DmeINT0034426 @ dm6
Intron Retention
Gene
FBgn0000036 | nAChRalpha1
Description
The gene nicotinic Acetylcholine Receptor alpha1 is referred to in FlyBase by the symbol Dmel
AChRalpha1 (CG5610, FBgn0000036). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (2 unique). Gene sequence location is 3R:24393896..24457157. Its molecular function is described by: neurotransmitter receptor activity; acetylcholine-gated cation-selective channel activity; acetylcholine receptor activity. It is involved in the biological process described with 8 unique terms, many of which group under: cellular process; cell communication; signaling; biological regulation; synaptic signaling. 26 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; chemical resistant; some die during pupal stage; memory defective; fertile; lethal - all die before end of pupal stage. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of no expression detected. Peak expression observed within 12-24 hour embryonic stages, during early larval stages.
Coordinates
chr3R:24403215-24404893:-
Coord C1 exon
chr3R:24404682-24404893
Coord A exon
chr3R:24403511-24404681
Coord C2 exon
chr3R:24403215-24403510
Length
1171 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGA
5' ss Score
10.03
3' ss Seq
ATTTTTATCTTTTTCCCCAGCAC
3' ss Score
8.98
Exon sequences
Seq C1 exon
ATCCCCTGTCACGCATCGCATGGCACCGTGGGTGCAGCGCCTCTTCATCCAGATCCTGCCCAAGCTGCTCTGCATCGAGCGGCCCAAGAAGGAGGAGCCCGAGGAGGACCAGCCGCCCGAAGTGCTCACCGATGTCTATCACCTGCCGCCGGATGTGGACAAGTTTGTCAACTACGATTCGAAGCGTTTCAGCGGCGACTACGGCATTCCAG
Seq A exon
GTACGAACCACTATCTCATCCATAAACCCAATTCCGTATAACAATGGTATGCCTTCTGGCGGGCGAATCCCATACAAAAGAAGCAAAAGTTTTCCACCCATTTTCCCGCTCCGCTTGATGCAAACTTTCTGTGTAGAACTTGGCATCTTGGGATTCGTGGGCTTCTTGTAGTTCCCCATCCTGCAGCTGAGAAATTTATGAATGTTTTCAACTGGCTTTAGTGGGCACATTACCAACGGTGCATGCAGCGAGCGACGGGAAACTTGCAACTTGCCAGTTTATATTCCATTTTAAATATGCACAACAACATGGAAATTATATGCATTCAGACACACCGCTTTATAATGATGCCGTGTTCGGAGGGCGGGGCGAAATAATTTATGACAATTAACAAGTGCATCTGCAAGGACGCCGGCCAAAAGGGAAAGTTTTGTCCAGGCATTATAAGTTCTAGGAAATGCCTTTCATGCTATTTTGTCGCCCCAAACTGACAGCATTTAGATGGCTCATTAAAATGGAGTCAAGATTAAAGAAGCAATTTTTTAATAAGGCGCACACTTGGTGTATACGTAATATTGCGCATACGCCGCGTGGAGCAATAATTTTAAGCTTACGGTCAAAGAATAAAATAATTTCTACTTCAAATGGCTTTCGAAGCGCGCGAAAATGAAAGGGAAATCGCAAAAGAAAAGACCTGAAACTTTCAAATGGCCCAGCAAAATAAATGGAAAACAGAATGCAGAAAACTATTTATTGAGTTTCCTTATTGTATCCCCGGACCTGAAGTCCTGCTTCTCTGCTTCTGTTGGGCCGCCCTCGAGGTTGAGGGTCCTTTGTCTACTCACTTCCTTCGGGGACATTGTGCCAAGGAGCATTGCGACGGCGAAGACAATGCAGAAAAGTTGCAAATTGCATTTACAACTTTATTTGCCTAATGCTGTTAATGCTGGCAAACACTCGGAAAAAAGTATCCACCCAGAATTGGGTCCCTGGTTTCGGTAAAAAGTAACGTAAAAGCAGCTTACTTAACAAGAAGCTATACTTTCTATGACACACCAGTAATTTCAACTTCAAAGAAAATGAAGGCTATGAAGTTAATTTCTGTTAAAAGAAGTGCGTTTTTTAAGGATTTTAAAGATTTTAATCAGTATATTTTTATCTTTTTCCCCAG
Seq C2 exon
CACTACCCGCTTCGCATCGCTTCGATTTGGCTGCGGCGGGCGGGATTAGCGCCCACTGTTTCGCAGAACCGCCGCTGCCCTCCTCACTGCCACTCCCGGGCGCCGACGACGATCTGTTCAGCCCGTCGGGCCTCAACGGAGACATCAGTCCCGGCTGCTGCCCGGCCGCTGCAGCCGCCGCTGCCGCCGATCTCAGTCCTACGTTCGAGAAGCCCTACGCCCGCGAAATGGAGAAGACCATCGAAGGATCCCGCTTCATCGCGCAGCACGTGAAGAACAAGGATAAGTTTGAGAGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000036:FBtr0084619:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.208 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=FE(24.9=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(34.4=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303342
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0084003, FBpp0306936
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:
CACCGATGTCTATCACCTGCC
R:
ATGAAGCGGGATCCTTCGATG
Band lengths:
345-1516
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)