Special

DmeALTD0000123-2/3 @ dm6

Alternative 5'ss

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:2027935-2029926:-
Coord C1 exon
chrX:2029841-2029926
Coord A exon
chrX:2029775-2029840
Coord C2 exon
chrX:2027935-2028027
Length
66 bp
Sequences
Splice sites
5' ss Seq
AATGTGACT
5' ss Score
3.25
3' ss Seq
GAAACCATGTGCAACAACAGGCG
3' ss Score
0.45
Exon sequences
Seq C1 exon
ATTTGATCAACACTCCGAAACCGGATGAACGTGCCATCATGACGTACGTCTCCTGCTACTACCACGCCTTCCAGGGAGCTCAACAG
Seq A exon
GTTGGAAATGTGACGCATGTACCCGAACCCACAAGACAATACACCTACGTCCCGAATAATTACAAT
Seq C2 exon
GCGGAAACCGCTGCCAACCGGATCTGCAAGGTGCTCAAGGTCAACCAGGAGAACGAACGCCTCATGGAGGAGTACGAGCGTCTGGCCAGTGAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000667-21-19,22-19,23-19-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact

Protein isoform when splice site is used (Ref)

No structure available
Features
Disorder rate (disopred):
  C1=0.102 A=NA C2=0.000
Domain overlap (PFAM):

C1:
PF0030726=CH=PD(23.1=82.8)
A:
NA
C2:
PF0043516=Spectrin=PU(9.9=35.5)


Main Inclusion Isoform:
FBpp0070331


Main Skipping Isoform:
FBpp0070329


Other Inclusion Isoforms:
FBpp0302778, FBpp0302779, FBpp0305936


Other Skipping Isoforms:
FBpp0292167, FBpp0305935
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGATCAACACTCCGAAACCG
R:
AGACGCTCGTACTCCTCCATG
Band lengths:
167-233
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Neural diversity
  • Neurogenesis
  • Neuronal activity
  • Splicing factor regulation (brain)
  • Splicing factor regulation (SL2)