HsaEX0058019 @ hg38
Exon Skipping
Gene
ENSG00000097033 | SH3GLB1
Description
SH3 domain containing GRB2 like endophilin B1 [Source:HGNC Symbol;Acc:HGNC:10833]
Coordinates
chr1:86724313-86730111:+
Coord C1 exon
chr1:86724313-86724405
Coord A exon
chr1:86728403-86728441
Coord C2 exon
chr1:86730088-86730111
Length
39 bp
Sequences
Splice sites
3' ss Seq
TCTCTTACTATGCACTTAAGCAA
3' ss Score
0.36
5' ss Seq
ATGGTAAAT
5' ss Score
6.41
Exon sequences
Seq C1 exon
AAAGAAAGGAAACTATTGCAAAATAAGAGACTGGATTTGGATGCTGCAAAAACGAGACTAAAAAAGGCAAAAGCTGCAGAAACTAGAAATTCA
Seq A exon
CAACTAAACTCAGCTCGCCTTGAAGGAGATAACATTATG
Seq C2 exon
ATTTGGGCAGAGGAGGTGACAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000097033-'19-16,'19-15,20-16
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.194 A=0.147 C2=0.000
Domain overlap (PFAM):
C1:
PF0311413=BAR=FE(12.2=100)
A:
PF0311413=BAR=FE(4.5=100)
C2:
PF0311413=BAR=FE(2.6=100)
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACTATTGCAAAATAAGAGACTGGA
R:
TGTCACCTCCTCTGCCCAAAT
Band lengths:
105-144
Functional annotations
There are 2 annotated functions for this event
PMID: 24523556
HsaEX0058019 and HsaEX0058023 are often included together. This splice isoform is associated with increased neuronal viability and mitochondrial elongation. The mitochondrial effect is associated with mitochondrial maintenance and function. Loss of this isoform is suggested to render neurons more susceptible to apoptotic stress.
PMID: 29759485
Isoforms 1b + 1c (represented by joint inclusion of this event and HsaEX0058023), show an antiapoptotic effect in human androgen-sensitive prostate cancer cell lines, while isoform 1a (corresponding to skipping of both exons) shows a pro-apoptotic effect. Isoforms 1b and 1c are up-regulated in patient-derived samples of treatment-induced neuroendocrine prostate cancer, which is a very aggressive and metastatic form of prostate cancer characterised by increased expression of SRRM4 (ENSG00000139767), a known master regulator of microexon inclusion in neuronal-related cell types. In contrast, prostate adenocarcinoma samples predominantly express isoform 1a.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development