DmeINT0009602 @ dm6
Intron Retention
Gene
FBgn0250819 | CG33521
Description
This gene is referred to in FlyBase by the symbol DmelCG33521 (FBgn0250819). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (3 unique). Gene sequence location is 4:1185768..1192985. Its molecular function is described by: actinin binding; structural constituent of muscle. It is involved in the biological process described with: sarcomere organization; muscle tissue development; actin cytoskeleton organization. 5 alleles are reported. No phenotypic data is available. The phenotypic class of alleles includes: viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of extremely low expression. Peak expression observed during late pupal stages.
Coordinates
chr4:1187522-1187880:+
Coord C1 exon
chr4:1187522-1187614
Coord A exon
chr4:1187615-1187734
Coord C2 exon
chr4:1187735-1187880
Length
120 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGC
5' ss Score
6.91
3' ss Seq
AATTTCCTTCCTTTTACCAGTCT
3' ss Score
6.71
Exon sequences
Seq C1 exon
AAAAAAAGTTTTACGAAATTCGATGATCTACAAAAACGTAATGTTATTCATGTACGTTCACGAGATTCTAAAAAAGCTCAATCACTTTTTCGA
Seq A exon
GTAAGCTAAGTATCATAAAGATAACGCATTACATTTACAAAATAACAAAAGGTGGTCGATTTTTTAACTTAAATCAATTTAATCAGCTGCTTGTAAATTTAATTTCCTTCCTTTTACCAG
Seq C2 exon
TCTACAATACCTGAGAAGGTTGAAAACTGCCACCAATGCAAGAAACCCGTGTACAAAATGGAGGAAGTCATTCTTAGTTTGAAGACAGCAACGACTATTTTCCATAAAACGTGCTTACGTTGCAAGGACTGTGGCAAACACCTTAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0250819:FBtr0091472:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0041217=LIM=PU(65.0=79.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0090952
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0090950, FBpp0090953, FBpp0306723
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:
ACGAAATTCGATGATCTACAAAAACG
R:
TAAGGTGTTTGCCACAGTCCT
Band lengths:
226-346
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)