|
||||||
|
 | |
| |
| |
| Open reading frame (ORF) annotation in the exon skipping event |
| |
| 3'-UTR located exon skipping events lost miRNA binding sites |
| |
| |
| Splicing Quantitative Trait Loci (sQTLs) in the skipped exons |
| |
| |
|
Gene summary for SDR39U1 |
 Gene summary |
| Gene information | Gene symbol | SDR39U1 | Gene ID | 56948 |
| Gene name | short chain dehydrogenase/reductase family 39U member 1 | |
| Synonyms | C14orf124|HCDI | |
| Cytomap | 14q12 | |
| Type of gene | protein-coding | |
| Description | epimerase family protein SDR39U1 | |
| 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 |
Top |
Gene structures and expression levels for SDR39U1 |
| 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. |
 |
ENSG00000100445
| 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. |
 |
| Tissue type | DEG direction | ENST | Transcript info. | Base mean exp. | log2FC(AD/control) | P-value | Adjc. p-value |
| DLPFC | UP | ENST00000556249.1 | SDR39U1-217:protein_coding:SDR39U1 | 1.698144e+00 | 1.444102e+00 | 9.891665e-06 | 1.402713e-03 |
| DLPFC | UP | ENST00000553546.1 | SDR39U1-205:retained_intron:SDR39U1 | 1.838946e+01 | 8.006635e-01 | 1.729236e-05 | 2.093227e-03 |
| CB | DOWN | ENST00000538105.6 | SDR39U1-202:protein_coding:SDR39U1 | 3.213701e+02 | -9.570758e-01 | 5.785274e-09 | 1.900126e-07 |
| CB | UP | ENST00000556249.1 | SDR39U1-217:protein_coding:SDR39U1 | 2.690668e+01 | 1.742132e+00 | 1.052164e-07 | 2.217890e-06 |
| CB | DOWN | ENST00000555355.5 | SDR39U1-211:protein_coding:SDR39U1 | 1.262234e+02 | -9.813393e-01 | 2.664091e-06 | 3.448128e-05 |
| CB | UP | ENST00000555778.1 | SDR39U1-214:retained_intron:SDR39U1 | 9.167451e+00 | 9.273526e-01 | 4.930842e-05 | 4.065363e-04 |
| TC | UP | ENST00000556249.1 | SDR39U1-217:protein_coding:SDR39U1 | 5.497331e+00 | 1.432738e+00 | 2.031527e-05 | 4.534296e-04 |
| Landscape of isoform expressions across multiple brain tissues between AD and control. |
 |
Top |
Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for SDR39U1 |
| Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap). |
 |
| All exon skipping events in AD cohorts. |
| Exon skip ID | chr | Exons involved in exon skipping | Skipped exon |
| exon_skip_107785 | chr14 | 24441678:24441795:24442178:24442260:24442346:24442375 | 24442178:24442260 |
| exon_skip_147317 | chr14 | 24440783:24440926:24442098:24442260:24442346:24442441 | 24442098:24442260 |
| exon_skip_153449 | chr14 | 24440854:24440926:24441674:24441795:24442346:24442375 | 24441674:24441795 |
| exon_skip_158432 | chr14 | 24440854:24440926:24441674:24441795:24442178:24442260 | 24441674:24441795 |
| exon_skip_160287 | chr14 | 24440783:24440926:24441674:24441795:24442346:24442441 | 24441674:24441795 |
| exon_skip_166178 | chr14 | 24441771:24441795:24442109:24442260:24442346:24442375 | 24442109:24442260 |
| exon_skip_17443 | chr14 | 24440854:24440926:24442098:24442260:24442346:24442375 | 24442098:24442260 |
| exon_skip_209818 | chr14 | 24440783:24440926:24442178:24442260:24442346:24442441 | 24442178:24442260 |
| exon_skip_221319 | chr14 | 24440854:24440926:24441674:24441795:24442098:24442177 | 24441674:24441795 |
| exon_skip_24293 | chr14 | 24441771:24441795:24442178:24442260:24442346:24442375 | 24442178:24442260 |
| exon_skip_262457 | chr14 | 24440854:24440926:24441678:24441795:24442109:24442260 | 24441678:24441795 |
| exon_skip_262941 | chr14 | 24441678:24441795:24442109:24442260:24442346:24442375 | 24442109:24442260 |
| exon_skip_294935 | chr14 | 24440854:24440926:24441678:24441795:24442178:24442260 | 24441678:24441795 |
| exon_skip_50287 | chr14 | 24440854:24440926:24441674:24441795:24442098:24442172 | 24441674:24441795 |
