DmeINT0034433 @ dm6
Intron Retention
Gene
FBgn0015519 | nAChRalpha3
Description
The gene nicotinic Acetylcholine Receptor alpha3 is referred to in FlyBase by the symbol Dmel
AChRalpha3 (CG2302, FBgn0015519). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is X:8276200..8367169. Its molecular function is described by: acetylcholine-gated cation-selective channel activity; neurotransmitter receptor activity; acetylcholine receptor activity. It is involved in the biological process described with 6 unique terms, many of which group under: transport; localization; biological regulation; signaling; system process. 25 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: sleep defective; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of low expression to a trough of extremely low expression. Peak expression observed within 18-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chrX:8365490-8367169:-
Coord C1 exon
chrX:8366804-8367169
Coord A exon
chrX:8365747-8366803
Coord C2 exon
chrX:8365490-8365746
Length
1057 bp
Sequences
Splice sites
5' ss Seq
GCTGTAGGT
5' ss Score
3.41
3' ss Seq
TCAATAAAAATAAAACCAAGGCT
3' ss Score
-2.71
Exon sequences
Seq C1 exon
ACGGCACGCGTTTCGCTTCGAGAGAGAGAGAGAGTTACCCGAAAAATAACCAAGCAAGCAGCACAAAAAACGCGCTAAAGTCGCCAATTGTTGTTGTTGTCGTCGAAAGTCGAAAGTCGGTTGTCGCTTGTCTCGTTGTTTCCCGTTGTTTCTCGTTGATTGTCGTTGTTGTTGTCGCCGCCGTCGTCGTCGGTTGTTGTCGTATTGTTGTTGTTGCTGGCTCTCTGTTTTTTTTTGCGTTATTTTGTTGTTGCCGTCGTCCCGCCGCCTCCGCCTTCGCCGCCCCGCCCCCTTTTCGTCTGACTGTCTGCGTGTGAGCGTGTGTTGGTGTGTTGTGTCTGTGTCGCGCATGTGACCGCCTCAGCT
Seq A exon
GTAGGTTTACCGTTATTTTTTTTTTGCATTCTCCACTTTGTTGTTTATAATTATTTATAATGCTAGCTTTACCGTTTGAATCCACTTTCTTGTGCCAGGCAATCAGGGAAGAGAAAAAAAAAAAAACAAATAATAATATATAGCCGCGATAAACAAAACAGAACAGCTGGGCAAACGGGCTGCGAGTTTGTGGGGTTAACAAATTTTTAGTTGCAACTTTGTCGCTTTTGGCGGATAAAACAGCGCCCGAAACGCGGGCAAAACGCGCACAAAACGCTTACATAAGTTGGCCATTTGTAAGCGCAACTGTGTGTGTGTGTGTGTGCGTGTGTTGCTATTTTAAGGCTAGAAAATTACCTAACCCAAATGCTTAATAAAAGTAAATGAAATTTTTGTTGGAAAACGTCACACTTCGAGAAAGACAAAAACCCGAAAAAAAGCGCGCGACTTCTTGGTGAAATAAAGAAAGAAAAAGGAGAAATGGTTTAAAAATAAGAAAATGGGGTGGAAGAAAAAAAAAAACGAAAGAAAAAGAAGGGGGCAAAGAAAACCGAAATTGTTACACGGTCATTGCGGAGGTCGCGCCAAACTAAAAGAGAGATTTTATTTGCGAGCTGCCAAGGCAAAACACAGCCAAGGGGAATTAGAAATCAATTGACATGCAATGTTTCGTAATAATAAATTGAAAAGGGGAATTCCCGTCAAAAGTTACAACTTGTTGATTGCCAGCAAAAGCGTCGTGGTTATTATTTTTTTTTTTACGAAACGTGACAATGCCAGATATGGTCTTAACTATTTATCAATGATTTGTGGTTATGCGAAAGTTTTGGCAACGAGCAGAGATTTGTAATTAAAGTTCTTAGTTGAGGCAGAAAGGCTTAAGTCGAGCTTGATTTATTAACAATTTAGTTAAAGGCATTTGTTCCATATTTTACTATGCTTTTCGTTTATTTTTCTTTTAAGTTCAGCTGAGAGCGAGACCAACCCACAACTTCTTTTTTTTGCTCTTTTTTTTAATGTTCCAAAACCAAACGAATTCAATAAAAATAAAACCAAG
Seq C2 exon
GCTGAAACTTCAAAACAAATATTGGAAAATTCCGAATAAAAAAAGGTGTGCCAGTTAGCCGAAGGAACCGAATGCAGATTGAAAGCTAAAGTTCGAGGAAGCCAACAGGAACCAAAACAAGGAAGCGAGCCCCTGTCCGTGCGAAGGACCTCCTGGGTCTGTGTGCGTGTGTGCGTGTGTGGGTGCGGCGACACCACTACCACTACCGCTATCACTACCACTATAGCAGCATCGGGCGAAATACTTTTTGTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0015519:FBtr0289988:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
TCGCTTGTCTCGTTGTTTCCC
R:
TCCTGTTGGCTTCCTCGAACT
Band lengths:
353-1410
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)