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| Open reading frame (ORF) annotation in the exon skipping event |
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| 3'-UTR located exon skipping events lost miRNA binding sites |
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| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
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Gene summary for ABCA7 |
 Gene summary |
| Gene information | Gene symbol | ABCA7 | Gene ID | 10347 |
| Gene name | ATP binding cassette subfamily A member 7 | |
| Synonyms | ABCA-SSN|ABCX|AD9 | |
| Cytomap | 19p13.3 | |
| Type of gene | protein-coding | |
| Description | phospholipid-transporting ATPase ABCA7ATP-binding cassette sub-family A member 7ATP-binding cassette, sub-family A (ABC1), member 7autoantigen SS-Nmacrophage ABC transporter | |
| Modification date | 20200320 | |
| UniProtAcc | ||
| Context | - 26079414(Loss-of-function Mutation in ABCA1 and Risk of Alzheimer's Disease and Cerebrovascular Disease) |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| ABCA7 | GO:0033344 | cholesterol efflux | 14570867 |
| ABCA7 | GO:0033700 | phospholipid efflux | 14570867 |
| ABCA7 | GO:0034380 | high-density lipoprotein particle assembly | 14570867 |
| ABCA7 | GO:0038027 | apolipoprotein A-I-mediated signaling pathway | 14570867 |
| ABCA7 | GO:0045332 | phospholipid translocation | 24097981 |
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Gene structures and expression levels for ABCA7 |
| Skipped exons in the ROSMAP, MSBB, and Mayo 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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ENSG00000064687
| Differentially expressed gene analysis across multiple brain tissues between AD and control. |
| Tissue type | DEG direction | Base mean exp. | log2FC(AD/control) | P-value | Adj. p-value |
| Differentially expressed isoform analysis across multiple brain tissues between AD and control. |
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| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| TC | DOWN | ENST00000531478.5 | ABCA7-215:retained_intron:ABCA7 | 2.020285e+01 | -1.101540e+00 | 1.271854e-04 | 1.958262e-03 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for ABCA7 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
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| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_110749 | chr19 | 1054193:1054341:1054570:1054694:1054780:1054878 | 1054570:1054694 |
| exon_skip_117706 | chr19 | 1052214:1052286:1053329:1053531:1053788:1053836 | 1053329:1053531 |
| exon_skip_11958 | chr19 | 1057314:1057429:1058146:1058269:1058618:1058740 | 1058146:1058269 |
| exon_skip_119919 | chr19 | 1057314:1057429:1057969:1058059:1058146:1058269 | 1057969:1058059 |
| exon_skip_120598 | chr19 | 1054780:1054878:1055097:1055351:1055907:1055939 | 1055097:1055351 |
| exon_skip_144518 | chr19 | 1054202:1054341:1054570:1054694:1054780:1054878 | 1054570:1054694 |
| exon_skip_155547 | chr19 | 1048895:1049005:1049266:1049437:1050921:1051052 | 1049266:1049437 |
| exon_skip_183000 | chr19 | 1063602:1063678:1063760:1063863:1064161:1064253 | 1063760:1063863 |
| exon_skip_190939 | chr19 | 1057314:1057429:1057915:1058059:1058146:1058157 | 1057915:1058059 |
| exon_skip_191804 | chr19 | 1058146:1058269:1058618:1058747:1058820:1058940 | 1058618:1058747 |
| exon_skip_215515 | chr19 | 1057314:1057429:1057969:1058059:1058146:1058157 | 1057969:1058059 |
| exon_skip_216737 | chr19 | 1055907:1055939:1056066:1056243:1056330:1056499 | 1056066:1056243 |
| exon_skip_217643 | chr19 | 1041516:1041603:1041831:1041972:1042064:1042176 | 1041831:1041972 |
