DmeEX6000296 @ dm6
Exon Skipping
Gene
FBgn0000667 | Actn
Description
The gene alpha actinin is referred to in FlyBase by the symbol DmelActn (CG4376, FBgn0000667). It is a protein_coding_gene from Dmel. It has 10 annotated transcripts and 10 polypeptides (4 unique). Gene sequence location is X:2023822..2042311. Its molecular function is described by: protein binding; actin filament binding; calcium ion binding; actin binding. It is involved in the biological process described with: sarcomere organization; actin filament bundle assembly; actin cytoskeleton reorganization. 48 alleles are reported. The phenotypes of these alleles manifest in: non-connected functional system; larva; somatic muscle; sensory system; pericardial cell. The phenotypic classes of alleles include: increased mortality; phenotype; some die during pupal stage; visible. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of moderately high expression. Peak expression observed within 12-24 hour embryonic stages, at stages throughout the larval period, during late pupal stages, in stages of adults of both sexes.
Coordinates
chrX:2027521-2029926:-
Coord C1 exon
chrX:2029775-2029926
Coord A exon
chrX:2027935-2028027
Coord C2 exon
chrX:2027521-2027871
Length
93 bp
Sequences
Splice sites
3' ss Seq
GAAACCATGTGCAACAACAGGCG
3' ss Score
0.45
5' ss Seq
GATGTAAGT
5' ss Score
9.11
Exon sequences
Seq C1 exon
ATTTGATCAACACTCCGAAACCGGATGAACGTGCCATCATGACGTACGTCTCCTGCTACTACCACGCCTTCCAGGGAGCTCAACAGGTTGGAAATGTGACGCATGTACCCGAACCCACAAGACAATACACCTACGTCCCGAATAATTACAAT
Seq A exon
GCGGAAACCGCTGCCAACCGGATCTGCAAGGTGCTCAAGGTCAACCAGGAGAACGAACGCCTCATGGAGGAGTACGAGCGTCTGGCCAGTGAT
Seq C2 exon
TTGCTGGAGTGGATCCGTCGCACCATGCCCTGGTTGAACTCGCGCCAGGCCGACAACTCGCTGGCAGGTGTGCAGAAGAAGCTGGAGGAGTACCGCACCTACCGTCGCAAGCACAAGCCACCACGTGTGGAGCAGAAGGCCAAGCTGGAGACCAACTTCAACACGCTGCAGACCAAGCTGCGCCTGTCCAACCGGCCCGCCTACCTGCCCACCGAGGGCAAGACCGTGTCCGACATCTCCAACTCGTGGAAGGGCCTGGAGCTGGCCGAGAAGGCCTTTGAGGAATGGCTGCTGGCCGAGACCATGCGCCTGGAGCGCCTTGAACATCTGGCCCAGAAGTTCAAGCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000667-'22-20,'22-19,25-20=AN
Average complexity
A_C2
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (disopred):
C1=0.123 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0030726=CH=PD(23.1=47.1)
A:
PF0043516=Spectrin=PU(9.9=35.5)
C2:
PF0043516=Spectrin=PD(88.3=83.8),PF0043516=Spectrin=PU(7.5=6.8)
Main Inclusion Isoform:
FBpp0070331
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
FBpp0070329, FBpp0070330, FBpp0292167, FBpp0302777, FBpp0302778, FBpp0302779, FBpp0305935, FBpp0305936
Other Skipping Isoforms:
NA
Associated events
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
AGGGAGCTCAACAGGTTGGAA
R:
ACTCCTCCAGCTTCTTCTGCA
Band lengths:
171-264
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]
SPECIAL DATASETS
- Neural diversity
- Neurogenesis
- Neuronal activity
- Splicing factor regulation (brain)
- Splicing factor regulation (SL2)