DmeINT0003537 @ dm6
Intron Retention
Gene
FBgn0035526 | CG1316
Description
This gene is referred to in FlyBase by the symbol DmelCG1316 (FBgn0035526). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 3L:4283851..4286865. Its molecular function is described by: nucleic acid binding; mRNA binding. The biological processes in which it is involved are not known. 7 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: some die during pupal stage; partially lethal - majority die. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of very high expression to a trough of moderately high expression. Peak expression observed within 00-06 hour embryonic stages.
Coordinates
chr3L:4283851-4284541:+
Coord C1 exon
chr3L:4283851-4284283
Coord A exon
chr3L:4284284-4284346
Coord C2 exon
chr3L:4284347-4284541
Length
63 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
CTCTTATCCTCCTCTTCCAGTCG
3' ss Score
9.59
Exon sequences
Seq C1 exon
GTTCACATCTCTATCTTGTCTGTATACGGCTGTGTGTCAAAGCGGCAAAAGCGAGAAAAGTCGAAGTGCAAATAATTTTAACGGAGCGGAAAAAATATAGATAAATCAGAACCATGTCGGACTATAGATCGCAATCGCGCAGTGGCGGGGGACGTGGCGGTCAGGAGTACTCGAACGACGACGATCCGCCGATGTCGCGTCTCTTCATCATTTGCAACAAGGCGCACACCGAGGAGGATTTCCGTGAAGCCTTCTCGCCATACGGCGAAATCGAGGATATCTGGGTGGTGAAGGACAAGCACACCCAGGAGAACAAGGGAATCGCGTACGTCAAGTTCTCCAAGACATCCGATGCTGCCAAGGCACAGGAGGAGATGAACGGCAAGACCATTGGCAAGATGGATCGCACCCTTAAAGTCCTGGTGGCAGCCAA
Seq A exon
GTAAGATTAGCTTCGAGAGTACTGGCCCAAAACCATGGTCTAACTCTTATCCTCCTCTTCCAG
Seq C2 exon
TCGCAATCAGGGCTCAAATAAGTCTGAGAACGAGCAGGAGAAGTACGTGAGACTCTTCATAGTGATCCCCAAAACAGCCACCGAGGAGGATATTCGCGAGGAATTCTCGCAGTGGGGCGATGTGGAATCTGTCACAATTGTCAAGGAGAAGAACAATGGCAATCCCAAGGGCTTCGGATATGTCCGCTTTACCAA
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0035526:FBtr0073233:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.355 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF0007617=RRM_1=WD(100=59.8)
A:
NA
C2:
PF0007617=RRM_1=PU(73.0=69.7)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
FBpp0073089
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:
AAGACATCCGATGCTGCCAAG
R:
TCACGTACTTCTCCTGCTCGT
Band lengths:
142-205
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)