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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 SMC1A |
 Gene summary |
| Gene information | Gene symbol | SMC1A | Gene ID | 8243 |
| Gene name | structural maintenance of chromosomes 1A | |
| Synonyms | CDLS2|DXS423E|SB1.8|SMC1|SMC1L1|SMC1alpha|SMCB | |
| Cytomap | Xp11.22 | |
| Type of gene | protein-coding | |
| Description | structural maintenance of chromosomes protein 1ASMC protein 1ASMC-1-alphaSMC1 (structural maintenance of chromosomes 1, yeast)-like 1epididymis secretory sperm binding proteinsegregation of mitotic chromosomes 1 | |
| Modification date | 20200329 | |
| UniProtAcc | ||
| Context |
| Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Gene | GO ID | GO term | PubMed ID |
| SMC1A | GO:0072423 | response to DNA damage checkpoint signaling | 11877377 |
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Gene structures and expression levels for SMC1A |
| 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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ENSG00000072501
| 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 |
| PCC | UP | ENST00000375340.10 | SMC1A-202:protein_coding:SMC1A | 1.264556e+02 | 9.123562e-01 | 2.002906e-06 | 4.220142e-04 |
| STG | UP | ENST00000463684.1 | SMC1A-204:nonsense_mediated_decay:SMC1A | 7.337230e+00 | 5.780194e+00 | 9.370938e-05 | 1.056776e-02 |
| PG | UP | ENST00000375340.10 | SMC1A-202:protein_coding:SMC1A | 4.051132e+01 | 1.597110e+00 | 4.801506e-03 | 4.441259e-02 |
| 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 SMC1A |
| 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_135022 | chrX | 53380620:53380730:53381018:53381087:53382232:53382383 | 53381018:53381087 |
| exon_skip_157835 | chrX | 53414985:53415169:53421895:53422040:53422492:53422669 | 53421895:53422040 |
| exon_skip_198180 | chrX | 53396472:53396617:53399589:53399730:53403566:53403668 | 53399589:53399730 |
| exon_skip_277173 | chrX | 53414981:53415169:53421895:53422040:53422492:53422669 | 53421895:53422040 |
| exon_skip_62486 | chrX | 53403777:53403893:53405012:53405149:53405245:53405391 | 53405012:53405149 |
| exon_skip_63493 | chrX | 53396472:53396617:53399589:53399730:53403566:53403672 | 53399589:53399730 |
| 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 SMC1A |
| 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 |
| ENST00000322213 | 53381018 | 53381087 | Frame-shift |
| ENST00000322213 | 53399589 | 53399730 | Frame-shift |
| 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 |
| ENST00000322213 | 53381018 | 53381087 | Frame-shift |
| ENST00000322213 | 53399589 | 53399730 | Frame-shift |
| 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 |
| ENST00000322213 | 53381018 | 53381087 | Frame-shift |
| ENST00000322213 | 53399589 | 53399730 | Frame-shift |
| ENST00000322213 | 53405012 | 53405149 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SMC1A |
p-ENSG00000072501_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 |
| 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 |
| 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 |
| ENST00000322213 | 9801 | 1233 | 53405012 | 53405149 | 2187 | 2323 | 686 | 731 |
| 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 |
| 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 |
| 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 |
| Q14683 | 686 | 731 | 1 | 1233 | Chain | ID=PRO_0000118989;Note=Structural maintenance of chromosomes protein 1A |
| Q14683 | 686 | 731 | 660 | 935 | Coiled coil | Ontology_term=ECO:0000255;evidence=ECO:0000255 |
| Q14683 | 686 | 731 | 713 | 713 | Modified residue | Note=N6-acetyllysine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:19608861;Dbxref=PMID:19608861 |
| Q14683 | 686 | 731 | 693 | 693 | Natural variant | ID=VAR_062795;Note=In CDLS2. R->G;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:19701948;Dbxref=PMID:19701948 |
| Q14683 | 686 | 731 | 693 | 693 | Natural variant | ID=VAR_078276;Note=In CDLS2. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:24124034;Dbxref=dbSNP:rs587784408,PMID:24124034 |
| Q14683 | 686 | 731 | 711 | 711 | Natural variant | ID=VAR_064542;Note=In CDLS2. R->Q;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:20358602;Dbxref=dbSNP:rs782176647,PMID:20358602 |
| Q14683 | 686 | 731 | 711 | 711 | Natural variant | ID=VAR_062796;Note=In CDLS2. R->W;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:17273969,ECO:0000269|PubMed:19701948;Dbxref=dbSNP:rs587784409,PMID:17273969,PMID:19701948 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SMC1A |
| 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 SMC1A |
| - 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 SMC1A |
| 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 SMC1A |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
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Correlation with RNA binding proteins (RBPs) for SMC1A |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SMC1A |
| 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 SMC1A |
| 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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