GgaEX0021047 @ galGal3
Exon Skipping
Description
NA
Coordinates
chrUn_random:38546836-38547745:-
Coord C1 exon
chrUn_random:38547664-38547745
Coord A exon
chrUn_random:38547316-38547401
Coord C2 exon
chrUn_random:38546836-38546921
Length
86 bp
Sequences
Splice sites
3' ss Seq
CCCTCACTGTTCACTTACAGACA
3' ss Score
9.47
5' ss Seq
AAGGTACCG
5' ss Score
9.67
Exon sequences
Seq C1 exon
GATGACCCCGTGACCAACCTGAACAACGCCTTTGAGGTGGCAGAGAAGTACCTGGACATCCCCAAGATGTTGGATGCCGAGG
Seq A exon
ACATTGTCAACACAGCTCGCCCCGACGAGAAGGCCATCATGACTTACGTGTCCAGCTTCTACCACGCCTTTTCAGGGGCTCAGAAG
Seq C2 exon
ATATTGTAGGCACTCTCAGGCCCGATGAGAAGGCCATCATGACATACGTTTCCTGCTTCTACCACGCTTTCTCGGGGGCTCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014305-'7-8,'7-7,8-8
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
In the CDS, with uncertain impact
Show structural model
Features
Disorder rate (disopred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0030726=CH=FE(29.3=100)
A:
PF0030726=CH=PD(26.1=82.8)
C2:
PF0030726=CH=PD(26.1=82.8)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGACCCCGTGACCAACCT
R:
CTTCTGAGCCCCCGAGAAAG
Band lengths:
168-254
Functional annotations
There are 5 annotated functions for this event
PMID: 15122314
HsaEX0002154 and HsaEX0002155 are mutually exclusive. Expression of the splice variant (containing HsaEX0002155 instead of HsaEX0002154) was highly specific to SCLC cell lines (10/10), biopsies (3/3), and testis. The variant encoded a peptide with a three amino-acid change in exon 8, where the germline missense mutation takes place in familial focal segmental glomerulosclerosis (FSGS). The variant protein showed high affinity to filamentous actin polymers and was not localized with cortical actin. Alternatively spliced actinin-4 may be a new diagnostic marker of SCLC and a candidate target for selective therapy.
PMID: 16980305
This study isolated a novel splice variant of alpha-actinin 4 (skipping exons 3-12; ENST00000424234) that is predominantly localized in the nucleus, a pattern distinct from the full-length alpha-actinin 4, which is primarily distributed in the cytoplasm and plasma membrane. Exon 3: HsaEX6094930, ex 4: HsaEX6094929, ex 5: HsaEX6094928, ex 6: HsaEX6094927, ex 7: HsaEX6094926, ex 8: HsaEX0002154, ex 9: HsaEX7010513, ex 10: HsaEX1002558, ex 11: HsaEX6094925, ex 12: HsaEX6094924.
PMID: 22887464
[Disease association only]. Variant actinin-4 (with Hsa0002155 instead of Hsa0002154) was expressed in 55% (96/176) of HGNTs, but in only 0.8% (3/378) of non-neuroendocrine (NE) lung cancers. The expression of variant actinin-4 was significantly associated with poorer overall survival in HGNT patients (P=0.00021, log-rank test). Multivariate analysis using the Cox proportional hazards model showed that the expression of variant actinin-4 was the most significant independent negative predictor of survival in HGNT patients (hazard ratio (HR), 2.15; P=0.00113) after the presence of lymph node metastasis (HR, 2.25; P=0.00023).
PMID: 22908231
ACTN4(Iso) overexpression increases transcriptional activity of the VDRE and ERE promoters. Both ACTN4(WT) and ACTN4(Iso) co-immunoprecipitate with estrogen receptors. Overexpression of ACTN4(Iso) fused to Gal4 increases basal transcription. The same is seen with overexpression of ACTN4(WT)-Gal4, but the effect is smaller.
PMID: 27998979
Overexpression of either ATN4(WT) or ACTN4(Iso) increases GRE reporter activity. Disruption of the LXXLL nuclear receptor-interacting motif present in ACTN4 results in reduced GR interaction and dexamethasone-mediated transactivation of a GRE reporter while still maintaining its actin-binding activity. In contrast, an ACTN4 isoform, ACTN4 (Iso), that loses its actin-binding domain is still capable of potentiating a GRE reporter.