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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 SNCB |
Gene summary |
Gene information | Gene symbol | SNCB | Gene ID | 6620 |
Gene name | synuclein beta | |
Synonyms | - | |
Cytomap | 5q35.2 | |
Type of gene | protein-coding | |
Description | beta-synucleinI(2)-synuclein | |
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 |
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Gene structures and expression levels for SNCB |
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. |
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 |
CB | DOWN | ENST00000310112.7 | SNCB-201:protein_coding:SNCB | 1.092263e+02 | -4.420306e+00 | 1.318582e-11 | 1.227979e-09 |
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 SNCB |
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_125636 | chr5 | 176626398:176626516:176626720:176626761:176629534:176629663 | 176626720:176626761 |
exon_skip_13635 | chr5 | 176629534:176629663:176629809:176629965:176630280:176630534 | 176629809:176629965 |
exon_skip_156976 | chr5 | 176629534:176629663:176629809:176629965:176630280:176630303 | 176629809:176629965 |
exon_skip_170524 | chr5 | 176626494:176626516:176626720:176626761:176629534:176629663 | 176626720:176626761 |
exon_skip_33983 | chr5 | 176629534:176629663:176629809:176629965:176630280:176630401 | 176629809:176629965 |
exon_skip_34425 | chr5 | 176629534:176629663:176629809:176629965:176630280:176630415 | 176629809:176629965 |
exon_skip_36372 | chr5 | 176626485:176626516:176626720:176626761:176629534:176629663 | 176626720:176626761 |
exon_skip_63701 | chr5 | 176621214:176621303:176626398:176626516:176626720:176626761 | 176626398:176626516 |
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 SNCB |
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 |
ENST00000310112 | 176629809 | 176629965 | 3UTR-3UTR |
ENST00000310112 | 176626398 | 176626516 | Frame-shift |
ENST00000393693 | 176626398 | 176626516 | Frame-shift |
ENST00000506696 | 176626398 | 176626516 | Frame-shift |
ENST00000510387 | 176626398 | 176626516 | Frame-shift |
ENST00000310112 | 176626720 | 176626761 | In-frame |
ENST00000393693 | 176626720 | 176626761 | In-frame |
ENST00000506696 | 176626720 | 176626761 | In-frame |
ENST00000510387 | 176626720 | 176626761 | 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 |
ENST00000310112 | 176629809 | 176629965 | 3UTR-3UTR |
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 |
ENST00000310112 | 176629809 | 176629965 | 3UTR-3UTR |
ENST00000310112 | 176626398 | 176626516 | Frame-shift |
ENST00000393693 | 176626398 | 176626516 | Frame-shift |
ENST00000506696 | 176626398 | 176626516 | Frame-shift |
ENST00000510387 | 176626398 | 176626516 | Frame-shift |
ENST00000310112 | 176626720 | 176626761 | In-frame |
ENST00000393693 | 176626720 | 176626761 | In-frame |
ENST00000506696 | 176626720 | 176626761 | In-frame |
ENST00000510387 | 176626720 | 176626761 | In-frame |
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Infer the effects of exon skipping event on protein functional features for SNCB |
p-ENSG00000074317_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 |
ENST00000310112 | 1400 | 134 | 176626720 | 176626761 | 373 | 413 | 40 | 54 |
ENST00000393693 | 1251 | 134 | 176626720 | 176626761 | 381 | 421 | 40 | 54 |
ENST00000506696 | 569 | 134 | 176626720 | 176626761 | 243 | 283 | 40 | 54 |
ENST00000510387 | 747 | 134 | 176626720 | 176626761 | 317 | 357 | 40 | 54 |
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 |
ENST00000310112 | 1400 | 134 | 176626720 | 176626761 | 373 | 413 | 40 | 54 |
ENST00000393693 | 1251 | 134 | 176626720 | 176626761 | 381 | 421 | 40 | 54 |
ENST00000506696 | 569 | 134 | 176626720 | 176626761 | 243 | 283 | 40 | 54 |
ENST00000510387 | 747 | 134 | 176626720 | 176626761 | 317 | 357 | 40 | 54 |
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 |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
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 |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 1 | 134 | Chain | ID=PRO_0000184035;Note=Beta-synuclein |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 20 | 67 | Region | Note=4 X 11 AA tandem repeats of [EGS]-K-T-K-[EQ]-[GQ]-V-X(4) |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 31 | 41 | Repeat | Note=2 |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
Q16143 | 40 | 54 | 42 | 56 | Repeat | Note=3%3B approximate |
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3'-UTR located exon skipping events that lost miRNA binding sites in SNCB |
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 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-3188 | chr5:176629825-176629832 | 8mer-1a | chr5:176629814-176629835 | 165.00 | -24.27 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-561-5p | chr5:176629854-176629861 | 8mer-1a | chr5:176629851-176629871 | 156.00 | -21.16 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-1471 | chr5:176629870-176629877 | 8mer-1a | chr5:176629862-176629883 | 168.00 | -33.79 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6836-5p | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6132 | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
Mayo | ENST00000310112 | 176629809 | 176629965 | hsa-miR-671-3p | chr5:176629925-176629932 | 8mer-1a | chr5:176629911-176629932 | 162.00 | -25.53 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-3188 | chr5:176629825-176629832 | 8mer-1a | chr5:176629814-176629835 | 165.00 | -24.27 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-561-5p | chr5:176629854-176629861 | 8mer-1a | chr5:176629851-176629871 | 156.00 | -21.16 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-1471 | chr5:176629870-176629877 | 8mer-1a | chr5:176629862-176629883 | 168.00 | -33.79 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6836-5p | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6132 | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
MSBB | ENST00000310112 | 176629809 | 176629965 | hsa-miR-671-3p | chr5:176629925-176629932 | 8mer-1a | chr5:176629911-176629932 | 162.00 | -25.53 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-3188 | chr5:176629825-176629832 | 8mer-1a | chr5:176629814-176629835 | 165.00 | -24.27 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-561-5p | chr5:176629854-176629861 | 8mer-1a | chr5:176629851-176629871 | 156.00 | -21.16 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-1471 | chr5:176629870-176629877 | 8mer-1a | chr5:176629862-176629883 | 168.00 | -33.79 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6836-5p | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-6132 | chr5:176629902-176629909 | 8mer-1a | chr5:176629885-176629909 | 159.00 | -31.87 |
ROSMAP | ENST00000310112 | 176629809 | 176629965 | hsa-miR-671-3p | chr5:176629925-176629932 | 8mer-1a | chr5:176629911-176629932 | 162.00 | -25.53 |
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SNVs in the skipped exons for SNCB |
- 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 SNCB |
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 |
CDR | MSBB | IFG | exon_skip_13635 | -4.390896e-01 | 1.940512e-02 | chr5 | - | 176629534 | 176629663 | 176629809 | 176629965 | 176630280 | 176630534 |
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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SNCB |
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 SNCB |
Correlated RBP and related information. |
Tissue type | RBP name | Exon skip ID | Correlation coeifficient | P-value |
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RelatedDrugs for SNCB |
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 SNCB |
Diseases associated with this gene. (DisGeNet 4.0) |
Gene | Disease ID | Disease name | # pubmeds | Source |