DmeINT0034493 @ dm6
Intron Retention
Gene
FBgn0000038 | nAChRbeta1
Description
The gene nicotinic Acetylcholine Receptor beta1 is referred to in FlyBase by the symbol Dmel
AChRbeta1 (CG11348, FBgn0000038). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3L:4429349..4435993. Its molecular function is described by: acetylcholine-gated cation-selective channel activity; transmembrane signaling receptor activity; neurotransmitter receptor activity. It is involved in the biological process described with 6 unique terms, many of which group under: signaling; cellular process; synaptic signaling; cell communication; anterograde trans-synaptic signaling. 15 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; partially lethal - majority die; some die during pupal stage; short lived. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr3L:4429566-4432522:+
Coord C1 exon
chr3L:4429566-4429715
Coord A exon
chr3L:4429716-4432385
Coord C2 exon
chr3L:4432386-4432522
Length
2670 bp
Sequences
Splice sites
5' ss Seq
TGGGTACGT
5' ss Score
7.7
3' ss Seq
GTTTCCGTTGTGTTTTTTAGTCA
3' ss Score
8.48
Exon sequences
Seq C1 exon
TTTTGGGGCGTGGGCCAGCGAAATCCCAATGCGAAAAAATATAAATTAGCCATGTCCCTGGAGTAAGTGAAAAGTGTGGAAAAATCATGGAGTCTTCCTGCAAATCCTGGCTGTTGTGCAGCATCCTGGTGCTTGTGGCCTTTTCGTTGG
Seq A exon
GTACGTATTTTGGGCTACGAAGAAGAAGACTGCCACGCCCCCTTTCGGGCAAGGGCCGTTATGTAATCGTAAAGGAAAGAAATGCAAATGAAGGCCTAAAAACTCTGTTAACTCTGCTAACCGTTTCTTAGTCCCCGAAAAACGAAAACTATCTCTCTATTTCTCTTCTCCTTAGCTAGCTTACGATTTTACAGCAATGATTTGATTTTTTTCTTAAATTTACGCTTTGCGCTGGCAGCGCCGCCTTAACAAGTTCTCCAAGCTCTCATTGCCAACCACCAAGTACCAAGTACCAACTACCACCGGCCCTCCAGCTCCTGGCATCCAACGTTTCGTGTATATAGCTTAGCCACACAACTCCCAAAAGAACAGCAACAACTACCAAATGTACTGGATTTAGTAGCTATATAGCAAATAGACCAGCAACAACAACCGCCACACAAATCTCGACTTGCGATTGCCCGAAAAAATGAGTCTTGGAGAATCTGTCAAAGCGTCGCTGCTGCAGCGCTGCAAAAAAAAAAAAAAAAAAAAAGAACCGAAAATTATAACCGAATCACAACTGCGCTAGTCATCAAAACTCTTTGTAAACTTTATATATATATATATATATAATTTGGAATCTCAAGTAGAACTCCTCATAGCACACCTCGCACTCTGTTAAGTGCCGCCCCACAGATTAGATATTTTGGCATAGCTATAACTTCTATCTCTATATAGATTCACTAAACATTAGCTTAGCTTTAGCTATCTCTCTCTCTCTCTCTCTTGCTCTCTCTTTCTCTCCCGCTCTCCGACTCTATATCCATTGCTCGACAACTGTAAACTTCTGTACCCGAACCGAACTATCAAACTATACGCCCAGTACACCTGCATACTTGTTTTACTCTATGAATATTTTACAAACAATATATAATATTCCCCAGCTATAATCGCTTTTGTAATTATTAACATTTCTCCAGAGTCCCCTCTGCATTTCTCTCGCTCGCTCTCTCTCTATGACTCTCTATCTCTCTGTCTTTGTCCACCCCCCAAAATAAATATTAAAAACCCCTGACTGTGTATCTACGAAAAGCGTGGTAGCCAAGGTCCTTGAGGGACCCGCAGGATGGGTGGTGGCACATTACATCCCGAACGACCACGGCAACCGAAATGAACAGCAACCAAAAGAAACAGAAAATGCAATACGAAAATGCAACGAACCGAAACAACAATGCATATATATATATACGTGTATATAAAGATTTCTGTATCAACTGCCGAATCTTAATTCATACTCCTTCTCTTCTGAGCAGTCCAAGAAGTAACGAAAAGAAAAGCAAATAGAAATTGTAGTCGAAGTTCGCATAGACAGAACCCCCCATTCAGGATTAGACTTAATTTGCTAAAGAAGAACTAAATATATTAGTGCATTCACTCACCCGCATAACAACATACACACACACACACTGATTTGCTTAGTATATCATCATCATATGTACCCACCCCAAAAAATCATAACGTTCACCTAGCGCAAAGTGCAACTCCAAAAACGAGTTTCGAAAGTCACGCACGCATACAGTAGCAGCAGTTCGTGCTCCATATATGAGACCACACACACACACACATGGACACACAAAGGGACGCGAACACACACTCAAAGAACAAGGATAACCCGGTCACACACACAAGCGGCCGAGAGTGTGGGCCCCAGCATCCCTGCGCTTTCGAAGAGCTCTCTCTTCTCCTCTCTCGAAGGACACCGTGTGGAGCTTTTCCGGATAAAGTTCGCTCAGCTGTCAAGCGGCGAGGAAAACAACGGGCACTATAGCCATCTCAGTCCCACGTAGAATATATAAGCAGAAACTCCCGTTAGGTTCTTAGATATCCCTGATCGGGCGCCACTTAAATGTTGCACTTTGTCAAGCACAAGTTACTGTATAACCATGTTATCATAGTACTTTTTACGAGTCAGGACTCTAGGACTGTAAGAATCACTAGGCACTTGCATTAAACCATCCACTATGTGGGGGGTGGGGGTTGGAAGGACCTCTTCCCCTGTTCATAGTTCTTGTTTAACGGAAGTGCCTCCCATGCGGCGTATACTCAACGTAGGCCAGAACAACAGCAACAACATCAACAGTGCCACTTCGCACACCACCTCCACCACCAAAACTGACAACCACCACCTGCACCACCAAAAACAGCAAAAACAGCAAAAACAGAAATATATACCACAATCGAGCGGTTCTCATGTGTCGTCCATTTTTGTTTAACTTTTCCCATCAAAATTCTAAAATGATGCTGATGCTGAAGACGAAGAATCGGTTTAAAAAGTCTGACAATGCCTCTGTCCTATCTGCCTATCTCTCTCAGTCTCTCTCTTCTACTCTTCCTCTCTCTCTCTCTATCTCGCTCTGTCTAAGTCTATCTGTCTATAAGCTAAATCATCCCAAAAACCCATTCAAAAATTAAAAAAAGAACAACAAGCAAAACTTAAACAATGAATACAACAACTTTGCTCATCCGTTCGTTTCTTTGTTTCTCTGTATTTTCTTTCATTACTTTTGTGTCTCTGTGTGCCCGCCATTTTGTTCTGATTAAACCTATATCCCGCCTCCGAATTCCTATATGTGTGTGTACACTCTTCCGTTGTTTTTCGTTCGCTTCCGTTTCCGTTGTGTTTTTTAG
Seq C2 exon
TCAGTGCATCCGAAGATGAAGAGCGCTTGGTGCGTGACCTCTTTCGAGGCTACAATAAACTCATACGACCCGTACAGAATATGACACAAAAAGTTGGAGTAAGATTTGGTTTGGCGTTCGTACAGCTAATCAATGTC
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000038:FBtr0073299:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0293118=Neur_chan_LBD=PU(18.7=84.8)
Main Inclusion Isoform:
FBpp0073156
Main Skipping Isoform:
FBpp0073155
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)