DmeINT0013220 @ dm6
Intron Retention
Gene
FBgn0039427 | CG5447
Description
This gene is referred to in FlyBase by the symbol DmelCG5447 (FBgn0039427). It is a protein_coding_gene from Dmel. It has 3 annotated transcripts and 3 polypeptides (2 unique). Gene sequence location is 3R:26452534..26454585. Its molecular function is described by: protein-cysteine S-palmitoyltransferase activity. It is involved in the biological process described with: Golgi to plasma membrane protein transport; peptidyl-L-cysteine S-palmitoylation; protein targeting to membrane. 8 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: fertile; 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 00-12 hour embryonic stages.
Coordinates
chr3R:26453089-26453908:+
Coord C1 exon
chr3R:26453089-26453241
Coord A exon
chr3R:26453242-26453568
Coord C2 exon
chr3R:26453569-26453908
Length
327 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCGT
5' ss Score
9.49
3' ss Seq
ATGCTCTTTCGCCCCCACAGACC
3' ss Score
11.06
Exon sequences
Seq C1 exon
ATTGAAAGACACGTCTTCGAGGCCACCATCAATAGGCTAAACGAGTTCTACGCCGAGGCGGAGGAGGGATCCTGCGGCACCTATTGCGAGGGCTGCATTGGCTGCATCACGGCCTACTTGATCTATATGTGCTCCGAAACGCACTATGAAAAG
Seq A exon
GTGCGTCATTTGGGTTTGGATTACACACATGTGGGTCAATGCAATAGAGTCTAGTTCCACTAGGGAACTATTAATAGGGATTAGAGTCAACAATTTCACAAATGTCGATATGCGATCGTATAAGTTATCAAAGTTATTCTCGTTAATGTCCTTGTACTCAAGGTTTTCATATCTGTTTAAGGTATAAAGGTCAGAGAACTTGATAAATCAAGTAGTAGTATTACTTGCTAATTAGTGATCGTGCTATCTGTTATACGAGTTTAAAATAAGGCAGTGGCACTTCCAGCTCTATTGCCTGCACATACTAATGCTCTTTCGCCCCCACAG
Seq C2 exon
ACCCTTCGCAAGATATCCAAATTTGTGGCTTCCCAAAATGAACGCATTTACAACACCAAGGGACTGCAGCTGATCGATCCCACTTATCGGGGACTTCGCGTCATAGAGATTACAATATTCGATCGTCCGGGGCGAACGTGACTTCCGCTTTCCCATTCAGCCAACGAGTTTTTCATGTGAGATCGAGCAGCTACAGTCGCATCAACAGGCATGTGAAGGAGAAGAGTCCGTTTCAGCAATTATCAAGCAAAAGTCAGCGCCATCAGAGTGCGTTTCCAAAAATATAAATCAATAAAAAGCTGTGGAAGCAGCTAAAGCTTTATAACCTATAACCATATGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0039427:FBtr0085012:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF102564=Erf4=FE(43.5=100)
A:
NA
C2:
PF102564=Erf4=PD(31.3=76.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303185
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0084384
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:
GTCTTCGAGGCCACCATCAAT
R:
GTTGATGCGACTGTAGCTGCT
Band lengths:
347-674
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)