Special

DmeINT0031794 @ dm6

Intron Retention

Gene
Description
The gene extradenticle is referred to in FlyBase by the symbol Dmelexd (CG8933, FBgn0000611). It is a protein_coding_gene from Dmel. It has 5 annotated transcripts and 5 polypeptides (1 unique). Gene sequence location is X:15992468..15996509. Its molecular function is described by 12 unique terms, many of which group under: binding; protein binding; DNA binding; transcription regulator activity; heterocyclic compound binding. It is involved in the biological process described with 12 unique terms, many of which group under: animal organ development; anatomical structure morphogenesis; embryo development; oenocyte differentiation; multicellular organism development. 65 alleles are reported. The phenotypes of these alleles manifest in: myofibril; organelle; adult abdominal segment 1; tarsal segment; midline crossing tract. The phenotypic classes of alleles include: embryonic/larval segmentation phenotype; some die during P-stage; increased mortality; phenotype. Summary of modENCODE Temporal Expression Profile: Temporal profile ranges from a peak of high expression to a trough of moderately high expression. Peak expression observed at stages throughout embryogenesis, during late larval stages, during early pupal stages.
Coordinates
chrX:15993965-15994605:+
Coord C1 exon
chrX:15993965-15994283
Coord A exon
chrX:15994284-15994346
Coord C2 exon
chrX:15994347-15994605
Length
63 bp
Sequences
Splice sites
5' ss Seq
GAGGTTGGT
5' ss Score
6.36
3' ss Seq
GTAATATAATCGTATTTCAGACC
3' ss Score
6.06
Exon sequences
Seq C1 exon
TCCTCTCGATTCGCAACACCCAGGAGGAGGAGCCCCCAGATCCGCAACTGATGCGCTTGGACAACATGCTGATTGCCGAGGGCGTGGCCGGACCCGAGAAGGGCGGTGGCGGAGCAGCGGCTGCCTCTGCGGCTGCGGCCAGCCAGGGCGGTTCCCTGTCCATCGATGGTGCTGACAATGCCATTGAGCATTCCGACTACCGTGCCAAGCTGGCACAGATCCGTCAAATATATCACCAGGAATTGGAGAAGTACGAGCAGGCATGCAACGAGTTCACCACGCATGTCATGAATCTTCTACGCGAACAGAGTCGCACGAG
Seq A exon
GTTGGTGTATATAGATAAATGCAAAATGATGGCCATCATTTGGGTAATATAATCGTATTTCAG
Seq C2 exon
ACCCATTACACCAAAGGAAATCGAGCGAATGGTGCAGATCATCCACAAAAAGTTTAGTTCCATACAAATGCAGCTGAAGCAGTCGACCTGCGAGGCTGTAATGATACTTCGTTCGCGTTTCCTGGACGCACGCCGCAAACGCCGCAATTTCAGCAAGCAGGCATCCGAGATTCTCAACGAGTACTTCTACAGTCACTTGAGCAACCCATATCCATCCGAAGAGGCCAAAGAGGAGTTGGCACGAAAGTGTGGCATCACG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0000611:FBtr0074135:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact

ORF disruption upon sequence inclusion

No structure available
Features
Disorder rate (Iupred):
  C1=0.477 A=NA C2=0.184
Domain overlap (PFAM):

C1:
PF037928=PBC=FE(51.7=100),PF070286=DUF1319=PU(60.5=48.6),PF040917=Sec15=PU(58.8=46.7)
A:
NA
C2:
PF037928=PBC=PD(20.5=48.3),PF070286=DUF1319=PD(38.4=37.9),PF040917=Sec15=PD(40.0=39.1),PF0004624=Homeobox=PU(70.0=48.3)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0073940


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0073942, FBpp0305514, FBpp0305515
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:
CGAGTTCACCACGCATGTCAT
R:
TCGACTGCTTCAGCTGCATTT
Band lengths:
137-200
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)