DmeINT0033358 @ dm6
Intron Retention
Gene
FBgn0265276 | l(3)neo38
Description
The gene lethal (3) neo38 is referred to in FlyBase by the symbol Dmell(3)neo38 (CG6930, FBgn0265276). It is a protein_coding_gene from Dmel. It has 11 annotated transcripts and 11 polypeptides (6 unique). Gene sequence location is 3R:11765038..11779128. Its molecular function is described by: transcription regulatory region sequence-specific DNA binding; DNA-binding transcription factor activity, RNA polymerase II-specific. It is involved in the biological process described with: regulation of chromatin silencing; positive regulation of transcription by RNA polymerase II. 33 alleles are reported. The phenotypes of these alleles manifest in: chaeta; mesothoracic tergum; wing. The phenotypic classes of alleles include: visible; lethal; viable; flight defective; partially lethal - majority die; pain response defective.
Coordinates
chr3R:11768611-11769154:-
Coord C1 exon
chr3R:11769058-11769154
Coord A exon
chr3R:11769001-11769057
Coord C2 exon
chr3R:11768611-11769000
Length
57 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTTATCGCTGCCACCTGCAGGTT
3' ss Score
9.04
Exon sequences
Seq C1 exon
ATCTGCATGAAGTCCTTCAAGCGCAAGGAGCAGCTCACTCTGCACATTGTCATCCATTCCGGCGAGAAGAAGCATGTTTGCATTGAGTGTGGAAAAG
Seq A exon
GTGAGTGGTCTGAAAAGCAATTTCGTTTACCTCGTTACTTATCGCTGCCACCTGCAG
Seq C2 exon
GTTTCTATCGCAAGGATCACTTGCGCAAGCACACACGATCGCACATCGCCCGGCGTGTCAAGTCGGAGGTGTCGGCGCAGAACGTTAACGGATCCGCCGGAGGCGGTGGCGGCGGTGGAGGCGGCAACAGTGCGCAGAGCAACGCGCTGCACGGCTCCTGAGGATCGTACAAGGACTTCTGGTAAACTCCCAGCCGAATTTCAAGCCATAAGGGGCGGCCAGCCTGCTGGCGGCGGTGGACAGGTGGTGTTCGTATACGGATACGACTGACTGCCGCCGGGAGCAGGCGAGCTGCCTTTGAAATTCGCTGGGGGCTTACCGGGGGTCCTGCTGAGCGTCACCCAACTCCAATTACAATAACCCTCAATAAACACGAGTTATACTTACTGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0265276:FBtr0082533:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.772
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=PD(26.9=21.2),PF134651=zf-H2C2_2=PU(84.6=66.7)
A:
NA
C2:
PF134651=zf-H2C2_2=PD(11.5=5.6)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0303203
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0082007, FBpp0110176, FBpp0110177, FBpp0293716, FBpp0297925, FBpp0297926, FBpp0297928, FBpp0297929, FBpp0297930
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:
ATTCCGGCGAGAAGAAGCATG
R:
GGCGGATCCGTTAACGTTCTG
Band lengths:
140-197
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)