BtaEX6082164 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000011215 | ACTN4
Description
Bos taurus actinin, alpha 4 (ACTN4), mRNA. [Source:RefSeq mRNA;Acc:NM_001098052]
Coordinates
chr18:48722388-48728805:+
Coord C1 exon
chr18:48722388-48722473
Coord A exon
chr18:48726887-48726979
Coord C2 exon
chr18:48728575-48728805
Length
93 bp
Sequences
Splice sites
3' ss Seq
AACCCCGTCCCCCGACCCAGGCT
3' ss Score
4.68
5' ss Seq
GACGTGAGT
5' ss Score
9.22
Exon sequences
Seq C1 exon
ACATCGTGAACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTGTCCAGCTTCTACCATGCCTTTTCGGGAGCGCAGAAG
Seq A exon
GCTGAGACCGCTGCCAACCGGATCTGCAAGGTGCTGGCCGTCAACCAGGAGAACGAGCACCTGATGGAAGATTATGAGAGGCTGGCCAGCGAC
Seq C2 exon
CTCCTGGAGTGGATCCGGCGCACCATCCCCTGGCTGGAGGACCGCGTGCCGCAGAAAACCATCCAGGAGATGCAGCAGAAGCTGGAGGACTTCCGCGACTACCGGCGGGTCCACAAGCCGCCGAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGCTGCGCCTCAGCAACCGGCCTGCCTTCATGCCCTCCGAGGGCAAGATGGTGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011215-'22-14,'22-13,25-14=AN
Average complexity
A_C1
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0030726=CH=PD(23.1=82.8)
A:
PF0043516=Spectrin=PU(9.9=35.5)
C2:
PF0043516=Spectrin=FE(68.5=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACCATGCCTTTTCGGGAGC
R:
TGATCTCCAGCTGGCACTTCT
Band lengths:
182-275
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]