Special

DmeINT0006603 @ dm6

Intron Retention

Gene
FBgn0033491 | CG18011
Description
This gene is referred to in FlyBase by the symbol DmelCG18011 (FBgn0033491). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:10142338..10146206. 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. 10 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: some die during pupal stage; partially lethal - majority die; 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 early pupal stages, in adult female stages.
Coordinates
chr2R:10143409-10143882:+
Coord C1 exon
chr2R:10143409-10143670
Coord A exon
chr2R:10143671-10143729
Coord C2 exon
chr2R:10143730-10143882
Length
59 bp
Sequences
Splice sites
5' ss Seq
TGAGTAATT
5' ss Score
0.85
3' ss Seq
ATGATGCTTGTATTACCTAGAAT
3' ss Score
5.08
Exon sequences
Seq C1 exon
AGGATGAAGTTGATAATATTCCGGAGTACTTGGCCACCGTGGTGAAGACGAGCTTTGAAAAGCTGACATTTCAGTGGTGCACTGTGTGCAAGCACTGCTCTCTGAAATGTCCCACATTCGAGAGCCTTTTTAGTCACTTGTCAAAGGCACACAAAAGCCGGAGAGATGTCTACGAGTGTCCCATCGAAGGATGCAACAAGGAGTTGAAAGGTCGCAAATTCCTAGCCATGCATCTTGTTTTGTTGCACGCGCCAGTGGCTGA
Seq A exon
GTAATTATATTTACTAAAGGAAATATTTGTGTAATATATATGATGCTTGTATTACCTAG
Seq C2 exon
AATTCCGATCTACGGCAGCTGTCCGGAATGTAAATTGACGTTCTCCAACATTCTGCAGTACAACAAGCATTCTTGCGCGCATGTAATAAAAAAGAAGCGAGGTTTTCGCTCTTATTGTGAAATGTGTTCGCTGGAGTTTCCTTCCTGGAAGCG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0033491:FBtr0088332:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0087421


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:
ACACAAAAGCCGGAGAGATGT
R:
TTTACATTCCGGACAGCTGCC
Band lengths:
148-207
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)