RnoINT0085169 @ rn6
Intron Retention
Gene
ENSRNOG00000018427 | Lhx3
Description
LIM homeobox 3 [Source:RGD Symbol;Acc:71078]
Coordinates
chr3:3656022-3656854:-
Coord C1 exon
chr3:3656652-3656854
Coord A exon
chr3:3656174-3656651
Coord C2 exon
chr3:3656022-3656173
Length
478 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TCACCGTTTGTCCCGCGCAGAAG
3' ss Score
8.32
Exon sequences
Seq C1 exon
GCGCTTCGGGACCAAGTGCGCCGCATGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGGCGCGCCCAGGACTTCGTGTACCACCTGCATTGCTTCGCCTGCGTGGTTTGCAAGCGGCAGCTGGCCACGGGGGACGAGTTCTACCTCATGGAAGACAGCCGGCTGGTGTGCAAGGCGGACTACGAAACAGCCAAGCAGCGAG
Seq A exon
GTCAGTGGGCGGAGATGGCCCTCACGGGCGAGGAGGGAAACTCTCAGGTCTAGAGGCTGGGGACGGGAATTGGTTTGGTCCTGGGAGGTGGGGCAACCTGAAGCCCCAGGCACTGAGCAGACTGCTCCGGGGAGCCTGCAGTAGCAGTCGCATCGGCGGAAACAGGAGGTTGCCCTCTTTGAGAGAATTAGCAGCGCAACACCCTTGATCGTGAAGACCTGATTCCCACAAACTCTTAGAATATGGGGGTCGAGGACCGTGTCTGGCAGCGAGGCGCACCGCTGCGGGTTCCTAATACAGAGCCCGTCTGCCGGCGCTCCGCGTTCCGGGAAGCGAGCGGGGCCACCGGCGGCCTTGGCTTGGGAGCCAGGACCTCAGGGGCATCCGGAGAACGACGCGGGGCTCTTGGGGTGAAGCACAGGGCGCAGGCTGGCGCAGCCGGAGCGGGCTGGCCGGCCTCACCGTTTGTCCCGCGCAG
Seq C2 exon
AAGCCGAGGCCACAGCCAAGCGGCCGCGCACCACCATCACCGCCAAGCAGCTGGAGACGCTGAAGAGCGCCTACAACACCTCGCCCAAGCCGGCGCGCCACGTGCGCGAGCAGCTCTCCTCCGAGACCGGCCTGGACATGCGCGTGGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000018427:ENSRNOT00000025047:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.667
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=86.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGCTTCGGGACCAAGTG
R:
ATGTCCAGGCCGGTCTCG
Band lengths:
342-820
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]