DmeINT0028543 @ dm6
Intron Retention
Gene
FBgn0030748 | Traf-like
Description
The gene TNF-receptor-associated factor-like is referred to in FlyBase by the symbol DmelTraf-like (CG4394, FBgn0030748). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (3 unique). Gene sequence location is X:16415046..16417585. Its molecular function is described by: protein binding. It is involved in the biological process described with: positive regulation of lipophagy. 6 alleles are reported. The phenotypes of these alleles manifest in: autophagosome; lipid droplet; embryonic/larval fat body; extracellular matrix; adult midgut. The phenotypic classes of alleles include: increased mortality; exocytosis defective; viable; size defective; immune response defective. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of extremely low expression. Peak expression observed within 18-24 hour embryonic stages.
Coordinates
chrX:16415046-16416085:+
Coord C1 exon
chrX:16415046-16415585
Coord A exon
chrX:16415586-16415656
Coord C2 exon
chrX:16415657-16416085
Length
71 bp
Sequences
Splice sites
5' ss Seq
ACGGTTATA
5' ss Score
-2.41
3' ss Seq
CTCTTTGGATGCGACTGCAGGAA
3' ss Score
4.41
Exon sequences
Seq C1 exon
CCATATAGTCGCTGGAAGATCTGGTGACGGTTACGATTTTAGTGGATTCTCGGTGGCTGTGTTTTCCTGGTCGTAGTTCGCCAAGTTAGTGGTCAATACGATTCGTTGGTTGCTCTCGCATTTCGAAATAGTGGTAATCGCACCAAATGGCAGTGCTATCAGTTCGAGGTTGTCGTATAGATTCCCATGGACGCCCTAATGCTAACACATGTGCAAAGCTATATCTAAACCATGTCTGTGTGCGCCGCGTATGACTATGCCCAAGGAAATTCTTAATCATTTTTGGCTGAGTTTAGTGTGCATAGGGCGGTGCTCGCAGCGCCAGAGAATTTGCTGATCCAAAGTTTCAATCGAATTTGCTTTCCTTTAATCAATATAATGTCACTGACCAAGTCGTCGTCGAGAAAGGATCTAACCGAGCAGAATCAGTATCAGAATCAGAATGAGAATCAGAATCAGCCCAAATCGACGACCATAGTCAAGTATGAGAAGTCGTCGTGCCTCTTCTGCAACGAATGGTTCGATGCCCAGACATTCACG
Seq A exon
GTTATAATCGTCCAACTTTTCAGTTCACCTTTGATTACTATTACATTACTCCTCTTTGGATGCGACTGCAG
Seq C2 exon
GAACACCTGATCCACTGCGGCCAGGTGCTGGAGGAGTGTCCCAACGGCTGTCAGGCCTTCATTCCACGCATCCGTATGCGATCCCATCTGAAGGAGTGTCCACGCAACCAGCACAATCTGAGCAATCAGCAACGCATGAGTGTCAGCATGGATCGCCTGGATAGGCAGTCGGATCAGCGTCTCCTGGTCATTGAACAGGACGTGGGCACCATTCGGTCCGTTCTCAACGAGGAGATACGACAGCGTTTGCATCTCATTACCGATGTGGGCAACATACGGAAGCAGAACCAGGTCGTCGAGGACTGGACCCGCGAAACCGAGAAGGCAATGGACGATCTGCGTCGCCAGATGGAGGAGGAAACCAATCGGAAGGCATTCGCCATCGAACAGAACCAGCTGGATGTCCAGTACTGCTGTGATATCACACAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0030748:FBtr0074275:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.374 A=NA C2=0.358
Domain overlap (PFAM):
C1:
PF0217613=zf-TRAF=WD(100=30.9)
A:
NA
C2:
PF0217613=zf-TRAF=WD(100=36.4)
Main Inclusion Isoform:
FBpp0074049
Main Skipping Isoform:
FBpp0074051
Other Inclusion Isoforms:
FBpp0300830, FBpp0300831
Other Skipping Isoforms:
FBpp0074050, FBpp0306152, FBpp0306153
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:
TTCGATGCCCAGACATTCACG
R:
ATCCATGCTGACACTCATGCG
Band lengths:
174-245
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)