DmeINT0010419 @ dm6
Intron Retention
Gene
FBgn0028497 | CG3530
Description
This gene is referred to in FlyBase by the symbol DmelCG3530 (FBgn0028497). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (3 unique). Gene sequence location is 2R:23389009..23396680. Its molecular function is described by: metal ion binding; phosphatidylinositol-3-phosphatase activity; protein tyrosine phosphatase activity; phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity. It is involved in the biological process described with: phosphatidylinositol dephosphorylation; mitotic cell cycle; regulation of autophagy. 8 alleles are reported. The phenotypes of these alleles manifest in: mesothoracic tergum; extracellular matrix; embryonic/larval fat body; trichogen cell; wing. The phenotypic classes of alleles include: planar polarity defective; visible; viable; female semi-sterile; exocytosis defective; flightless. 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 00-06 and 18-24 hour embryonic stages.
Coordinates
chr2R:23393364-23395421:-
Coord C1 exon
chr2R:23394917-23395421
Coord A exon
chr2R:23393481-23394916
Coord C2 exon
chr2R:23393364-23393480
Length
1436 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
CTCTGTTTTTGTTTTTGCAGGTG
3' ss Score
12.12
Exon sequences
Seq C1 exon
CTGAGTTCCATTCCATCGTTTGACGGAAGCACTTCGCGCTGCCCCAAGCAAACCACACACACTCATATCCGTGGGGTAAAATCGCACAAAAAGGCACAGCAAGTCGCCAGTGAATAGCGCGAGTTTCGCGCTCGTTAGGCAGGCGAAAAGTGAAAGTCCCAGGCCATTCCACCCATACAAACTTGGATTGATTCCATTTGAGTTGCCAGCACACGATTGCTGCTGCTGATTCAAAATCAATAAAGCGGCCCGCCAGTCTCCCGCAATGGACATCACCCGATTCATGAACAAGTTCAACGAGATCGAGCGCCAATTGTCCCCGACCTCCGCGCTGCGGCTGAGCTTCGACAACATCTCGCCGGAGACGGAGGAGCCGCCGGACGGCAATAAGAGGCTGTGGGGCGTGCCAGTGCCGCCCTTCGTCTCCGAAAAGGTGGTCTCCTGGATCGAGGAGGAGTTCAACGAGGCTCCGGTCTTCTACAACGGCAACAGTGTGCTCAAGAAG
Seq A exon
GTAAACCCGCCCAACAGACCAACATCCTGCTCCCCAGTTTCCCATGCAAATCATGGCGAGCAAATCGTGCTAATTTTCCCATCTCACCCATGGCCACCGGCTACTGGCCACTGGCCGGAAAATATGCAAATCAGCACACAGGCAGTATGTTCGGGGGCCTGCCAAAAGCTGACTTCCCCTTCTTCCCGAAACCCGTTTCCTATGTGGGTCATGTGTGGGAACGAGGAGCAGGTCTGCATCCGGGCGCCAAGTGCGTCACCACAATCACTCCTCGGGGCACCCACAAGTCTGACAGATTGTTGCATTGTCAGCGGGATACTCGGGTGCGGAGCTGGGTCAATTAATGGAATGGGTTTTCCATCAAAGTCGCAGATGCAACTGCCATCGGCTGGCAAATTGCACTCGTACATCAAGAGCAGGCCACCGGACTTGGCAATTGTCAAGGTTACCCATGTTGATTACCAATGGACAATGGCACCAACTCCCCATGTGCACTATACGCAGATTGAATTAATGCAGTTCGTTTGTCTTTATTTGTGTGTATCTGATAATTTCGAAATTCAAAATATAATTAAGTTTTATGGCTCAGTTCGTTTGATAATCGTGCATCAAGTATGCGCCATGTTGCCAACAAACTGATTGAGCTTCTGCATGTGCAACTTAACCATTATAAATCTAATCAAATACTCGTGCTATGCATTATGCTTATATATGCTACAGTTTCTGAATCTGAAAGCTTATGAAGGTTCATTTATACAAATGATTAGTTAGGCAAATTTGTTTATCTTAAATCCACGCTTTAATTTGCCTGCCCGCTGGGCGAGGGTAATGAACTCGCACTGGCTAAATCAGACAATTAACTAACCTTATCTATCTCGACAATGGACCCGGCTCAAACAAGGGCCTCAATCTAAGTGACATGAAAGGAAATTAGTCCGATGATGAACGGCTCTAGGGAAATGGAATATGTATAGACCTCCTGGGCAATAAAAGCCGGCGCAGATGGGGAAGCGGCGGCATGGGTTGGTTTGGGGAATCCGGCCTGCAGGACCATCAAAGGAATTAATGTGCCGCTGGTCGGCCGACGGTTTTGTTAAATGGATGCCAAACAACTAACCGCAAGGGGCACATATTGTGGTGCCTATATTTAGGTGGTGCTTTAAAGTTGACATATCCTCGGCTTTGATGAATCTTTGATGAAGTTTCCATTCACTTCAGCCGGGTATTCGCTGAAAGTTGATTGAAAAAGTTTGCTCCTTTCTTCGTACTCATGCAGTTTATTCTTTCTCGTATGCAATGTGTACGTACGAGTGGGTTTCCACAAAACTATATGGATTCCGCTGACGTCAGCCGGGGGCGCAGCTGAAATGAAATAGCGAATTTAAACCCAATTGTAATCATTTCCATTCTCTCTGTCTCTGTTTTTGTTTTTGCAG
Seq C2 exon
GTGGAAAATGTGCGGATGATAGATCGCTACAATACCAAAAATCCCACGGTTGGCACACTCTATCTAACGGCCACCCATCTGATATTCGTGGAGCCCGACAGCAACAAGGAGACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0028497:FBtr0072029:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0289315=GRAM=PU(22.2=20.0)
A:
NA
C2:
PF0289315=GRAM=FE(64.4=100)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0071938
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:
CAGTCTCCCGCAATGGACATC
R:
TCGGGCTCCACGAATATCAGA
Band lengths:
350-1786
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)