DmeINT0010437 @ dm6
Intron Retention
Gene
FBgn0031492 | CG3542
Description
The gene pre-mRNA processing factor 40 is referred to in FlyBase by the symbol DmelPrp40 (CG3542, FBgn0031492). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2L:3023226..3026439. Its molecular function is described by: RNA binding. It is involved in the biological process described with: mRNA cis splicing, via spliceosome; mRNA splicing, via spliceosome. 17 alleles are reported. The phenotypes of these alleles manifest in: trichogen cell; mesothoracic tergum. The phenotypic classes of alleles include: visible; lethal; flightless; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderately high expression to a trough of low expression. Peak expression observed within 00-18 hour embryonic stages, in adult female stages.
Coordinates
chr2L:3025689-3026439:+
Coord C1 exon
chr2L:3025689-3025769
Coord A exon
chr2L:3025770-3025831
Coord C2 exon
chr2L:3025832-3026439
Length
62 bp
Sequences
Splice sites
5' ss Seq
GGTGTACGT
5' ss Score
4.36
3' ss Seq
TAACATGGCTTACATTTCAGTCC
3' ss Score
5.05
Exon sequences
Seq C1 exon
CATTCCCTGACCTCAATTGGCAGCATCGAGAGCGAAAAATTGCTGAAGAAGAAAAAGAAGCGCAAGAACAAACTGCGAGGT
Seq A exon
GTACGTAGCAAGTCGGCCCAGTCCTTGGACAACTATACTATCTAACATGGCTTACATTTCAG
Seq C2 exon
TCCTCCTGCGAATCGGATGTTCCAGGCATTCAATCGCCGGGAACTCAAGCTCTACTTCAGAACGACTCAAACTCGCACTCACCCGCAAAGAAAAAGAAGAAGGAGAAGCGAGCTAAGAAGGACAAGCGACACAACAGGCACAATCGATCCGGCACGCCCCTTAGTCCTGCCCAGTCCGTCGAGTCGTCTGGATCGCGAAACGAGGAGCTGACGTTAAGTGACGGCGAGCTGGAATCGAAGCGAGCGGCTCTTCTAGCCCAACTCAGCGAGCAGCTCGACGAGTGACCAGCTGACAGGCGTTGAGTCAAAGCCGACATCGACATCGTGTGGCACTCTCTAGCTCTAGCTTAAGGAGGATCGGGAGAGGTAGCTAGCCCTGGACTCAGTTGCTGGACAAGTTCTCTTTTCAGTCCTTGCCTTCCACTGCACTCTGCTTCGTTTGGTTTAGATACTGTCCTGGTCCCAGCACAAACCACACAGCGAACCACAATTGTAATTTCTTAGTCTCAATAAGTTTCAATGTATAAATGAGAATTAAACCTAACGAGTCAAATTTTAAGTTATACGCAAATGATTTTGATTCTGCATCAAAATAAACAAATTACGAT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0031492:FBtr0077648:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0077333
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
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:
CCTGACCTCAATTGGCAGCAT
R:
AGTAGAGCTTGAGTTCCCGGC
Band lengths:
132-194
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)