DmeINT0033869 @ dm6
Intron Retention
Gene
FBgn0051004 | mesh
Description
The gene mesh is referred to in FlyBase by the symbol Dmelmesh (CG31004, FBgn0051004). It is a protein_coding_gene from Dmel. It has 6 annotated transcripts and 6 polypeptides (3 unique). Gene sequence location is 3R:31178389..31195762. Its molecular function is described by: protein binding. It is involved in the biological process described with: smooth septate junction assembly; cell-matrix adhesion. 6 alleles are reported. The phenotypes of these alleles manifest in: smooth septate junction; embryonic/larval midgut. The phenotypic classes of alleles include: viable; lethal - all die before end of first instar larval stage; some die during pupal stage; partially lethal - majority die; some die during first instar larval stage; short lived. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of very low expression. Peak expression observed within 12-24 hour embryonic stages.
Coordinates
chr3R:31180459-31180818:-
Coord C1 exon
chr3R:31180579-31180818
Coord A exon
chr3R:31180510-31180578
Coord C2 exon
chr3R:31180459-31180509
Length
69 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGT
5' ss Score
6.84
3' ss Seq
ACCGCAAATTGATTTTCCAGCTA
3' ss Score
6.02
Exon sequences
Seq C1 exon
GTGAGGTGTACTACACGCGTCGCGTCGCTTTCATAGCAATTGGCATTATCTTCCTGGTGATCTGCCCACTGATGCTGTGCATCGTGTGTGGAGTATATCGCTATCGCCAGAAGCAGCTCAAGGAGGATCCGCAGTGGCAGATGCCCATGCTGCCCCGTTCGAGGGCTAGTTCGGCTCGTAATTTAAGGACACTTAACTACGACGACGACAGCGATACGGATGCCAGCACATTGAAGAAAA
Seq A exon
GTAGGTCCTACGACAAAGTATATCGCACGAACGAACCATTACCGGGCAAACCGCAAATTGATTTTCCAG
Seq C2 exon
CTAAGAAATGGGATCTGGATGAGAACGACGAGGATGTGACCTCATCGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0051004:FBtr0085779:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.367 A=NA C2=0.738
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
FBpp0290183
Main Skipping Isoform:
FBpp0085140
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0085141
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:
GAAGCAGCTCAAGGAGGATCC
R:
AGGTCACATCCTCGTCGTTCT
Band lengths:
173-242
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)