| exon_skip_2303 | chr19 | 1057314:1057429:1057915:1058059:1058146:1058269 | 1057915:1058059 |
| exon_skip_236933 | chr19 | 1056934:1057084:1057314:1057429:1057915:1058059 | 1057314:1057429 |
| exon_skip_257328 | chr19 | 1049266:1049437:1050921:1051052:1051155:1051294 | 1050921:1051052 |
| exon_skip_257822 | chr19 | 1056066:1056243:1056330:1056499:1056907:1057084 | 1056330:1056499 |
| exon_skip_263558 | chr19 | 1043725:1043841:1044577:1044744:1045002:1045231 | 1044577:1044744 |
| exon_skip_59937 | chr19 | 1049318:1049437:1050921:1051052:1051155:1051294 | 1050921:1051052 |
| exon_skip_82388 | chr19 | 1063544:1063678:1063760:1063863:1064161:1064253 | 1063760:1063863 |
| exon_skip_90467 | chr19 | 1061782:1061888:1062172:1062313:1063544:1063678 | 1062172:1062313 |
| exon_skip_96213 | chr19 | 1056934:1057084:1057314:1057429:1058146:1058157 | 1057314:1057429 |
| Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control. |
| Exon skipping information | Tissue type | Avg(PSIs) in AD | Avg(PSIs) in control | Difference (PSI) | Adj. p-value |
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Open reading frame (ORF) annotation in the exon skipping event for ABCA7 |
| Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000263094 | 1041831 | 1041972 | Frame-shift |
| ENST00000433129 | 1041831 | 1041972 | Frame-shift |
| ENST00000263094 | 1049266 | 1049437 | Frame-shift |
| ENST00000433129 | 1049266 | 1049437 | Frame-shift |
| ENST00000263094 | 1053329 | 1053531 | Frame-shift |
| ENST00000433129 | 1053329 | 1053531 | Frame-shift |
| ENST00000263094 | 1054570 | 1054694 | Frame-shift |
| ENST00000433129 | 1054570 | 1054694 | Frame-shift |
| ENST00000263094 | 1057314 | 1057429 | Frame-shift |
| ENST00000433129 | 1057314 | 1057429 | Frame-shift |
| ENST00000263094 | 1057915 | 1058059 | Frame-shift |
| ENST00000433129 | 1057915 | 1058059 | Frame-shift |
| ENST00000263094 | 1058618 | 1058747 | Frame-shift |
| ENST00000433129 | 1058618 | 1058747 | Frame-shift |
| ENST00000263094 | 1062172 | 1062313 | Frame-shift |
| ENST00000433129 | 1062172 | 1062313 | Frame-shift |
| ENST00000263094 | 1063760 | 1063863 | Frame-shift |
| ENST00000433129 | 1063760 | 1063863 | Frame-shift |
| ENST00000263094 | 1050921 | 1051052 | In-frame |
| ENST00000433129 | 1050921 | 1051052 | In-frame |
| ENST00000263094 | 1055097 | 1055351 | In-frame |
| ENST00000433129 | 1055097 | 1055351 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000263094 | 1041831 | 1041972 | Frame-shift |
| ENST00000433129 | 1041831 | 1041972 | Frame-shift |
| ENST00000263094 | 1054570 | 1054694 | Frame-shift |
| ENST00000433129 | 1054570 | 1054694 | Frame-shift |
| ENST00000263094 | 1057915 | 1058059 | Frame-shift |
| ENST00000433129 | 1057915 | 1058059 | Frame-shift |
| ENST00000263094 | 1063760 | 1063863 | Frame-shift |
| ENST00000433129 | 1063760 | 1063863 | Frame-shift |
| ENST00000263094 | 1050921 | 1051052 | In-frame |
| ENST00000433129 | 1050921 | 1051052 | In-frame |
| Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms. |
| ENST | Start of skipped exon | End of skipped exon | ORF |
| ENST00000263094 | 1041831 | 1041972 | Frame-shift |
| ENST00000433129 | 1041831 | 1041972 | Frame-shift |
| ENST00000263094 | 1053329 | 1053531 | Frame-shift |
| ENST00000433129 | 1053329 | 1053531 | Frame-shift |
| ENST00000263094 | 1054570 | 1054694 | Frame-shift |
| ENST00000433129 | 1054570 | 1054694 | Frame-shift |
| ENST00000263094 | 1056066 | 1056243 | Frame-shift |
| ENST00000433129 | 1056066 | 1056243 | Frame-shift |
| ENST00000263094 | 1056330 | 1056499 | Frame-shift |
| ENST00000433129 | 1056330 | 1056499 | Frame-shift |
| ENST00000263094 | 1057314 | 1057429 | Frame-shift |
| ENST00000433129 | 1057314 | 1057429 | Frame-shift |
| ENST00000263094 | 1057915 | 1058059 | Frame-shift |
