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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 ABCA4 |
 Gene summary |
| Gene information | Gene symbol | ABCA4 | Gene ID | 24 |
| Gene name | ATP binding cassette subfamily A member 4 | |
| Synonyms | ABC10|ABCR|ARMD2|CORD3|FFM|RMP|RP19|STGD|STGD1 | |
| Cytomap | 1p22.1 | |
| Type of gene | protein-coding | |
| Description | retinal-specific ATP-binding cassette transporterATP binding cassette transporterATP-binding cassette sub-family A member 4ATP-binding cassette transporter, retinal-specificATP-binding cassette, sub-family A (ABC1), member 4ATP-binding transporter, r | |
| Modification date | 20180523 | |
| UniProtAcc | P78363 | |
| Context | PubMed: ABCA4 [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 |
| ABCA4 | GO:0045332 | phospholipid translocation | 24097981 |
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Exon skipping events across known transcript of Ensembl for ABCA4 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 ABCA4 |
| 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 ABCA4 |
| Information of exkip skipping event in TCGA. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_28587 | 1 | 94463416:94463666:94466391:94466484:94466557:94466661 | 94466391:94466484 | ENSG00000198691.7 | ENST00000370225.3,ENST00000535881.1,ENST00000536513.1 |
| exon_skip_28592 | 1 | 94485137:94485315:94486795:94486965:94487195:94487270 | 94486795:94486965 | ENSG00000198691.7 | ENST00000370225.3,ENST00000460514.1 |
| exon_skip_28595 | 1 | 94495000:94495187:94495983:94496082:94496551:94496676 | 94495983:94496082 | ENSG00000198691.7 | ENST00000370225.3 |
| exon_skip_28597 | 1 | 94520666:94520871:94522156:94522378:94526092:94526315 | 94522156:94522378 | ENSG00000198691.7 | ENST00000370225.3 |
| PSI values of skipped exons in TCGA. |
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Exon skipping events with PSIs in GTEx for ABCA4 |
| Information of exkip skipping event in GTEx |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon | ENSG | ENSTs |
| exon_skip_28592 | 1 | 94485137:94485315:94486795:94486965:94487195:94487270 | 94486795:94486965 | ENSG00000198691.7 | ENST00000370225.3,ENST00000460514.1 |
| exon_skip_28595 | 1 | 94495000:94495187:94495983:94496082:94496551:94496676 | 94495983:94496082 | ENSG00000198691.7 | ENST00000370225.3 |
| exon_skip_28597 | 1 | 94520666:94520871:94522156:94522378:94526092:94526315 | 94522156:94522378 | ENSG00000198691.7 | ENST00000370225.3 |
| 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 ABCA4 |
| 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 |
| ENST00000370225 | 94486795 | 94486965 | Frame-shift |
| ENST00000370225 | 94466391 | 94466484 | In-frame |
| ENST00000370225 | 94495983 | 94496082 | In-frame |
| ENST00000370225 | 94522156 | 94522378 | 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 |
| ENST00000370225 | 94486795 | 94486965 | Frame-shift |
| ENST00000370225 | 94495983 | 94496082 | In-frame |
| ENST00000370225 | 94522156 | 94522378 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ABCA4 |
| 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 |
| ENST00000370225 | 7326 | 2273 | 94522156 | 94522378 | 2248 | 2469 | 720 | 794 |
| ENST00000370225 | 7326 | 2273 | 94495983 | 94496082 | 4341 | 4439 | 1418 | 1450 |
| ENST00000370225 | 7326 | 2273 | 94466391 | 94466484 | 6474 | 6566 | 2129 | 2159 |
| 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 |
| ENST00000370225 | 7326 | 2273 | 94522156 | 94522378 | 2248 | 2469 | 720 | 794 |
| ENST00000370225 | 7326 | 2273 | 94495983 | 94496082 | 4341 | 4439 | 1418 | 1450 |