| exon_skip_71738 | chr14 | 24440854:24440926:24442109:24442260:24442346:24442375 | 24442109:24442260 |
| exon_skip_78157 | chr14 | 24440854:24440926:24442178:24442260:24442346:24442375 | 24442178:24442260 |
| exon_skip_79643 | chr14 | 24441674:24441795:24442178:24442260:24442346:24442452 | 24442178:24442260 |
| exon_skip_94070 | chr14 | 24440854:24440926:24441674:24441795:24442098:24442260 | 24441674:24441795 |
| exon_skip_94590 | chr14 | 24440897:24440926:24441674:24441795:24442178:24442260 | 24441674:24441795 |
| 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 |
| exon_skip_122309 | Mayo_CB | 8.340244e-01 | 9.449351e-01 | -1.109107e-01 | 2.974783e-08 |
| exon_skip_78157 | Mayo_CB | 5.765854e-01 | 8.222368e-01 | -2.456515e-01 | 3.138870e-08 |
| exon_skip_252532 | Mayo_CB | 7.000000e-01 | 8.144595e-01 | -1.144595e-01 | 1.755380e-04 |
| exon_skip_78157 | Mayo_TC | 7.945122e-01 | 9.032432e-01 | -1.087310e-01 | 1.552722e-04 |
Top |
Open reading frame (ORF) annotation in the exon skipping event for SDR39U1 |
| 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 |
| 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 |
| 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 |
Top |
Infer the effects of exon skipping event on protein functional features for SDR39U1 |
p-ENSG00000100445_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 |
| 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 |
Top |
3'-UTR located exon skipping events that lost miRNA binding sites in SDR39U1 |
| 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 |
Top |
SNVs in the skipped exons for SDR39U1 |
| - 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 |
Top |
AD stage-associated exon skippint events for SDR39U1 |
| 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 |
Top |
Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SDR39U1 |
| sQTL information located at the skipped exons. |
| Tissue type | Exon skip ID | SNP id | Location | P-value | FDR |
| HCC | exon_skip_158432 | rs1956896 | chr14:24456995 | 7.894053e-10 | 2.396011e-07 |
| HCC | exon_skip_158432 | rs1043831 | chr14:24440156 | 1.698371e-09 | 4.842950e-07 |
| HCC | exon_skip_158432 | rs1956898 | chr14:24447098 | 1.698371e-09 | 4.842950e-07 |
| HCC | exon_skip_158432 | rs12884447 | chr14:24460857 | 1.698371e-09 | 4.842950e-07 |
| HCC | exon_skip_158432 | rs7152372 | chr14:24461670 | 1.292950e-06 | 2.055448e-04 |
| HCC | exon_skip_158432 | rs3759635 | chr14:24509229 | 3.810703e-05 | 3.992267e-03 |
| HCC | exon_skip_158432 | rs5248 | chr14:24506608 | 3.810703e-05 | 3.992267e-03 |
| HCC | exon_skip_158432 | rs11158709 | chr14:24444802 | 4.126202e-05 | 4.269012e-03 |
| HCC | exon_skip_158432 | rs11628094 | chr14:24456583 | 4.126202e-05 | 4.269012e-03 |
| HCC | exon_skip_158432 | rs4982925 | chr14:24460665 | 4.126202e-05 | 4.269012e-03 |
| HCC | exon_skip_158432 | rs2076946 | chr14:24482617 | 2.280305e-04 | 1.806362e-02 |
| HCC | exon_skip_158432 | rs8020496 | chr14:24484544 | 2.280305e-04 | 1.806362e-02 |
| HCC | exon_skip_158432 | rs10083509 | chr14:24438841 | 4.218978e-04 | 2.955503e-02 |
| HCC | exon_skip_158432 | rs10083382 | chr14:24438911 | 4.218978e-04 | 2.955503e-02 |
| HCC | exon_skip_158432 | rs987629 | chr14:24536379 | 5.783440e-04 | 3.796132e-02 |
| PCC | exon_skip_94590 | rs1043831 | chr14:24440156 | 1.799994e-04 | 2.754773e-02 |
| PCC | exon_skip_94590 | rs1956898 | chr14:24447098 | 1.799994e-04 | 2.754773e-02 |
| PCC | exon_skip_94590 | rs12884447 | chr14:24460857 | 1.799994e-04 | 2.754773e-02 |
| DLPFC | exon_skip_158432 | rs1043831 | chr14:24440156 | 1.667013e-10 | 5.234264e-08 |
