DmeINT0037286 @ dm6
Intron Retention
Gene
FBgn0003656 | sws
Description
The gene swiss cheese is referred to in FlyBase by the symbol Dmelsws (CG2212, FBgn0003656). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (3 unique). Gene sequence location is X:7956820..7968236. Its molecular function is described by: lysophospholipase activity; protein binding; protein kinase A catalytic subunit binding. It is involved in the biological process described with 11 unique terms, many of which group under: multicellular organismal process; programmed cell death; cellular lipid metabolic process; apoptotic process; cellular process. 32 alleles are reported. The phenotypes of these alleles manifest in: cellular anatomical entity; cytoplasm; organelle; adult sense organ; cell body rind of lamina. The phenotypic classes of alleles include: short lived; phenotype; phototaxis defective; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderate expression. Peak expression observed within 00-06 hour embryonic stages, during late pupal stages, in stages of adults of both sexes.
Coordinates
chrX:7962570-7964142:-
Coord C1 exon
chrX:7963208-7964142
Coord A exon
chrX:7963142-7963207
Coord C2 exon
chrX:7962570-7963141
Length
66 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TTGCTTTATTTCCTCGACAGGAT
3' ss Score
8.98
Exon sequences
Seq C1 exon
GCATTCGAAGAGGTGTTCCAGGACAATCCGGACGTAATGATTCGCGTCATCCAGGTGATTATGATCCGGCTACAACGCGTACTGTTCACCGCTTTGCGCAACTACCTCGGTCTAAATGCCGAACTGGTGCAGAATCACATGCGCTACAAGAGCGTATCCACAATGAGTGGACCGATTAACTCGCAGACCTCGCAATCCTCACGCCAGGCGCCCAATGGGCCGCCCATGGTGATCAGCCAGATGAATCTGATGCAGTCCGCTGTTTCGGGAACGGGATCATCGGGTGTCTCGGTGACCGTAACTCGACCACCATCCTCGCCATCGCGACACTCGCGCGAGGAGCACACGCTATCCGATCCGAATCCAAATCCGGATGGTAGTTTTCACGGCACTACCAATCTGTTCACCGAGGTGCATGGCGATGCGCCCAATGCAGATCTATTCCATCAGCAGCAGCAGCAGCATTCGGTGGGCAACCTATCCACGCGTCGCAGTTCCATAACTCTGATGGCACCCGATGGTTCGCACTCGTGTCTACAGACACCCGGTGTGACAACCTCGATAGACATGCGCCTGGTGCAATCCTCAGCGGTGGACAGCCTACGCAAGGAATTGGGTCTGTCCGAGGAGGATTCCCACATCATTGAGCCTTTTGTAGAGTTAAGGGAACTGGAGCCGAATGTCACCCTGATTACGGAGGGCAATGCGGACGATGTTTGCGTTTGGTTTGTGATGACGGGCACATTGGCTGTTTACCAGAGCAATCAGGATGCCACGCGGGCCAAGCAGGATAAGAGCGACATGCTCATTCACTTTGTGCATCCCGGCGAAATCGTTGGTGGACTGGCCATGCTAACGGGAGAGGCCAGTGCGTATACCATTCGATCGAGAAGCATCACCAGAATAGCCTTCATCCGACGAGCAGCTATTTACCA
Seq A exon
GTAAGTTTGGGCGTTTACATAATGAAGTAAAATGATTGCTTTATGATTGCTTTATTTCCTCGACAG
Seq C2 exon
GATCATGCGACAACGACCACGCATTGTTTTGGATCTGGGCAACGGAGTAGTACGCCGTCTATCGCCTCTGGTGAGGCAGTGTGACTATGCCTTGGACTGGATCTTTCTGGAATCGGGCAGAGCTGTCTATCGGCAGGACGAGAGCAGCGACAGCACATATATTGTGCTTAGCGGGCGAATGCGTTCGGTTATCACGCATCCTGGTGGCAAAAAGGAGATCGTCGGCGAATACGGCAAGGGGGATCTTGTGGGCATCGTTGAAATGATCACGGAAACGTCGCGCACCACGACGGTGATGGCTGTGCGCGACTCGGAGCTGGCCAAGCTGCCCGAGGGCCTGTTCAATGCCATCAAGCTGCGCTACCCCATCGTGGTGACCAAGCTGATTAGCTTCCTTAGCCACCGCTTCCTCGGCTCGATGCAGACGCGCTCGGGCAGCGGGGCGCCGGGCGCGCCCGTCGAGGCCAATCCCGTCACGCACAAGTACTCCACGGTGGCCCTGGTGCCCATCACCGACGAGGTGCCGATGACGCCCTTCACCTACGAGCTCTACCACTCGCTCTGTGCCATAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0003656:FBtr0071125:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.407 A=NA C2=0.042
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(10.2=3.2),PF0002724=cNMP_binding=PU(91.9=29.2)
A:
NA
C2:
PF0002724=cNMP_binding=PD(7.1=3.6),PF0002724=cNMP_binding=WD(100=47.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0071077

Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0290889
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:
AGAGGCCAGTGCGTATACCAT
R:
AGGCATAGTCACACTGCCTCA
Band lengths:
167-233
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)