HsaEX6094925 @ hg19
Exon Skipping
Gene
ENSG00000130402 | ACTN4
Description
actinin, alpha 4 [Source:HGNC Symbol;Acc:166]
Coordinates
chr19:39207726-39212328:+
Coord C1 exon
chr19:39207726-39207956
Coord A exon
chr19:39208567-39208714
Coord C2 exon
chr19:39212178-39212328
Length
148 bp
Sequences
Splice sites
3' ss Seq
CTGCTCCTGCCCTGCCCCAGGAC
3' ss Score
8.55
5' ss Seq
ACGGTACGG
5' ss Score
9.91
Exon sequences
Seq C1 exon
CTCCTGGAGTGGATCCGGCGCACCATCCCCTGGCTGGAGGACCGTGTGCCCCAAAAGACTATCCAGGAGATGCAGCAGAAGCTGGAGGACTTCCGCGACTACCGGCGTGTGCACAAGCCGCCCAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGCTGCGCCTCAGCAACCGGCCCGCCTTCATGCCCTCCGAGGGCAAGATGGTCTCG
Seq A exon
GACATCAACAATGGCTGGCAGCACTTGGAGCAGGCTGAGAAGGGCTACGAGGAGTGGCTGCTGAATGAGATCCGCAGGCTGGAGCGGCTCGACCACCTGGCAGAGAAGTTCCGGCAGAAGGCCTCCATCCACGAGGCCTGGACTGACG
Seq C2 exon
GGAAGGAAGCCATGCTGAAGCACCGGGACTACGAGACGGCCACACTATCGGACATCAAAGCCCTCATTCGCAAGCACGAGGCCTTCGAGAGCGACCTGGCTGCGCACCAGGACCGCGTGGAGCAGATCGCCGCCATTGCCCAGGAGCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130402-'21-24,'21-20,24-24=AN
Average complexity
A_S
Mappability confidence:
91%=100=83%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (disopred):
C1=0.091 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF131021=Phage_int_SAM_5=PD(58.0=66.2),PF0043516=Spectrin=FE(85.4=100),PF0103115=Dynamin_M=PD(76.1=70.1)
A:
PF0043516=Spectrin=PD(18.9=42.0),PF0043516=Spectrin=PU(17.0=36.0)
C2:
PF0043516=Spectrin=FE(47.2=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGTGTGCCCCAAAAGACTAT
R:
TTGATGTCCGATAGTGTGGCC
Band lengths:
248-396
Functional annotations
There are 3 annotated functions for this event
PMID: 16980305
This event
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: 22908231
This event
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
This event
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.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)