Special

DmeINT0034506 @ dm6

Intron Retention

Gene
FBgn0004118 | nAChRbeta2
Description
The gene nicotinic Acetylcholine Receptor beta2 is referred to in FlyBase by the symbol Dmel AChRbeta2 (CG6798, FBgn0004118). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:24509228..24515106. Its molecular function is described by: acetylcholine-gated cation-selective channel activity; neurotransmitter receptor activity; transmembrane signaling receptor activity. It is involved in the biological process described with 7 unique terms, many of which group under: cellular process; biological regulation; cell communication; response to stimulus; synaptic signaling. 19 alleles are reported. The phenotype of these alleles manifest in: chaeta. The phenotypic classes of alleles include: flight defective; chemical resistant; visible; lethal; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, during early larval stages, at stages throughout the pupal period.
Coordinates
chr3R:24510902-24511225:-
Coord C1 exon
chr3R:24511073-24511225
Coord A exon
chr3R:24510982-24511072
Coord C2 exon
chr3R:24510902-24510981
Length
91 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGT
5' ss Score
11.37
3' ss Seq
GGGCTGGTTTTCCCCTGCAGTGA
3' ss Score
7.71
Exon sequences
Seq C1 exon
ATCTCCATCTACGCACAATATGTCGCCGCTGGTGCGGAAACTCTTCCTGCACTTCATGCCCAAGCTGATGATGATGCGGCGGACGCAGTACACTCTGCCCGACTACGATGACTCCACTCCGAGCAATGGGTACACCAACGAGATCGATGTGCG
Seq A exon
GTAAGTGGCAACCAACTCGCGAAATTGAAAGTAAACACTTGACTTTGGCCTGCCTGTTTGTGTTGTGGCATGGGCTGGTTTTCCCCTGCAG
Seq C2 exon
TGACAGCATCAGCGATTTTCCCAGCGAGTTTAAGGACAGCCAGGATGGCGCTTACGATAATGGCATGCAGAACTCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0004118:FBtr0084681:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.019 A=NA C2=0.071
Domain overlap (PFAM):

C1:
PF0293211=Neur_chan_memb=FE(22.3=100)
A:
NA
C2:
PF0293211=Neur_chan_memb=FE(11.8=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0084061


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:
TCTACGCACAATATGTCGCCG
R:
CTCGCTGGGAAAATCGCTGAT
Band lengths:
174-265
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)