| 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 |
| P78363 | 720 | 794 | 1 | 2273 | Chain | ID=PRO_0000093301;Note=Retinal-specific ATP-binding cassette transporter |
| P78363 | 720 | 794 | 752 | 752 | Natural variant | ID=VAR_014703;Note=S->I;Dbxref=dbSNP:rs1801369 |
| P78363 | 720 | 794 | 762 | 762 | Natural variant | ID=VAR_067427;Note=In ARMD2. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19028736;Dbxref=PMID:19028736 |
| P78363 | 720 | 794 | 764 | 764 | Natural variant | ID=VAR_012532;Note=In STGD1. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61749428,PMID:10958763 |
| P78363 | 720 | 794 | 765 | 765 | Natural variant | ID=VAR_012534;Note=In STGD1. S->N;Dbxref=dbSNP:rs61749429 |
| P78363 | 720 | 794 | 765 | 765 | Natural variant | ID=VAR_012533;Note=In STGD1. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61752404,PMID:10958763 |
| P78363 | 720 | 794 | 767 | 767 | Natural variant | ID=VAR_012535;Note=In STGD1. V->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10711710,ECO:0000269|PubMed:11527935,ECO:0000269|PubMed:18977788;Dbxref=dbSNP:rs61751395,PMID:10711710,PMID:11527935,PMID:18977788 |
| P78363 | 720 | 794 | 722 | 722 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P78363 | 720 | 794 | 700 | 720 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 720 | 794 | 731 | 751 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 720 | 794 | 760 | 780 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 1418 | 1450 | 1 | 2273 | Chain | ID=PRO_0000093301;Note=Retinal-specific ATP-binding cassette transporter |
| P78363 | 1418 | 1450 | 1428 | 1428 | Natural variant | ID=VAR_008447;Note=In ARMD2. T->M;Dbxref=dbSNP:rs1800549 |
| P78363 | 1418 | 1450 | 1429 | 1429 | Natural variant | ID=VAR_008448;Note=In STGD1. V->A;Dbxref=dbSNP:rs61752432 |
| P78363 | 1418 | 1450 | 1430 | 1430 | Natural variant | ID=VAR_012572;Note=In STGD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=PMID:10958763 |
| P78363 | 1418 | 1450 | 1433 | 1433 | Natural variant | ID=VAR_008449;Note=In STGD1. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18977788;Dbxref=dbSNP:rs56357060,PMID:18977788 |
| P78363 | 1418 | 1450 | 1439 | 1439 | Natural variant | ID=VAR_008450;Note=In STGD1. G->D;Dbxref=dbSNP:rs61750140 |
| P78363 | 1418 | 1450 | 1440 | 1440 | Natural variant | ID=VAR_008451;Note=In STGD1. F->S;Dbxref=dbSNP:rs61750141 |
| P78363 | 1418 | 1450 | 1440 | 1440 | Natural variant | ID=VAR_012573;Note=In STGD1. F->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61752433,PMID:10958763 |
| P78363 | 1418 | 1450 | 1443 | 1443 | Natural variant | ID=VAR_012574;Note=In STGD1. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61750142,PMID:10958763 |
| P78363 | 1418 | 1450 | 1398 | 1727 | Topological domain | Note=Extracellular |
| P78363 | 2129 | 2159 | 1 | 2273 | Chain | ID=PRO_0000093301;Note=Retinal-specific ATP-binding cassette transporter |
| P78363 | 2129 | 2159 | 1938 | 2170 | Domain | Note=ABC transporter 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| P78363 | 2129 | 2159 | 2131 | 2131 | Natural variant | ID=VAR_008487;Note=In STGD1. E->K;Dbxref=dbSNP:rs61750652 |
| P78363 | 2129 | 2159 | 2137 | 2137 | Natural variant | ID=VAR_067430;Note=In ARMD2. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19028736;Dbxref=PMID:19028736 |
| P78363 | 2129 | 2159 | 2139 | 2139 | Natural variant | ID=VAR_008488;Note=In STGD1. R->W;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11527935;Dbxref=dbSNP:rs61750653,PMID:11527935 |