| ENST00000433129 | 1057915 | 1058059 | Frame-shift |
| ENST00000263094 | 1058618 | 1058747 | Frame-shift |
| ENST00000433129 | 1058618 | 1058747 | Frame-shift |
| ENST00000263094 | 1062172 | 1062313 | Frame-shift |
| ENST00000433129 | 1062172 | 1062313 | Frame-shift |
| ENST00000263094 | 1063760 | 1063863 | Frame-shift |
| ENST00000433129 | 1063760 | 1063863 | Frame-shift |
| ENST00000263094 | 1044577 | 1044744 | In-frame |
| ENST00000433129 | 1044577 | 1044744 | In-frame |
| ENST00000263094 | 1050921 | 1051052 | In-frame |
| ENST00000433129 | 1050921 | 1051052 | In-frame |
| ENST00000263094 | 1055097 | 1055351 | In-frame |
| ENST00000433129 | 1055097 | 1055351 | In-frame |
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Infer the effects of exon skipping event on protein functional features for ABCA7 |
p-ENSG00000064687_img4.png |
| Loci of skipped exons in ROSMAP 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 |
| ENST00000263094 | 6833 | 2146 | 1050921 | 1051052 | 2785 | 2915 | 851 | 894 |
| ENST00000433129 | 6721 | 2146 | 1050921 | 1051052 | 2670 | 2800 | 851 | 894 |
| ENST00000263094 | 6833 | 2146 | 1055097 | 1055351 | 4183 | 4436 | 1317 | 1401 |
| ENST00000433129 | 6721 | 2146 | 1055097 | 1055351 | 4068 | 4321 | 1317 | 1401 |
| Loci of skipped exons in MSBB 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 |
| ENST00000263094 | 6833 | 2146 | 1050921 | 1051052 | 2785 | 2915 | 851 | 894 |
| ENST00000433129 | 6721 | 2146 | 1050921 | 1051052 | 2670 | 2800 | 851 | 894 |
| Loci of skipped exons in Mayo 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 |
| ENST00000263094 | 6833 | 2146 | 1044577 | 1044744 | 1280 | 1446 | 349 | 405 |
| ENST00000433129 | 6721 | 2146 | 1044577 | 1044744 | 1165 | 1331 | 349 | 405 |
| ENST00000263094 | 6833 | 2146 | 1050921 | 1051052 | 2785 | 2915 | 851 | 894 |
| ENST00000433129 | 6721 | 2146 | 1050921 | 1051052 | 2670 | 2800 | 851 | 894 |
| ENST00000263094 | 6833 | 2146 | 1055097 | 1055351 | 4183 | 4436 | 1317 | 1401 |
| ENST00000433129 | 6721 | 2146 | 1055097 | 1055351 | 4068 | 4321 | 1317 | 1401 |
| Lost protein functional features of individual exon skipping events in ROSMAP. |
| 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 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8IZY2 | 1317 | 1401 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 1317 | 1401 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 1317 | 1401 | 1345 | 1359 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1345 | 1359 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1349 | 1349 | Natural variant | ID=VAR_027586;Note=R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10873640,ECO:0000269|PubMed:11355874,ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3745842,PMID:10873640,PMID:11355874,PMID:12111378 |
| Q8IZY2 | 1317 | 1401 | 1349 | 1349 | Natural variant | ID=VAR_027586;Note=R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10873640,ECO:0000269|PubMed:11355874,ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3745842,PMID:10873640,PMID:11355874,PMID:12111378 |
| Q8IZY2 | 1317 | 1401 | 1264 | 1537 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1264 | 1537 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Lost protein functional features of individual exon skipping events in MSBB. |
| 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 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Lost protein functional features of individual exon skipping events in Mayo. |
| 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 |