| DLPFC | exon_skip_158432 | rs1956898 | chr14:24447098 | 1.667013e-10 | 5.234264e-08 |
| DLPFC | exon_skip_158432 | rs12884447 | chr14:24460857 | 1.667013e-10 | 5.234264e-08 |
| DLPFC | exon_skip_158432 | rs1956896 | chr14:24456995 | 2.050550e-09 | 5.385693e-07 |
| DLPFC | exon_skip_158432 | rs7152372 | chr14:24461670 | 1.414073e-07 | 2.545378e-05 |
| DLPFC | exon_skip_158432 | rs11158709 | chr14:24444802 | 1.179344e-06 | 1.693905e-04 |
| DLPFC | exon_skip_158432 | rs11628094 | chr14:24456583 | 1.179344e-06 | 1.693905e-04 |
| DLPFC | exon_skip_158432 | rs4982925 | chr14:24460665 | 1.179344e-06 | 1.693905e-04 |
| DLPFC | exon_skip_158432 | rs3759635 | chr14:24509229 | 3.111750e-06 | 3.986166e-04 |
| DLPFC | exon_skip_158432 | rs5248 | chr14:24506608 | 6.623530e-05 | 5.920691e-03 |
| DLPFC | exon_skip_158432 | rs1951139 | chr14:24474636 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs11627992 | chr14:24478487 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs8015404 | chr14:24478558 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs6573825 | chr14:24478591 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs6573826 | chr14:24478761 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs8015027 | chr14:24483240 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs8015201 | chr14:24483339 | 1.220477e-04 | 9.983947e-03 |
| DLPFC | exon_skip_158432 | rs7159031 | chr14:24472151 | 4.735208e-04 | 3.090986e-02 |
| DLPFC | exon_skip_158432 | rs8015553 | chr14:24478622 | 5.075811e-04 | 3.263582e-02 |
| DLPFC | exon_skip_158432 | rs10083509 | chr14:24438841 | 6.858850e-04 | 4.148164e-02 |
| DLPFC | exon_skip_158432 | rs10083382 | chr14:24438911 | 6.858850e-04 | 4.148164e-02 |
Top |
Correlation with RNA binding proteins (RBPs) for SDR39U1 |
| Correlated RBP and related information. |
| Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
| CB | TARDBP | exon_skip_122309 | -4.939429e-01 | 3.684774e-11 |
| CB | PABPN1 | exon_skip_122309 | -4.360348e-01 | 9.195664e-09 |
| CB | ELAVL1 | exon_skip_122309 | -4.506835e-01 | 2.505107e-09 |
| CB | RBM6 | exon_skip_122309 | -5.187373e-01 | 2.480926e-12 |
| CB | CNOT4 | exon_skip_122309 | -5.181187e-01 | 2.660789e-12 |
| CB | PCBP1 | exon_skip_122309 | -4.871286e-01 | 7.452445e-11 |
| CB | PCBP4 | exon_skip_122309 | 5.633269e-01 | 1.076548e-14 |
| CB | FUBP1 | exon_skip_122309 | -4.664639e-01 | 5.751951e-10 |
| CB | KHSRP | exon_skip_122309 | -4.559891e-01 | 1.540286e-09 |
| CB | HNRNPA2B1 | exon_skip_122309 | -5.194073e-01 | 2.299414e-12 |
| CB | NUP42 | exon_skip_122309 | 4.237266e-01 | 2.617250e-08 |
| CB | PTBP1 | exon_skip_122309 | -5.009184e-01 | 1.762888e-11 |
| CB | RBM23 | exon_skip_122309 | -4.322069e-01 | 1.278802e-08 |
| CB | HNRNPF | exon_skip_122309 | -4.425468e-01 | 5.197811e-09 |
| CB | PCBP4 | exon_skip_78157 | 5.585596e-01 | 2.422121e-14 |
| CB | PCBP4 | exon_skip_252532 | 4.000958e-01 | 2.496978e-07 |
| CB | PCBP4 | exon_skip_24293 | 5.238785e-01 | 1.379025e-12 |
| IFG | HNRNPK | exon_skip_158432 | -4.433923e-01 | 2.053159e-02 |
| IFG | EWSR1 | exon_skip_158432 | -5.337867e-01 | 4.136262e-03 |
| IFG | SRSF5 | exon_skip_158432 | -4.556491e-01 | 1.691842e-02 |
| IFG | EIF4B | exon_skip_158432 | -4.127501e-01 | 3.238151e-02 |
| IFG | ESRP1 | exon_skip_158432 | -4.936942e-01 | 8.868885e-03 |
| TC | PTBP1 | exon_skip_158432 | 4.065163e-01 | 9.611678e-08 |
Top |
RelatedDrugs for SDR39U1 |
| Approved drugs targeting this gene. (DrugBank Version 5.1.0 2018-04-02) |
| UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
RelatedDiseases for SDR39U1 |
| 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)
|