DmeINT0011378 @ dm6
Intron Retention
Gene
FBgn0034598 | CG4266
Description
This gene is referred to in FlyBase by the symbol DmelCG4266 (FBgn0034598). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (4 unique). Gene sequence location is 2R:21161713..21168659. Its molecular function is described by: mRNA binding; nucleic acid binding. The biological processes in which it is involved are not known. 13 alleles are reported. The phenotypes of these alleles manifest in: chaeta; mesothoracic tergum. The phenotypic classes of alleles include: viable; visible; body color defective; partially lethal - majority die; some die during pupal stage. 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
chr2R:21166890-21168183:-
Coord C1 exon
chr2R:21167596-21168183
Coord A exon
chr2R:21167043-21167595
Coord C2 exon
chr2R:21166890-21167042
Length
553 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
CTTTTAAATAACTCTTTCAGGAG
3' ss Score
7.2
Exon sequences
Seq C1 exon
CTCTCCGGACTCTATGACAGCCGACCGCCCATTTCCAAAGCGAAGATGGCCGCCATCACCAAGTCGGCGATGCGGGCCATCAAGCTGTATAAGCACGTCGTCCAGAGTGTGGAGAAGTTCATCTTGAAGTGCAAGCCGGAGTACAAAGTACCCGGGCTGTATGTAATCGACTCGATAGTGCGCCAGTCGCGCCACCAGTACGGTATGGACAAGGATCTGTTCGCGCCCCGATTCCAGCGTAATCTCACGGAGACCTTTGCCAACTTGTTCCGGTGCGCTCCGGAGGACAAGAGTCGCATCATCCGGGTACTGAACCTGTGGCAGAAAAACAACGTCTTCAAGTCCGAGGTCATTCAGCCGATCTTCGACCTGGCCGACCCAAACCACCCAATCTACCACCAGATGCCTCCGGTGGGTGGCAGTGGAGGACAGGGCGGCGGCGTGGGTCCAGGACCCAGCAGCAGCGGTGCTCTTAGCCTGGCGGACATATCGAGCGGTCCGAACGGTCTAAACAGCTCCGGAATGGAGATAAGCATGAACAGCTCCGGGGGCGACGATAAGATGGGCGGTGCCATGCCCGACTTGTCG
Seq A exon
GTAAGTGATGCTTTCGGTTGAGGCTTCTACAGGTGTCTAGTATTGGATAATGGCTTAACTAACATCGTCTACAATTCTGCTGCATTTACATTTCTCTGTCTCTCATGTCTTGCCCACTAACCGCCCATTTTGCCCTTCGCCCAATCGCTAGCTGGGCCATGAGAAGTTCGGCGGTGGCAGCAGCAGCTCCAAGCGTCACTACTCGGAGCAACACTATTCCAAACGACAGTCGGTGGTCTCGTGCTCGTCGAAGACCAGCAAGTCGCATCATCACAAACGGGAATATGTCAAGAGCTCGCACGACATTGACTACCAGGTGCGGGAGATCATCGAGGAAGAAGATGAAGGCCTGCAGATGCTGATGGCAGATGATCACCACTGTATGGGCGACGACTCACCGCCCACTTCTTCAAACCTGTTAGACGTATGGCGAACCCCATTAACACATCTCTTCATTTAGATAGTTTTGTTTATCTTAAGTTTCTATTTGTTGCTTTTGTTGCTCACATTAGATCGATCCCATTTTGAATAACCTTTTAAATAACTCTTTCAG
Seq C2 exon
GAGAAGAAGATCAAGCAGCTGCTAAACAATCCGAATGTGCTGCGGCAGCTCCATACGCTGCAGAACTTCCAAAATTTGAAGCCGCAGGAGGAGAACCAGAAGCATCGCTATCAGGACGAGGCACTGCAGCAGCATTTCCAGAACGTAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0034598:FBtr0071629:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.324 A=NA C2=0.903
Domain overlap (PFAM):
C1:
PF048188=CTD_bind=WD(100=33.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0071554
Other Inclusion Isoforms:
FBpp0112013, FBpp0302570
Other Skipping Isoforms:
FBpp0309673
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:
CAAGTCCGAGGTCATTCAGCC
R:
CTCCTCCTGCGGCTTCAAATT
Band lengths:
343-896
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)