| Q8IZY2 | 349 | 405 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 349 | 405 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 349 | 405 | 395 | 395 | Natural variant | ID=VAR_027583;Note=H->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3764647,PMID:12111378 |
| Q8IZY2 | 349 | 405 | 395 | 395 | Natural variant | ID=VAR_027583;Note=H->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3764647,PMID:12111378 |
| Q8IZY2 | 349 | 405 | 43 | 549 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 349 | 405 | 43 | 549 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 807 | 1038 | Domain | Note=ABC transporter 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00434 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8IZY2 | 851 | 894 | 849 | 869 | Transmembrane | Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q8IZY2 | 1317 | 1401 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 1317 | 1401 | 1 | 2146 | Chain | ID=PRO_0000250674;Note=ATP-binding cassette sub-family A member 7 |
| Q8IZY2 | 1317 | 1401 | 1345 | 1359 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1345 | 1359 | Disulfide bond | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1349 | 1349 | Natural variant | ID=VAR_027586;Note=R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10873640,ECO:0000269|PubMed:11355874,ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3745842,PMID:10873640,PMID:11355874,PMID:12111378 |
| Q8IZY2 | 1317 | 1401 | 1349 | 1349 | Natural variant | ID=VAR_027586;Note=R->Q;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:10873640,ECO:0000269|PubMed:11355874,ECO:0000269|PubMed:12111378;Dbxref=dbSNP:rs3745842,PMID:10873640,PMID:11355874,PMID:12111378 |
| Q8IZY2 | 1317 | 1401 | 1264 | 1537 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q8IZY2 | 1317 | 1401 | 1264 | 1537 | Topological domain | Note=Extracellular;Ontology_term=ECO:0000250;evidence=ECO:0000250 |
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3'-UTR located exon skipping events that lost miRNA binding sites in ABCA7 |
| 3'-UTR exon skipping evnets lost miRNA binding. |
| Tissue type | ENST | Exon skip start | Exon skip end | microRNA | Binding site by TargetScan | Binding type by TargetScan | Bdinding site by miRanda | Score of miRanda | Energy by miRanda |
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SNVs in the skipped exons for ABCA7 |
| - Differential PSIs between mutated versus non-mutated samples. |
| - Depth of Coverage in the skipped exon of the mutated samples. |
| - Sashimi plot in the skipped exon of the mutated samples. |
| - Non-synonymous mutations located in the skipped exons. |
| Cancer type | Sample | ESID | Skipped exon start | Skipped exon end | Mutation start | Mutation end | Mutation type | Reference seq | Mutation seq | AAchange |
| - 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 |
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AD stage-associated exon skippint events for ABCA7 |
| Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR). |
| AD stage info | Cohort | Tissue | SE id | Coefficient | P-value | Chromosome | Strand | E1 start | E1 end | Skipped start | Skipped end | E2 start | E2 end |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ABCA7 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| CB | exon_skip_144518 | rs8110452 | chr19:998127 | 8.541056e-05 | 1.528493e-02 |
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Correlation with RNA binding proteins (RBPs) for ABCA7 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | RBM6 | exon_skip_82388 | -4.343879e-01 | 1.060274e-08 |
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RelatedDrugs for ABCA7 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for ABCA7 |
| 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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