DmeINT0002879 @ dm6
Intron Retention
Gene
FBgn0043458 | CG12084
Description
This gene is referred to in FlyBase by the symbol DmelCG12084 (FBgn0043458). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3L:1490951..1496643. Its molecular function is unknown. The biological processes in which it is involved are not known. 7 alleles are reported. The phenotypes of these alleles manifest in: eye; head; external compound sense organ; scutum; dorsocentral bristle. The phenotypic classes of alleles include: visible; 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.
Coordinates
chr3L:1493094-1494268:-
Coord C1 exon
chr3L:1493329-1494268
Coord A exon
chr3L:1493266-1493328
Coord C2 exon
chr3L:1493094-1493265
Length
63 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
CTAAATTTCATCTTCATTAGTGC
3' ss Score
3.47
Exon sequences
Seq C1 exon
GCTTGGAGACTCTGATGCGGCACAAACTGTTCGCTTTGTCCTTGTGGTACTGTGACATGATATCCGTTGGTTCCCACCACCTTCTGGCCCACTACGGCGACAGTCTGCGATCCCTGGAATTGGGCATCAGTTCCCATCTGCTGCAGTACGCGGAGCCCAACGAGAAGGAGCCAGTGGACTTCCAGTTGACTTGTCCGCATCTGCGGCGGCTGGTGCTCAACGGTGTTGTGATGCACCACCGCCTGCAGTTCGCTCACCTCCACGACTTGGGCCACCTGGACCTGACCTCCTGCGTGCTGGCCAACTTCAGCCTTGAGGCATTGGGCTCGCTGCCCAATCTGCACACGCTCATCCTGTTCAATGTGTGGCCCATCGCCAACCAGCTGCATGCGATCTGCTGCCTGAGGCGTCTGTGCACACTGGACATATCCATCTCCAGTTCCGGAAATGGCCACGGCACCTACGACCTGCCCGATCAGACGCTGGAGATGCTGATGGACAACTTGCGACATCTCACACATTTGGATATCTCTGGCACGAATTTGGCCGGCAACGGTGTGGCCACCAAGGAGTCGACAACTACCAGTGGCATGCAGCAGAGCCCCAAAATGGAGCAACACTTTGCCCTCACAGACATCCCGGGGCTAGCGTCCCGCACCCAGCGACCGCTGCAGTTCCTAGGCCTCTATCACACGGCCCACTGGGCCTGCAAAAGACACGATATTCCAGCTTTGGAGGTAGCTGGCGATGCCAACGAGCAGCAAATCCTTACTGCGGCGCGTTATTACCACGACAGACCAGTGCTTCTGACAAGAGTTCTCAACGACTTGTACCATCTCTTCCGCTTCGAGAACTGCAAGGACATACACACAGCACTGGATGTTGTGCTCTCCGCCATGGATCGGCATCTCAAGTTCAAGCACATGCAAATCTCCGGCAG
Seq A exon
GTGGGTTTATAGCTTTGAAGTTAAGTGAAAATAGTATTTAATTCTAAATTTCATCTTCATTAG
Seq C2 exon
TGCCACGCTGTTCTACATTGTCAAGGGCAGGGATCGATCCAAGTTTGGAGCACTACTGCGCAATCACATCATTCGCACGCTGCTCAATGGCATGGAGATGCACATCACCGACGACACCATGCTGCGGAATGGTTACCTCACGCTCACCCAGTTTCACATGCCAGTCGATGTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0043458:FBtr0072711:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0072595
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0304902
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:
ACCATCTCTTCCGCTTCGAGA
R:
CGATCCCTGCCCTTGACAATG
Band lengths:
145-208
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)