BtaEX6082165 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000011215 | ACTN4
Description
Bos taurus actinin, alpha 4 (ACTN4), mRNA. [Source:RefSeq mRNA;Acc:NM_001098052]
Coordinates
chr18:48720283-48722473:+
Coord C1 exon
chr18:48720283-48720361
Coord A exon
chr18:48721584-48721665
Coord C2 exon
chr18:48722388-48722473
Length
82 bp
Sequences
Splice sites
3' ss Seq
CTCTCGCCTCCCTCCCCCAGGAC
3' ss Score
11.71
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
Exon sequences
Seq C1 exon
CTGGAAGGATGGTCTTGCCTTCAATGCCCTGATCCACCGGCACAGACCAGAGCTGATCGAGTACGACAAGCTGAGAAAG
Seq A exon
GACGACCCCGTCACCAACCTGAACAATGCCTTCGAAGTGGCTGAGAAATACCTCGACATCCCCAAGATGCTAGATGCAGAGG
Seq C2 exon
ACATCGTGAACACGGCCCGGCCCGACGAGAAGGCCATAATGACCTATGTGTCCAGCTTCTACCATGCCTTTTCGGGAGCGCAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011215-'20-10,'20-9,21-10=AN
Average complexity
A_C1
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0030726=CH=FE(25.0=100)
A:
PF0030726=CH=FE(26.0=100)
C2:
PF0030726=CH=PD(23.1=82.8)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAGGATGGTCTTGCCTTCA
R:
CTTCTGCGCTCCCGAAAAGG
Band lengths:
163-245
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]