DmeINT0003998 @ dm6
Intron Retention
Gene
FBgn0033368 | CG13743
Description
This gene is referred to in FlyBase by the symbol DmelCG13743 (FBgn0033368). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (3 unique). Gene sequence location is 2R:9044850..9060608. Its molecular function is described by: amino acid transmembrane transporter activity. It is involved in the biological process described with: amino acid transmembrane transport. 8 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: lethal - all die before end of pupal stage; some die during pupal stage. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 18-24 hour embryonic stages, during early larval stages, during late pupal stages, in adult male stages.
Coordinates
chr2R:9050515-9051151:-
Coord C1 exon
chr2R:9050843-9051151
Coord A exon
chr2R:9050630-9050842
Coord C2 exon
chr2R:9050515-9050629
Length
213 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
AAGCCTCATTTCATTTGCAGGTC
3' ss Score
9.01
Exon sequences
Seq C1 exon
AACAACCATCAGACACATCAGCAACAGGGCCAGCCGCAACAGCCACATCAGCAGCAGCAGCAGCCGCCGCAGCAGCAGCAGCAGCAACAGCATCGCCAGCATTCGCAGCAGCAGCAGCAAGCACAGCAGGATGCCGGACTGGGGGACACGCTGTCCTCGCTGCCACAGGCCTCGTTCAACTACATCAACTCCATCGTGGGCAGCGGCGTCATCGGCATACCCTACGCCCTTCACAGGGCCGGATTCGGACTGGGCCTGGCCCTGCTCATCCTGGTGGCCTACATCACCGACTACTCACTCATCCTGATG
Seq A exon
GTGAGTGGCAGGCCCCCCTAACTCGATGCCTTTCCCAAATCGGTTTTAAAGTTCCAATCAGGCAATCTGGACATCTGACCAGACCGAAGCGACCAAAGTCACATGCCAAACGCATTTCCGCTCGACTCCGGGCATTAGCATTTGCTGCATAATTAACGAGCCCACTCATTTGCGAGGGCGTGTGCTGCCGTTTAAGCCTCATTTCATTTGCAG
Seq C2 exon
GTCAGATGCGGCCACATCTGCGGTCGGTTCAGCTATCCGGGCATCATGGAGGCGGCCTACGGCAAGTACGGCTATTACCTGCTCTCCCTGCTGCAGTTCATGTATCCATTCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0033368:FBtr0088662:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.466 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF046958=Pex14_N=PD(72.5=84.5),PF0149013=Aa_trans=PU(13.0=51.5)
A:
NA
C2:
PF0149013=Aa_trans=FE(21.0=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0087743
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0300980, FBpp0308396
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:
AACAGCCACATCAGCAGCAG
R:
ATAGCTGAACCGACCGCAGAT
Band lengths:
308-521
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)