Special

DmeINT0022379 @ dm6

Intron Retention

Gene
FBgn0002023 | Lim3
Description
The gene Lim3 is referred to in FlyBase by the symbol DmelLim3 (CG10699, FBgn0002023). It is a protein_coding_gene from Dmel. It has 8 annotated transcripts and 8 polypeptides (4 unique). Gene sequence location is 2L:19079256..19108427. Its molecular function is described by: sequence-specific DNA binding. It is involved in the biological process described with: motor neuron axon guidance; regulation of transcription, DNA-templated; positive regulation of gene expression; nervous system development. 37 alleles are reported. The phenotypes of these alleles manifest in: circulatory system; tagmatic subdivision of integument; segmental nerve; melanotic mass; adult. The phenotypic classes of alleles include: lethal; phenotype; increased mortality; increased mortality during development. 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 06-24 hour embryonic stages, during early larval stages.
Coordinates
chr2L:19081492-19081994:-
Coord C1 exon
chr2L:19081820-19081994
Coord A exon
chr2L:19081695-19081819
Coord C2 exon
chr2L:19081492-19081694
Length
125 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CCAATGTTCGGGTCGAACAGACG
3' ss Score
1.97
Exon sequences
Seq C1 exon
CCACAATCCCGAAATGCGGCGGCTGCCACGAGCTGATCCTTGACCGCTTCATCCTCAAAGTGCTGGAGAGGACGTGGCACGCCAAGTGCCTGCAGTGCAGCGAGTGTCATGGCCAGCTGAACGACAAGTGCTTCGCGCGGAATGGCCAGCTCTTCTGCAAGGAGGACTTCTTCAA
Seq A exon
GTAAGTAAATTTCTCAAATGCCAAGGTCGTTGGCAGGGGGTGAACATTGGACGCTTTGGTAGGCCAAATTGGTTTAATGAAAAATCTCCTTCCATGTCGCACTTGCCAATGTTCGGGTCGAACAG
Seq C2 exon
ACGTTACGGTACAAAGTGTTCCGCTTGTGATATGGGCATTCCGCCCACGCAGGTGGTGCGTCGGGCGCAGGACAACGTCTACCATCTGCAGTGCTTCCTGTGCGCCATGTGCTCCCGCACCCTGAACACCGGCGACGAGTTCTACCTGATGGAGGATCGTAAGCTGATCTGCAAGCGGGACTACGAGGAGGCCAAGGCCAAGG
VastDB Features
Vast-tools module Information
Secondary ID
FBgn0002023:FBtr0081170:2
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:
PF0041217=LIM=PU(94.6=89.8)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)


Main Inclusion Isoform:
NA


Main Skipping Isoform:
FBpp0302972


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
FBpp0080712, FBpp0080713, FBpp0301566, FBpp0301567, FBpp0301568, FBpp0301569
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:
CCAGCTGAACGACAAGTGCTT
R:
GTAGTCCCGCTTGCAGATCAG
Band lengths:
247-372
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)