Special

DmeINT0002522 @ 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:20843421-20844024:+
Coord C1 exon
chr3L:20843421-20843586
Coord A exon
chr3L:20843587-20843926
Coord C2 exon
chr3L:20843927-20844024
Length
340 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGC
5' ss Score
7.79
3' ss Seq
TTAAAAATCTACTCTGCCAGCGA
3' ss Score
3.55
Exon sequences
Seq C1 exon
ATTTCAGCTGACTGTTTTATGCCGTTGGAGAGCGTGGATTCATTGCCCCATGAACCAGCTCTGGATACGGGTGGTGTAACCATACCAGCTCCTCCATCTGAAGATACTCAATTTCCCACGTACTTAAAGGACTAAAATTATAACATTTTAAGTTGATAGATTAGGG
Seq A exon
GTAAGCGTTGAGTTGATTCACTTCCCATTTTTTATTGATTACTTTGTTTTTATGTCCTATGTATTTATGTACAATTCAATTTGTTGAATATGGCGTGTCCAATGCGCTGTAAAGAGTTTTGTATAAAATAATGTTCTCATGCAGTTTGTTTTGGGGATTTAAATGCTTGTTTATTAAGTTGTTCAGTTTTCCATTTAAATTTAATATCATTTTAGAATCTGATATGATTTTTTTGTTCAACATTCGAATTATTTAGTCATGCTGGTTTACCGTGTTCCGTTTAATTATCAGTTACGCTTTACTTTAAACTAATTTAAAATTTAAAAATCTACTCTGCCAG
Seq C2 exon
CGATAATCATCCGGTTTCAGTTCGGTTTCAAGATCAGCGCCGTTAAATCTAGTTTACGACAGAAATGTTTTCATTTGGGCAGTTCACTAATAACTTGT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0037031:FBtr0078264:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact

3' UTR

No structure available
Features
Disorder rate (Iupred):
  C1=0.568 A=NA C2=NA
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NA


Main Inclusion Isoform:
NA


Main Skipping Isoform:
NA


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0077922, 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:
TTCAGCTGACTGTTTTATGCCGT
R:
ACAAGTTATTAGTGAACTGCCCA
Band lengths:
262-602
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)