RnoINT0085186 @ rn6
Intron Retention
Gene
ENSRNOG00000005996 | Lhx6
Description
LIM homeobox 6 [Source:RGD Symbol;Acc:1306174]
Coordinates
chr3:15419393-15419779:-
Coord C1 exon
chr3:15419679-15419779
Coord A exon
chr3:15419489-15419678
Coord C2 exon
chr3:15419393-15419488
Length
190 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
TGCCCTTCTGCGCCCTACAGGTT
3' ss Score
10.22
Exon sequences
Seq C1 exon
GGAACGGTCTCACGTTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCAGCTAAGCGCGCGCGGACGTCCTTCACGGCAGAGCAATTGCAG
Seq A exon
GTACCCCGGGCAAGCCCCGAAGCGTGTGGGCGGGGCCTCGGAGTGGGCGTGGTTGTGCGGGATTTGTGACTCCGCCCCTTGTGCTGGGACCCGCGGGAGGCCGCTCCAGGGCTGAAGCTGTCTGGGGCGTGGCCTCGGACCCTGAGCTTCTGATTGGGCGGAGGTCTCAGTGCCCTTCTGCGCCCTACAG
Seq C2 exon
GTTATGCAGGCTCAGTTCGCGCAGGACAACAACCCCGACGCGCAGACGCTGCAGAAGCTAGCGGACATGACGGGCCTCAGTCGCAGGGTCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005996:ENSRNOT00000008817:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.824 A=NA C2=0.594
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(21.1=35.3)
A:
NA
C2:
PF0004624=Homeobox=FE(54.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGTCTCACGTTGGAGGG
R:
CTGGATGACCCTGCGACTGAG
Band lengths:
194-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]