 | 155 | 191 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00740,ECO:0000269|PubMed:2584229;Dbxref=PMID:2584229 |
| P11279 | 134 | 187 | 165 | 165 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2243102,ECO:0000269|PubMed:8323299;Dbxref=PMID:2243102,PMID:8323299 |
| P11279 | 134 | 187 | 181 | 181 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2243102,ECO:0000269|PubMed:8323299;Dbxref=PMID:2243102,PMID:8323299 |
| P11279 | 134 | 187 | 29 | 194 | Region | Note=First lumenal domain |
| P11279 | 134 | 187 | 29 | 382 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11279 | 314 | 371 | 29 | 417 | Chain | ID=PRO_0000017104;Note=Lysosome-associated membrane glycoprotein 1 |
| P11279 | 314 | 371 | 338 | 375 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00740,ECO:0000269|PubMed:2584229;Dbxref=PMID:2584229 |
| P11279 | 314 | 371 | 322 | 322 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8323299;Dbxref=PMID:8323299 |
| P11279 | 314 | 371 | 228 | 382 | Region | Note=Second lumenal domain |
| P11279 | 314 | 371 | 29 | 382 | Topological domain | Note=Lumenal;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 |
| P11279 | 134 | 187 | 135 | 187 | Alternative sequence | ID=VSP_056032;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039 |
| P11279 | 134 | 187 | 29 | 417 | Chain | ID=PRO_0000017104;Note=Lysosome-associated membrane glycoprotein 1 |
| P11279 | 134 | 187 | 155 | 191 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00740,ECO:0000269|PubMed:2584229;Dbxref=PMID:2584229 |
| P11279 | 134 | 187 | 165 | 165 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2243102,ECO:0000269|PubMed:8323299;Dbxref=PMID:2243102,PMID:8323299 |
| P11279 | 134 | 187 | 181 | 181 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:2243102,ECO:0000269|PubMed:8323299;Dbxref=PMID:2243102,PMID:8323299 |
| P11279 | 134 | 187 | 29 | 194 | Region | Note=First lumenal domain |
| P11279 | 134 | 187 | 29 | 382 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P11279 | 314 | 371 | 29 | 417 | Chain | ID=PRO_0000017104;Note=Lysosome-associated membrane glycoprotein 1 |
| P11279 | 314 | 371 | 338 | 375 | Disulfide bond | Ontology_term=ECO:0000255,ECO:0000269;evidence=ECO:0000255|PROSITE-ProRule:PRU00740,ECO:0000269|PubMed:2584229;Dbxref=PMID:2584229 |
| P11279 | 314 | 371 | 322 | 322 | Glycosylation | Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:8323299;Dbxref=PMID:8323299 |
| P11279 | 314 | 371 | 228 | 382 | Region | Note=Second lumenal domain |
| P11279 | 314 | 371 | 29 | 382 | Topological domain | Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
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SNVs in the skipped exons for LAMP1 |
| - 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. |
LAMP1_KIRC_exon_skip_101596_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 |
| LIHC | TCGA-DD-A1EG-01 | 113960800 | 113960921 | 113960838 | 113960838 | Frame_Shift_Del | A | - | p.K34fs | |
| LIHC | TCGA-DD-A1EG-01 | 113960800 | 113960921 | 113960838 | 113960838 | Frame_Shift_Del | A | - | p.V33fs | |
| LIHC | TCGA-DD-A3A0-01 | 113960800 | 113960921 | 113960913 | 113960913 | Frame_Shift_Del | G | - | p.G59fs | |
| LIHC | TCGA-G3-A3CJ-01 | exon_skip_101595 | 113963958 | 113964177 | 113964130 | 113964130 | Frame_Shift_Del | T | - | p.V119fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_101595 | 113963958 | 113964177 | 113964158 | 113964158 | Frame_Shift_Del | C | - | p.F128fs |
| KIRC | TCGA-B0-5098-01 | exon_skip_101596 | 113965024 | 113965182 | 113965071 | 113965071 | Frame_Shift_Del | A | - | p.K152fs |
| LIHC | TCGA-DD-AAD5-01 | exon_skip_101600 | 113975872 | 113976042 | 113975888 | 113975888 | Frame_Shift_Del | T | - | p.A320fs |
| PAAD | TCGA-IB-7651-01 | exon_skip_101600 | 113975872 | 113976042 | 113975904 | 113975904 | Nonsense_Mutation | C | T | p.R326* |
| PAAD | TCGA-IB-7651-01 | exon_skip_101600 | 113975872 | 113976042 | 113975904 | 113975904 | Nonsense_Mutation | C | T | p.R326X |
| LUAD | TCGA-78-7149-01 | exon_skip_101600 | 113975872 | 113976042 | 113975949 | 113975949 | Nonsense_Mutation | G | T | p.E341* |
| - Depth of coverage in the three exons composing exon skipping event |
| Depth of coverage in three exons | Mutation description |
 | Sample: TCGA-B0-5098-01 |
| Cancer type: KIRC | |
| ESID: exon_skip_101596 | |
| Skipped exon start: 113965024 | |
| Skipped exon end: 113965182 | |
| Mutation start: 113965071 | |
| Mutation end: 113965071 | |
| Mutation type: Frame_Shift_Del | |
| Reference seq: A | |
| Mutation seq: - | |
| AAchange: p.K152fs | |
exon_skip_101596_KIRC_TCGA-B0-5098-01.png | |
exon_skip_311289_KIRC_TCGA-B0-5098-01.png | |
exon_skip_84604_KIRC_TCGA-B0-5098-01.png | |
exon_skip_84605_KIRC_TCGA-B0-5098-01.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 |
| TGBC11TKB_STOMACH | 113965024 | 113965182 | 113965071 | 113965071 | Frame_Shift_Del | A | - | p.K152fs |
| CORL32_LUNG | 113960800 | 113960921 | 113960878 | 113960878 | Missense_Mutation | C | G | p.S47C |
| KLE_ENDOMETRIUM | 113960800 | 113960921 | 113960899 | 113960899 | Missense_Mutation | A | G | p.Y54C |
| NCIH196_LUNG | 113963958 | 113964177 | 113963965 | 113963965 | Missense_Mutation | C | T | p.T64I |
| HS819T_FIBROBLAST | 113963958 | 113964177 | 113964007 | 113964007 | Missense_Mutation | G | A | p.S78N |
| MFHINO_SOFT_TISSUE | 113963958 | 113964177 | 113964027 | 113964027 | Missense_Mutation | A | G | p.T85A |
| SNU475_LIVER | 113963958 | 113964177 | 113964088 | 113964088 | Missense_Mutation | C | T | p.T105M |
| HCC2998_LARGE_INTESTINE | 113965024 | 113965182 | 113965122 | 113965122 | Missense_Mutation | G | A | p.V168I |
| SNU1066_UPPER_AERODIGESTIVE_TRACT | 113975872 | 113976042 | 113975908 | 113975908 | Missense_Mutation | C | T | p.A327V |
| RH30_SOFT_TISSUE | 113975872 | 113976042 | 113975964 | 113975964 | Missense_Mutation | G | A | p.V346I |
| SJRH30_SOFT_TISSUE | 113975872 | 113976042 | 113975964 | 113975964 | Missense_Mutation | G | A | p.V346I |
| OUMS23_LARGE_INTESTINE | 113975872 | 113976042 | 113975873 | 113975873 | Splice_Site | C | A | p.D315E |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for LAMP1 |
| 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 LAMP1 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for LAMP1 |
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RelatedDrugs for LAMP1 |
| 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 LAMP1 |
| 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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