DmeINT0001840 @ dm6
Intron Retention
Gene
FBgn0037440 | CG1041
Description
The gene Carnitine O-Acetyl-Transferase is referred to in FlyBase by the symbol DmelCRAT (CG1041, FBgn0037440). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (3 unique). Gene sequence location is 3R:6371026..6376044. Its molecular function is described by: carnitine O-acetyltransferase activity. It is involved in the biological process described with: fatty acid beta-oxidation; carnitine metabolic process, CoA-linked. 8 alleles are reported. The phenotypes of these alleles manifest in: mitochondrion; embryonic/larval fat body. The phenotypic classes of alleles include: fertile; size defective; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of moderate expression. Peak expression observed within 06-18 hour embryonic stages, at stages throughout the larval period, at stages throughout the pupal period, in adult male stages.
Coordinates
chr3R:6373302-6374025:-
Coord C1 exon
chr3R:6373814-6374025
Coord A exon
chr3R:6373381-6373813
Coord C2 exon
chr3R:6373302-6373380
Length
433 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
ACCATTTCTCCGTTTTGCAGCCC
3' ss Score
10.23
Exon sequences
Seq C1 exon
CTTTAAAGAAGTTTTGGAATTGCTTGTGATTTTAATCGATTGTTATCCATTATTGATAGCACAGTTAAACCAACAACAGGGAGTGCTTATTTACTTGTTGCTGTTTGACAACAGCTGTTTCTTGTTTTGATTTGAACATACAAACATATATAAACATATATGTTTATATAGAATCTATAGATGTTAATTAACCGGAGCAAAACAAGAGTGAG
Seq A exon
GTAAACTTAAATTCTTTATTTGAACTGATGGGCAAGGACAGTCGAACCAGTTAAGGATTATATAAAAAGTGGTTATATATCTAGATGGTAATCATCGTGTATTTCGCTGGTATGGTATGGATATTAAGAGACGCACTCTTGGGAGAGCGAAAGTAAATAAACCGGTCGCTGATAGCATTTAAGTTGGGCTCCACTCCACTCCCACCCTTCTGCCTACGTGGACTGCTCTTTCGATGGCCAGTTGATTGGCAACTGCCGTTTTGCTTGCACTTGCCTCCTCCGCTGGCTGCTAATCGTGAGCCATTAGTTTATCGCTCCTTATAGCTAGAAGTAGATTATGTACAAATATCAAAGGTTAATTCAGTGCCACAGGCACACCAACCGGTGGTTGGACTTTAAAGTAACACTCGAATACCATTTCTCCGTTTTGCAG
Seq C2 exon
CCCAACGTCTGAGCGAATCCTCGAGAAAACCGAAGCCGAGATGAAGTTCCGTGGCAATGGAAAGCTTTTGTGGAATTTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0037440:FBtr0081734:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.364 A=NA C2=0.266
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0081231
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0310697, FBpp0312437
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:
AAGAAGTTTTGGAATTGCTTGTGA
R:
CAAATTCCACAAAAGCTTTCCATTGC
Band lengths:
286-719
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)