RnoEX0049901 @ rn6
Exon Skipping
Gene
ENSRNOG00000005996 | Lhx6
Description
LIM homeobox 6 [Source:RGD Symbol;Acc:1306174]
Coordinates
chr3:15411939-15419209:-
Coord C1 exon
chr3:15419035-15419209
Coord A exon
chr3:15415252-15415355
Coord C2 exon
chr3:15411939-15411959
Length
104 bp
Sequences
Splice sites
3' ss Seq
AGGCACCCTCTCGTCCACAGGTC
3' ss Score
9.14
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
Exon sequences
Seq C1 exon
GTGTGGTTTCAAAACTGCCGAGCGCGTCATAAAAAGCATACACCGCAGCACCCAGTGCCGCCCTCTGGGGCACCCCCGTCCCGCCTCCCCTCCTCCCTGTCCGACGACATCCACTATTCTCCGTTCAGCAGCCCAGAGCGGGCACGCATGGTCACCTTGCACGGCTACATCGAGA
Seq A exon
GTCAGGTACAGTGCGGGCAGGTGCACTGCCGACTGCCTTACACCGCGCCCCCTGTCCACCTCAAAGCCGACATGGATGGGCCGCTCTCCAGCCGGGGTGAGAAG
Seq C2 exon
GTCATCCTTTTTCAGTACTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005996_MULTIEX1-2/2=1-C2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (No Ref, Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.610 A=0.200 C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(19.3=18.6)
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 1 annotated functions for this event
PMID: 10393337
[Negative results]. LHX6 splice variant with/without cassette exon HsaEX0035746 interacts with Ldb1 in co-IP assay performed on lysate from transfected COS7 cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]