DmeINT0011377 @ dm6
Intron Retention
Gene
FBgn0034598 | CG4266
Description
This gene is referred to in FlyBase by the symbol DmelCG4266 (FBgn0034598). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 2R:21161713..21168659. Its molecular function is described by: mRNA binding; nucleic acid binding. The biological processes in which it is involved are not known. 13 alleles are reported. The phenotypes of these alleles manifest in: chaeta; mesothoracic tergum. The phenotypic classes of alleles include: viable; visible; body color defective; partially lethal - majority die; some die during pupal stage. 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 00-12 hour embryonic stages.
Coordinates
chr2R:21167596-21168659:-
Coord C1 exon
chr2R:21168432-21168659
Coord A exon
chr2R:21168184-21168431
Coord C2 exon
chr2R:21167596-21168183
Length
248 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGC
5' ss Score
9.85
3' ss Seq
ACATCTATATTTCTCCTTAGCTC
3' ss Score
7.41
Exon sequences
Seq C1 exon
TACAGGTCTGGCAACGCTTCAGGCTTTAGGGCAGCCATTTTTTTCACGCTTTGTAAAAAGTTTTTTTAAAAGCCGTGGAAACCGCAGAAAGGTCGAGAAAATTGTTTTTCGCCAGTTTTAAACGATTGTGTTGACCAACCAAAGTATGCAAAACTAAATATTGTGTGTGCGTGCCGTGAGTGAACCAAGCAATTGAACATGGAAACCGTGGTTGCCTTCAACAATGAG
Seq A exon
GTAAGCTATAGATGCATTAGAAACGAGGTTCGTTATGGAGCAGCCGGCGTGGTTGCACAATGTCCGCTTGAAGTCGGTATTCGGATTGTCCAATGTGCGGGAGGTATACAGATCCTGCTGGAGGCGCAGGCAGAGCACCGAACAGCACCGCTCAGGGTTGCTTTTTGGCCAGCACCCGATAACGATAACTCCATGTCCCAGATATCCGTAAACTATAGCCGTACTGTAACATCTATATTTCTCCTTAG
Seq C2 exon
CTCTCCGGACTCTATGACAGCCGACCGCCCATTTCCAAAGCGAAGATGGCCGCCATCACCAAGTCGGCGATGCGGGCCATCAAGCTGTATAAGCACGTCGTCCAGAGTGTGGAGAAGTTCATCTTGAAGTGCAAGCCGGAGTACAAAGTACCCGGGCTGTATGTAATCGACTCGATAGTGCGCCAGTCGCGCCACCAGTACGGTATGGACAAGGATCTGTTCGCGCCCCGATTCCAGCGTAATCTCACGGAGACCTTTGCCAACTTGTTCCGGTGCGCTCCGGAGGACAAGAGTCGCATCATCCGGGTACTGAACCTGTGGCAGAAAAACAACGTCTTCAAGTCCGAGGTCATTCAGCCGATCTTCGACCTGGCCGACCCAAACCACCCAATCTACCACCAGATGCCTCCGGTGGGTGGCAGTGGAGGACAGGGCGGCGGCGTGGGTCCAGGACCCAGCAGCAGCGGTGCTCTTAGCCTGGCGGACATATCGAGCGGTCCGAACGGTCTAAACAGCTCCGGAATGGAGATAAGCATGAACAGCTCCGGGGGCGACGATAAGATGGGCGGTGCCATGCCCGACTTGTCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0034598:FBtr0071629:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.324
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF048188=CTD_bind=WD(100=33.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0112013
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0071554, FBpp0302570, FBpp0309673
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:
TTAAAAGCCGTGGAAACCGCA
R:
GTACTCCGGCTTGCACTTCAA
Band lengths:
307-555
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)