Special

DmeINT0002869 @ dm6

Intron Retention

Gene
FBgn0039808 | CG12071
Description
This gene is referred to in FlyBase by the symbol DmelCG12071 (FBgn0039808). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (2 unique). Gene sequence location is 3R:30877084..30881027. Its molecular function is described by: RNA polymerase II cis-regulatory region sequence-specific DNA binding; DNA-binding transcription repressor activity, RNA polymerase II-specific. It is involved in the biological process described with: negative regulation of transcription by RNA polymerase II; regulation of gene expression. 6 alleles are reported. No phenotypic data is available. No phenotypic class data is available. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of extremely low expression. Peak expression observed within 12-24 hour embryonic stages, at stages throughout the larval period, at stages throughout the pupal period, in adult male stages.
Coordinates
chr3R:30877569-30878581:-
Coord C1 exon
chr3R:30878147-30878581
Coord A exon
chr3R:30877998-30878146
Coord C2 exon
chr3R:30877569-30877997
Length
149 bp
Sequences
Splice sites
5' ss Seq
GAAGTAACT
5' ss Score
4.11
3' ss Seq
CCTTTTCCCTGCAAATCCAGGTG
3' ss Score
7.31
Exon sequences
Seq C1 exon
TATTGACAGCCGGAACGGCTAGTCGCAGAGTCAACAAAACCAGCAGCAGCGGCGGCAGGAGTCATTGCTAAGACCACCAGCAGCAACAACAGTCGCAACTATCAAATGGATGCTAATCAAAACCAAATTCAGATGGAGGCCCAAGCACGAAAACAGAAGATAATCATTCAAAACCAGATGATACTCAATGCCAGCCACCAGCAGCAGCAGCAGCCGCAGCAACATCCGCAACAGCAGCAGCACCAACAGCAGCAGCAGCAACACGTGGCCCACGGAAAGAAGGCAGCCAGAAAACACCAGCAACATCTGCAGCAACAGCAGCAGCAACAGCAACAGCAACAGCAACAGCAACAGCAGCAGCAGCAACAGACCAGTGCGCCTATGTACAATAACAATAGTAGTAGCAACCACAACGGCAACAACCAAAGCCAAGAA
Seq A exon
GTAACTACCTATTAAACAGACCAAATGAACTGAAACCACAGCAACACCAACAGCCAACAGCAACATTGAACACCAAAAAAAAAAACTCACCATTTCCGCATTCTGTATTCTGTTACCCTTCCGTTTACCCCTTTTCCCTGCAAATCCAG
Seq C2 exon
GTGTCGGTGCCGGTGTCGCACATCATTGCCAATTCGCCGACGGCCGCCACGTATATGCAGGCCCAGCTGAGCGAGCACGCCAGCAACATGCAGCACGGCATGCCCATTGTCACGTACAATGGGAACCAGTACTGCGTGATTACCCGTGCCCCGGATCTGGATGTGGAGGCGATGCAGAAGCCGCTGGACTATGGCCACGCAGCCGGAGGAGCCACCAACATAATAGTAATGTCGCCGATGCAACTGCTGCCCCCCCAGCAGCAGCAGCAGCAGCCGCAACAGCAACAGCAGCAGCAGTAAGCACCATCGAAGAGAAAGGCTAACTGACTGGCCAATCAGCTATAAATACGAATTGTAAATAAAGTCTTAAGCAGCCGAGAGCAACCCTAAGTATATGTTTAACAACACTACCCAGCAAAACTAAAAACT
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0039808:FBtr0344715:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact

Alternative protein isoforms

No structure available
Features
Disorder rate (Iupred):
  C1=0.972 A=NA C2=0.838
Domain overlap (PFAM):

C1:
NO
A:
NA
C2:
NO


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0311048


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0311049, FBpp0312354, FBpp0312355
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:
CAACAGCAACAGCAACAGCAG
R:
CGGGTAATCACGCAGTACTGG
Band lengths:
245-394
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)