Special

DmeINT0034430 @ dm6

Intron Retention

Gene
FBgn0000039 | nAChRalpha2
Description
The gene nicotinic Acetylcholine Receptor alpha2 is referred to in FlyBase by the symbol Dmel AChRalpha2 (CG6844, FBgn0000039). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (1 unique). Gene sequence location is 3R:24485428..24491147. 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 7 unique terms, many of which group under: cellular process; cell communication; biological regulation; ion transport; signaling. 10 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: chemical resistant; viable. 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, at stages throughout the pupal period, in adult male stages.
Coordinates
chr3R:24487423-24488611:+
Coord C1 exon
chr3R:24487423-24487603
Coord A exon
chr3R:24487604-24488451
Coord C2 exon
chr3R:24488452-24488611
Length
848 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
GGGCTTTTCTCGATTCACAGATC
3' ss Score
7.73
Exon sequences
Seq C1 exon
TGCCGATGGCGAGTACGTGGTCACCACCATGACGAAGGCCATCCTCCACTATACCGGCAAAGTGGTCTGGACTCCGCCGGCCATCTTCAAGTCCAGCTGTGAGATTGATGTGCGCTACTTTCCCTTCGATCAGCAGACCTGCTTCATGAAGTTCGGCTCGTGGACCTACGACGGTGATCAG
Seq A exon
GTGAGTGGTGGCGTCATTGTCTTCTATCTGCTGCCAGTGCCATGCCAGTTGAGCCTCAGATAAATGGGCGTGGCGAACGATTTATGGTACACCATTTATCTGAGAGATGAGATGAGGAGATGAGGTAGCGACTTACACGCCTAAGACGCGGTAAGAACATCGAAAAGGCGTCGTTGGCAACTCGCAGATTAAAATGTGAGAAATTGTAAAAGTGTAATTGAAACTTGTCTAACCGCTGCACACACAAACACAGCCATGCACGCACACTGGCGCTGAAAGAGAGCGGCACTAACTCACACAGAGGCACTCGACTGTGTGTGTCGCTGTCATAAAAATGCGCGGCCATAAATTAAGCCAAAGTGCGACTTCCACCCAACCCAAGCAGCTTCCGTTTCCGCTGACCCTTCGCAGTGCTGCGAAGAGGGACAGGTGCACTGAGAAAAATATGAAATCAATATTGAGATGGAGTATGTCACATTTGCAATTAGTAACTACTTAAAGACGAAGTGTGCACATAGAATTTATAAGATGTATAGAATGTTATAAGATTAGTTAAACTATTAGAGAGCTACACATTAAAGGCACTAGATTTTTTTTTGAGTGCTGCGATGGGTTTTAGGACAGGCTACGGAACAGAGCTCTTTTTCACCGGGCGTTTGTCAACGCATTTAAATTTCGCTACTCTTTTAACGACTGCACTTTGGCTGCCGGTCGCCTGGTTGGAGGAGATTGGAGGGAGTGGGATGCGCCAGGTGGCGTTGTCACGGCAAGTGGCAGTGAGCCGGACAAAGGAGCCAAAGGAGCGTAACTTTAACGGCTCCATCAACGGGGCTTTTCTCGATTCACAG
Seq C2 exon
ATCGATTTGAAGCACATCAGCCAGAAAAACGACAAGGACAACAAGGTGGAGATAGGCATCGACCTGCGTGAGTACTATCCCAGTGTGGAGTGGGACATTCTCGGCGTTCCGGCTGAGCGGCACGAGAAGTACTATCCCTGCTGTGCCGAACCGTATCCGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000039:FBtr0084639:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

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

C1:
PF0293118=Neur_chan_LBD=FE(27.6=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(24.4=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0084023


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0084024
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:
GATGGCGAGTACGTGGTCAC
R:
GATACGGTTCGGCACAGCAG
Band lengths:
334-1182
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)