DmeINT0000566 @ dm6
Intron Retention
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:2025775-2027462:-
Coord C1 exon
chrX:2027284-2027462
Coord A exon
chrX:2026910-2027283
Coord C2 exon
chrX:2025775-2026909
Length
374 bp
Sequences
Splice sites
5' ss Seq
TAAGTAAGT
5' ss Score
8.07
3' ss Seq
ATCCGAGCTTTGATCCACAGCAC
3' ss Score
3.84
Exon sequences
Seq C1 exon
GCCGATGCCCACGAGGACTGGACGCGTGGCAAGGAGGAGATGCTGCAGTCGCAGGACTTCCGCCAGTGCAAGCTCAACGAGCTGAAGGCCCTAAAGAAGAAGCACGAAGCCTTTGAGTCTGACCTGGCCGCCCACCAGGATCGTGTGGAGCAGATTGCCGCCATCGCCCAGGAGCTTAA
Seq A exon
GTAAGTGTCTGCCCCGGGCGAACCCATTATCTAATCTCGATTTATCCCCGCCTGCTGCCACCGATGGTCAATGGTGATTCTGATCTGTGTCCAGCGTGAGGTTAGGTAGAATTCCACATTCTCGATCAGTCATCTATCCACACACCAAAATTTGCCAGACATTTTGCATACGGATGTTCCTTCCATGTCTCCTTTAGGCTAATCTTTTGTTTGCCAATTGTGCCTATATCAGGCTTTTGTCCTAACGGAAATGGGTTAGGCTTACTGGCAATACTATCCCATCTACTCTCGCAGCGTTCACCATTCCATCTGAAATCACATTTCCTCAGCCTGTTCGAACAGAGATCCCCACTAATCCGAGCTTTGATCCACAG
Seq C2 exon
CACTCTGGAGTACCATGACTGTGTGTCTGTGAACGCCAGGTGCCAGCGCATCTGCGACCAATGGGATCGCTTGGGTGCTCTTACCCAGCGCAGGCGCACCGCCTTAGACGAGGCCGAGCGAATCCTGGAGAAGATCGACATCTTGCATTTGGAGTTCGCGAAGCGTGCGGCGCCGTTCAACAACTGGCTGGATGGTACGCGCGAGGATCTTGTGGACATGTTTATTGTACACACCATGGAGGAAATCCAAGGCCTGATCCAGGCGCACGACCAGTTCAAGGCGACCCTGGGTGAGGCCGACAAGGAGTTCAACCTGATCGTGAACCTGGTCCGCGAAGTGGAGTCGATTGTGAAGCAGCACCAGATCCCCGGCGGCCTAGAGAACCCCTACACCACCCTGACCGCCAACGACATGACGCGCAAGTGGAGCGACGTCCGCCAACTGGTGCCCCAACGCGACCAGACTTTGGCCAACGAGCTGCGCAAGCAACAGAACAACGAAATGCTCCGCCGTCAGTTTGCCGAGAAGGCCAACATTGTCGGCCCCTGGATCGAGCGGCAAATGGATGCTGTTACGGCCATCGGTATGGGACTGCAGGGATCGCTGGAGGACCAACTGCACCGGCTCAAGGAGTACGAGCAGGCCGTCTACGCCTACAAGCCGAACATTGAGGAGCTGGAGAAGATCCACCAAGCGGTGCAGGAATCGATGATCTTCGAGAACCGATACACCAACTACACGATGGAAACGCTGCGCGTCGGCTGGGAGCAGCTGCTTACATCTATCAACCGCAACATCAACGAGGTGGAGAACCAGATTCTCACCCGCGACTCCAAGGGCATTAGCCAGGAGCAGCTGAACGAATTCCGCAGCAGCTTCAACCACTTCGACAAGAACCGCACCGGCCGACTGTCGCCCGAGGAGTTCAAGTCGTGCTTGGTCTCGTTGGGCTACTCGATTGGCAAGGATCGCCAGGGTGATTTGGACTTCCAGCGCATCCTCGCCGTCGTCGATCCCAACAACACTGGCTACGTGCACTTCGACGCCTTCCTCGACTTCATGACCCGCGAGAGCACCGATACCGACACTGCCGAACAAGTCATCGACTCCTTCCGAATCCTGGCAGCCGACAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000667:FBtr0070344:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043516=Spectrin=FE(55.7=100)
A:
NA
C2:
PF0043516=Spectrin=PD(34.9=9.8),PF0043516=Spectrin=WD(100=29.3),PF0043516=Spectrin=WD(100=27.4),PF134991=EF-hand_7=WD(100=25.3),PF087265=EFhand_Ca_insen=PU(26.9=4.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0070331
Other Inclusion Isoforms:
FBpp0302777
Other Skipping Isoforms:
FBpp0070329, FBpp0070330, FBpp0292167, FBpp0302778, FBpp0302779, FBpp0305935, FBpp0305936
Associated events
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:
CAAGGAGGAGATGCTGCAGTC
R:
ATCCAGCCAGTTGTTGAACGG
Band lengths:
343-717
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)