RnoEX0006375 @ rn6
Exon Skipping
Gene
ENSRNOG00000020433 | Actn4
Description
actinin alpha 4 [Source:RGD Symbol;Acc:61816]
Coordinates
chr1:87086677-87090507:-
Coord C1 exon
chr1:87090277-87090507
Coord A exon
chr1:87089571-87089718
Coord C2 exon
chr1:87086677-87086827
Length
148 bp
Sequences
Splice sites
3' ss Seq
TGCTTTCTCCTACCCCACAGGAC
3' ss Score
10.96
5' ss Seq
ATGGTATGC
5' ss Score
7.14
Exon sequences
Seq C1 exon
CTTCTAGAGTGGATCCGGCGCACCATCCCCTGGCTGGAAGACCGTGTGCCTCAGAAGACCATCCAGGAGATGCAGCAGAAGCTGGAGGACTTCCGAGACTATAGGCGTGTGCACAAGCCCCCCAAGGTACAGGAGAAGTGTCAGCTGGAGATCAACTTCAACACCCTGCAGACCAAGCTGCGGCTGAGCAACCGGCCTGCCTTCATGCCCTCCGAGGGCAGGATGGTCTCG
Seq A exon
GACATCAACAATGGGTGGCAACATCTGGAGCAGGCTGAGAAGGGCTATGAAGAATGGCTCTTGAATGAAATCCGTAGGCTGGAACGACTTGATCACCTGGCAGAGAAATTCCGGCAGAAGGCTTCCATCCATGAGGCCTGGACCGATG
Seq C2 exon
GGAAGGAGGCCATGCTGAAGCACCGGGACTATGAGACAGCCACCCTGTCAGACATCAAAGCTCTGATCCGAAAGCATGAGGCCTTTGAGAGTGACCTGGCGGCGCACCAGGACCGCGTGGAGCAGATCGCGGCTATTGCCCAGGAGCTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020433-'35-21,'35-18,37-21
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (disopred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(68.5=100)
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
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTGTGCCTCAGAAGACCATC
R:
TTGATGTCTGACAGGGTGGCT
Band lengths:
247-395
Functional annotations
There are 3 annotated functions for this event
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: 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.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]