| P78363 | 2129 | 2159 | 2146 | 2146 | Natural variant | ID=VAR_012611;Note=In CORD3. G->D;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11527935;Dbxref=dbSNP:rs61753044,PMID:11527935 |
| P78363 | 2129 | 2159 | 2149 | 2149 | Natural variant | ID=VAR_012612;Note=In STGD1. R->L;Dbxref=dbSNP:rs61750655 |
| P78363 | 2129 | 2159 | 2150 | 2150 | Natural variant | ID=VAR_012613;Note=In STGD1. C->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:11527935;Dbxref=dbSNP:rs61750656,PMID:11527935 |
| P78363 | 2129 | 2159 | 2150 | 2150 | Natural variant | ID=VAR_008489;Note=In STGD1 and CORD3. C->Y;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10206579,ECO:0000269|PubMed:11527935,ECO:0000269|PubMed:18977788;Dbxref=dbSNP:rs61751384,PMID:10206579,PMID:11527935,PMID:18977788 |
| P78363 | 2129 | 2159 | 1895 | 2273 | Topological domain | Note=Cytoplasmic |
| 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 |
| P78363 | 720 | 794 | 1 | 2273 | Chain | ID=PRO_0000093301;Note=Retinal-specific ATP-binding cassette transporter |
| P78363 | 720 | 794 | 752 | 752 | Natural variant | ID=VAR_014703;Note=S->I;Dbxref=dbSNP:rs1801369 |
| P78363 | 720 | 794 | 762 | 762 | Natural variant | ID=VAR_067427;Note=In ARMD2. A->E;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19028736;Dbxref=PMID:19028736 |
| P78363 | 720 | 794 | 764 | 764 | Natural variant | ID=VAR_012532;Note=In STGD1. C->Y;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61749428,PMID:10958763 |
| P78363 | 720 | 794 | 765 | 765 | Natural variant | ID=VAR_012534;Note=In STGD1. S->N;Dbxref=dbSNP:rs61749429 |
| P78363 | 720 | 794 | 765 | 765 | Natural variant | ID=VAR_012533;Note=In STGD1. S->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61752404,PMID:10958763 |
| P78363 | 720 | 794 | 767 | 767 | Natural variant | ID=VAR_012535;Note=In STGD1. V->D;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10711710,ECO:0000269|PubMed:11527935,ECO:0000269|PubMed:18977788;Dbxref=dbSNP:rs61751395,PMID:10711710,PMID:11527935,PMID:18977788 |
| P78363 | 720 | 794 | 722 | 722 | Sequence conflict | Note=G->V;Ontology_term=ECO:0000305;evidence=ECO:0000305 |
| P78363 | 720 | 794 | 700 | 720 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 720 | 794 | 731 | 751 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 720 | 794 | 760 | 780 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| P78363 | 1418 | 1450 | 1 | 2273 | Chain | ID=PRO_0000093301;Note=Retinal-specific ATP-binding cassette transporter |
| P78363 | 1418 | 1450 | 1428 | 1428 | Natural variant | ID=VAR_008447;Note=In ARMD2. T->M;Dbxref=dbSNP:rs1800549 |
| P78363 | 1418 | 1450 | 1429 | 1429 | Natural variant | ID=VAR_008448;Note=In STGD1. V->A;Dbxref=dbSNP:rs61752432 |
| P78363 | 1418 | 1450 | 1430 | 1430 | Natural variant | ID=VAR_012572;Note=In STGD1. L->P;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=PMID:10958763 |
| P78363 | 1418 | 1450 | 1433 | 1433 | Natural variant | ID=VAR_008449;Note=In STGD1. V->I;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:18977788;Dbxref=dbSNP:rs56357060,PMID:18977788 |
| P78363 | 1418 | 1450 | 1439 | 1439 | Natural variant | ID=VAR_008450;Note=In STGD1. G->D;Dbxref=dbSNP:rs61750140 |
| P78363 | 1418 | 1450 | 1440 | 1440 | Natural variant | ID=VAR_008451;Note=In STGD1. F->S;Dbxref=dbSNP:rs61750141 |
| P78363 | 1418 | 1450 | 1440 | 1440 | Natural variant | ID=VAR_012573;Note=In STGD1. F->V;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61752433,PMID:10958763 |
| P78363 | 1418 | 1450 | 1443 | 1443 | Natural variant | ID=VAR_012574;Note=In STGD1. R->H;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:10958763;Dbxref=dbSNP:rs61750142,PMID:10958763 |
