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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 SPEN |
 Gene summary |
| Gene information | Gene symbol | SPEN | Gene ID | 23013 |
| Gene name | spen family transcriptional repressor | |
| Synonyms | HIAA0929|MINT|RBM15C|SHARP | |
| Cytomap | 1p36.21-p36.13 | |
| Type of gene | protein-coding | |
| Description | msx2-interacting proteinMsx2 interacting nuclear target (MINT) homologSMART/HDAC1-associated repressor proteinnuclear receptor transcription cofactorspen homolog, transcriptional regulator | |
| Modification date | 20200313 | |
| 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 |
| SPEN | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16287852 |
| SPEN | GO:0045892 | negative regulation of transcription, DNA-templated | 16129689 |
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Gene structures and expression levels for SPEN |
| 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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ENSG00000065526
| 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 |
| CB | UP | ENST00000442985.1 | SPEN-203:protein_coding:SPEN | 1.378869e+01 | 8.422366e-01 | 6.545915e-05 | 5.166931e-04 |
| 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 SPEN |
| 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_113434 | chr1 | 15922249:15922349:15928091:15936266:15937163:15937645 | 15928091:15936266 |
| exon_skip_176546 | chr1 | 15920870:15920983:15922249:15922349:15928091:15936266 | 15922249:15922349 |
| exon_skip_19924 | chr1 | 15919404:15919517:15920870:15920983:15922249:15922349 | 15920870:15920983 |
| exon_skip_209019 | chr1 | 15872816:15873136:15876202:15876678:15909321:15909481 | 15876202:15876678 |
| exon_skip_47955 | chr1 | 15918926:15919051:15919404:15919517:15920870:15920906 | 15919404:15919517 |
| exon_skip_69953 | chr1 | 15937812:15938006:15938718:15938876:15939296:15939544 | 15938718:15938876 |
| 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 SPEN |
| 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 |
| ENST00000375759 | 15922249 | 15922349 | Frame-shift |
| ENST00000375759 | 15928091 | 15936266 | Frame-shift |
| ENST00000375759 | 15876202 | 15876678 | In-frame |
| ENST00000375759 | 15919404 | 15919517 | In-frame |
| ENST00000375759 | 15938718 | 15938876 | 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 |
| ENST00000375759 | 15876202 | 15876678 | 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 |
| ENST00000375759 | 15922249 | 15922349 | Frame-shift |
| ENST00000375759 | 15876202 | 15876678 | In-frame |
| ENST00000375759 | 15919404 | 15919517 | In-frame |
| ENST00000375759 | 15920870 | 15920983 | In-frame |
| ENST00000375759 | 15938718 | 15938876 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SPEN |
p-ENSG00000065526_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 |
| ENST00000375759 | 12249 | 3664 | 15876202 | 15876678 | 610 | 1085 | 135 | 293 |
| ENST00000375759 | 12249 | 3664 | 15919404 | 15919517 | 1727 | 1839 | 507 | 545 |
| ENST00000375759 | 12249 | 3664 | 15938718 | 15938876 | 10910 | 11067 | 3568 | 3621 |
| 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 |
| ENST00000375759 | 12249 | 3664 | 15876202 | 15876678 | 610 | 1085 | 135 | 293 |
| 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 |
| ENST00000375759 | 12249 | 3664 | 15876202 | 15876678 | 610 | 1085 | 135 | 293 |
| ENST00000375759 | 12249 | 3664 | 15919404 | 15919517 | 1727 | 1839 | 507 | 545 |
| ENST00000375759 | 12249 | 3664 | 15920870 | 15920983 | 1841 | 1953 | 545 | 583 |
| ENST00000375759 | 12249 | 3664 | 15938718 | 15938876 | 10910 | 11067 | 3568 | 3621 |
| 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 |
| Q96T58 | 135 | 293 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 135 | 293 | 125 | 277 | Compositional bias | Note=Arg-rich |
| Q96T58 | 135 | 293 | 240 | 325 | Compositional bias | Note=Ser-rich |
| Q96T58 | 135 | 293 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 135 | 293 | 188 | 188 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q96T58 | 135 | 293 | 190 | 190 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q96T58 | 507 | 545 | 507 | 510 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 517 | 522 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 543 | 549 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 507 | 545 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 507 | 545 | 438 | 513 | Domain | Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q96T58 | 507 | 545 | 517 | 589 | Domain | Note=RRM 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q96T58 | 507 | 545 | 530 | 537 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 538 | 540 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 3568 | 3621 | 3573 | 3580 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3608 | 3614 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 3568 | 3621 | 3498 | 3664 | Domain | Note=SPOC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00249 |
| Q96T58 | 3568 | 3621 | 3585 | 3598 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3600 | 3606 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3570 | 3572 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3617 | 3619 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2RT5 |
| 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 |
| Q96T58 | 135 | 293 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 135 | 293 | 125 | 277 | Compositional bias | Note=Arg-rich |
| Q96T58 | 135 | 293 | 240 | 325 | Compositional bias | Note=Ser-rich |
| Q96T58 | 135 | 293 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 135 | 293 | 188 | 188 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q96T58 | 135 | 293 | 190 | 190 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| 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 |
| Q96T58 | 135 | 293 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 135 | 293 | 125 | 277 | Compositional bias | Note=Arg-rich |
| Q96T58 | 135 | 293 | 240 | 325 | Compositional bias | Note=Ser-rich |
| Q96T58 | 135 | 293 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 135 | 293 | 188 | 188 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q96T58 | 135 | 293 | 190 | 190 | Modified residue | Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163 |
| Q96T58 | 507 | 545 | 507 | 510 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 517 | 522 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 543 | 549 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 507 | 545 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 507 | 545 | 438 | 513 | Domain | Note=RRM 3;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q96T58 | 507 | 545 | 517 | 589 | Domain | Note=RRM 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q96T58 | 507 | 545 | 530 | 537 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 507 | 545 | 538 | 540 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 543 | 549 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 554 | 560 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 575 | 577 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 583 | 586 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 545 | 583 | 1 | 573 | DNA binding | Ontology_term=ECO:0000250;evidence=ECO:0000250 |
| Q96T58 | 545 | 583 | 517 | 589 | Domain | Note=RRM 4;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176 |
| Q96T58 | 545 | 583 | 562 | 572 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 545 | 583 | 550 | 553 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:4P6Q |
| Q96T58 | 3568 | 3621 | 3573 | 3580 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3608 | 3614 | Beta strand | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 1 | 3664 | Chain | ID=PRO_0000081627;Note=Msx2-interacting protein |
| Q96T58 | 3568 | 3621 | 3498 | 3664 | Domain | Note=SPOC;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00249 |
| Q96T58 | 3568 | 3621 | 3585 | 3598 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3600 | 3606 | Helix | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3570 | 3572 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:1OW1 |
| Q96T58 | 3568 | 3621 | 3617 | 3619 | Turn | Ontology_term=ECO:0000244;evidence=ECO:0000244|PDB:2RT5 |
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3'-UTR located exon skipping events that lost miRNA binding sites in SPEN |
| 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 SPEN |
| - 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 SPEN |
| 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 SPEN |
| 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 SPEN |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SPEN |
| 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 SPEN |
| 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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