DmeINT0002520 @ dm6
Intron Retention
Gene
FBgn0037031 | CG11456
Description
This gene is referred to in FlyBase by the symbol DmelCG11456 (FBgn0037031). It is a protein_coding_gene from Dmel. It has 4 annotated transcripts and 4 polypeptides (2 unique). Gene sequence location is 3L:20841987..20844340. Its molecular function is described by: DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding. It is involved in the biological process described with: regulation of transcription by RNA polymerase II. 6 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: pain response defective; viable. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of low expression. Peak expression observed within 00-18 hour embryonic stages, during late larval stages, at stages throughout the pupal period, in adult female stages.
Coordinates
chr3L:20842403-20843358:+
Coord C1 exon
chr3L:20842403-20842928
Coord A exon
chr3L:20842929-20842980
Coord C2 exon
chr3L:20842981-20843358
Length
52 bp
Sequences
Splice sites
5' ss Seq
ATAGTGAGT
5' ss Score
6.97
3' ss Seq
CTACCTAATACTCTTTCCAGATT
3' ss Score
6.85
Exon sequences
Seq C1 exon
GTGCTCCTTTGGAAAGGAATGCCCCTTCAAGTTCCAAGATGCTACCAAAATGGAGCTCCACTGTAGTTGCCATAAGGGTGGCAGTTTTTCCTGCTGCGAATGTGGCATGGAACTGCCCAACTGGCGGCGGTGCTCGGCTCACCTGTGGAAAGCCCACCAGGTGGATGTGGACCTACTAGTGTGTCCCGTTTTCGAATGCAACTACAAGTCGCCCATATCCGCTCTCGTGTGGCGCCACATGCAGGTTCACAAAAAGTGGCGACCCAGGGTGCTCCGGTCACTGGCTGCCGTTCAGCGGAGAAGAAAGCTCAAGGAACAGTCCGCAGAGATGGCCGCGCAACCTGCTGCTCTGCCACCATCGTCAAAGAAAAACAAATACTATGCCGAGAAGACTTGCGAGATTTGCAATCGCAAGTTTGTCAACGGTAAAACGCTCTCTAAACACGTGAAGACTGTTCACAACAAAATCAAGCCATTTATCTGCAATGTGTGTGGCAAAAAGACGGCTCGCAAGGCTAGCTTAATA
Seq A exon
GTGAGTTCAGATAGCACTTTACGATCTTCTTGCTACCTAATACTCTTTCCAG
Seq C2 exon
ATTCACATGCGTCAGCACACGGGCGAGAAGCCGCTGCAATGTGGCGAATGCAAGTTCTCCACTCGCGATCCCAGTGTCCTGCACAAGCATCGGCAGCGTCATGATAGCCAGGACACAAGGAGCAGCCTGAAATGTAGTCAGTGCGACTACTTCTGCATCCAAGCCAATGCTCTTAAGCGCCACATGCGGCTCAATCATGCCGAAGCCTATAGGGACTTGTGCTGTGATATCTGCAGCTTCACCTCAATTAATGTAGAACGACTACGAGCCCACAAACAGGATCATCGACAGGGCTTGATCACAAATTGTGAGGATTCTATGGATGCACGTGCCGCTGGCTTCAAGTATCCTCGAAAAGTGGGCGACAAGAACGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0037031:FBtr0078264:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.064 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF134651=zf-H2C2_2=WD(100=15.3),PF134651=zf-H2C2_2=PU(8.0=1.1)
A:
NA
C2:
PF134651=zf-H2C2_2=PD(84.0=16.7),PF139091=zf-H2C2_5=WD(100=19.8)
Main Inclusion Isoform:
FBpp0290095
Main Skipping Isoform:
FBpp0077922
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
FBpp0305563
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:
GGCTCGCAAGGCTAGCTTAAT
R:
GTCCTGGCTATCATGACGCTG
Band lengths:
136-188
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)