Special

DmeINT0024259 @ dm6

Intron Retention

Gene
FBgn0050443 | Opbp
Description
The gene Optix-binding protein is referred to in FlyBase by the symbol DmelOpbp (CG30443, FBgn0050443). It is a protein_coding_gene from Dmel. It has 2 annotated transcripts and 2 polypeptides (1 unique). Gene sequence location is 2R:6653217..6655267. Its molecular function is described by: DNA-binding transcription factor activity, RNA polymerase II-specific; sequence-specific DNA binding; RNA polymerase II regulatory region sequence-specific DNA binding. It is involved in the biological process described with: regulation of transcription by RNA polymerase II. 9 alleles are reported. No phenotypic data is available. The phenotypic classes of alleles include: viable; fertile. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of moderate expression to a trough of low expression. Peak expression observed at stages throughout embryogenesis, at stages throughout the larval period, at stages throughout the pupal period, in stages of adults of both sexes.
Coordinates
chr2R:6654117-6655110:+
Coord C1 exon
chr2R:6654117-6654509
Coord A exon
chr2R:6654510-6654563
Coord C2 exon
chr2R:6654564-6655110
Length
54 bp
Sequences
Splice sites
5' ss Seq
GCGGTGGGT
5' ss Score
6.6
3' ss Seq
TAAATAACTTATTATTTTAGCTT
3' ss Score
6.08
Exon sequences
Seq C1 exon
CTTCGATGAAACCCTCCTGACGGTACACAAACAGATGCACCAACAGGAATCTAGTGAGATTATGTGCAGCATTTGCAACCGGAAGTTTGAGAACGAAGTTACCTATCAGATGCACCAAAAAATCCATGAGAAACCGCGCGACTCCGAGTCCTCCCGTAAATTAGCCCAGCGTACTAGTCTCGATAAGGAGAAACCCGGGTTTCCCTGCCAGTACTGCGAGAGGGTGTTCACCCGCCCCTTTGAAAAAGTCAAGCACGAACGGGTCCACACCGGAGAAAAGCCTTACGCCTGCGAGGTCTGCGGCAAGACATTTCGGGTGTCATATTCCCTGACCCTTCATCTGCGTACCCACACCAACATTCGGCCGTATGTGTGCACGGTGTGCAACAAGCG
Seq A exon
GTGGGTAAAATCAAGTTTCATAGAATTACAGTTTTAAATAACTTATTATTTTAG
Seq C2 exon
CTTTAAATCGCACCAAGTGTACTCCCACCACCTGCGCATCCACAGCTCCGAACGACAGTTTTCATGCGATGCGTGCCCCAAGACTTTTCGGACCTCCGTGCAGCTGTACGCCCACAAAAACACCCACACCAAGCCTTACCGGTGTGCCGTGTGCAATCGCCCATTTTCTTCGATGTACGCCGTCAAGAATCACATGCAGACCCATAAGGAGATCAGCAGCAAAGGAAGTGTCGGCTCTGGTACGCCGAACATTAAGAGTGCGGCCACCTCGAAGAGCCAGGCAGCTGGGAAGTTCTATTGTAATACTTGTGGAGCTGAGTACGCACGTCTCTTCGCCCTGCGCCTGCACATGAAGTCGGCTCACGGTTTGGTGGAGGAGCAGGAGAATCCCGCCACCTCAACTGATGCTGCACACGTCGCTGAGACCGATGATTCCGAGACTGCGGTGTTGATAGCGGCAGCCGAGGCAGATGCCGCTTACATAAACGCTGTGGTAAACGATGTAGACATCGTGGGCACCGTACCCACCTACGAAGAGTGCGTTGTG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0050443:FBtr0086109:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.189 A=NA C2=0.191
Domain overlap (PFAM):

C1:
PF056057=zf-Di19=PD(80.0=33.3),PF134651=zf-H2C2_2=WD(100=17.4),PF134651=zf-H2C2_2=PU(84.6=16.7)
A:
NA
C2:
PF134651=zf-H2C2_2=PD(11.5=1.6),PF134651=zf-H2C2_2=WD(100=14.2),PF0009621=zf-C2H2=WD(100=12.6)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0085444


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:
CTTCATCTGCGTACCCACACC
R:
CGCATCGCATGAAAACTGTCG
Band lengths:
132-186
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)