| P78363 | 1418 | 1450 | 1398 | 1727 | Topological domain | Note=Extracellular |
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SNVs in the skipped exons for ABCA4 |
| - 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 |
| KIRP | TCGA-MH-A561-01 | exon_skip_28597 | 94522157 | 94522378 | 94522320 | 94522320 | Frame_Shift_Del | A | - | p.F740fs |
| LIHC | TCGA-DD-A3A0-01 | exon_skip_28597 | 94522157 | 94522378 | 94522350 | 94522350 | Frame_Shift_Del | G | - | p.P730fs |
| PAAD | TCGA-XN-A8T3-01 | exon_skip_28587 | 94466392 | 94466484 | 94466426 | 94466426 | Nonsense_Mutation | G | A | p.R2149* |
| PAAD | TCGA-XN-A8T3-01 | exon_skip_28587 | 94466392 | 94466484 | 94466426 | 94466426 | Nonsense_Mutation | G | A | p.R2149X |
| READ | TCGA-F5-6814-01 | exon_skip_28587 | 94466392 | 94466484 | 94466426 | 94466426 | Nonsense_Mutation | G | A | p.R2149X |
| SKCM | TCGA-EE-A2A2-06 | exon_skip_28592 | 94486796 | 94486965 | 94486960 | 94486960 | Nonsense_Mutation | C | T | p.W1618* |
| SKCM | TCGA-EE-A2A2-06 | exon_skip_28592 | 94486796 | 94486965 | 94486960 | 94486960 | Nonsense_Mutation | C | T | p.W1618X |
| SKCM | TCGA-D3-A3ML-06 | exon_skip_28595 | 94495984 | 94496082 | 94495990 | 94495990 | Nonsense_Mutation | C | T | p.W1449* |
| SKCM | TCGA-D3-A3ML-06 | exon_skip_28595 | 94495984 | 94496082 | 94495990 | 94495990 | Nonsense_Mutation | C | T | p.W1449X |
| HNSC | TCGA-F7-A624-01 | exon_skip_28595 | 94495984 | 94496082 | 94496004 | 94496004 | Nonsense_Mutation | G | T | p.C1444* |
| - 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 |
| SKNMC_BONE | 94466392 | 94466484 | 94466422 | 94466422 | Missense_Mutation | C | T | p.C2150Y |
| MCIXC_AUTONOMIC_GANGLIA | 94466392 | 94466484 | 94466422 | 94466422 | Missense_Mutation | C | T | p.C2150Y |
| HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 94466392 | 94466484 | 94466428 | 94466428 | Missense_Mutation | A | G | p.F2148S |
| LOVO_LARGE_INTESTINE | 94466392 | 94466484 | 94466456 | 94466456 | Missense_Mutation | G | A | p.R2139W |
| BT474_BREAST | 94486796 | 94486965 | 94486837 | 94486837 | Missense_Mutation | T | G | p.Q1659H |
| AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 94486796 | 94486965 | 94486859 | 94486859 | Missense_Mutation | T | C | p.Y1652C |
| JHH4_LIVER | 94522157 | 94522378 | 94522354 | 94522354 | Missense_Mutation | C | T | p.D729N |
| TK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE | 94466392 | 94466484 | 94466426 | 94466426 | Nonsense_Mutation | G | A | p.R2149* |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ABCA4 |
| 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 ABCA4 |
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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ABCA4 |
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RelatedDrugs for ABCA4 |
| 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 ABCA4 |
| Diseases associated with this gene. (DisGeNet 4.0) |
| Gene | Disease ID | Disease name | # pubmeds | Source |
| ABCA4 | C1855465 | STARGARDT DISEASE 1 (disorder) | 17 | CTD_human;UNIPROT |
| ABCA4 | C1858806 | CONE-ROD DYSTROPHY 3 (disorder) | 4 | CTD_human;UNIPROT |
| ABCA4 | C3495438 | Macular Degeneration, Age-Related, 2 | 4 | CTD_human;UNIPROT |
| ABCA4 | C0008924 | Cleft Lip | 1 | CTD_human |
| ABCA4 | C0009404 | Colorectal Neoplasms | 1 | CTD_human |
| ABCA4 | C0035334 | Retinitis Pigmentosa | 1 | CTD_human;HPO;ORPHANET |
| ABCA4 | C0242383 | Age related macular degeneration | 1 | CTD_human |
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