RnoALTA0022006-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000005996 | Lhx6
Description
LIM homeobox 6 [Source:RGD Symbol;Acc:1306174]
Coordinates
chr3:15419679-15422531:-
Coord C1 exon
chr3:15422311-15422531
Coord A exon
chr3:15419780-15419833
Coord C2 exon
chr3:15419679-15419779
Length
54 bp
Sequences
Splice sites
5' ss Seq
ACGGTACCC
5' ss Score
6.32
3' ss Seq
CCCCACCCCGTCCTTTCCAGGCT
3' ss Score
8.83
Exon sequences
Seq C1 exon
CCGATTTGGAACCAAGTGTGCCCGGTGCGGCAGACAAATCTATGCCAGTGACTGGGTGCGGCGCGCGCGCGGCAATGCCTACCACCTGGCCTGCTTCGCTTGCTTTTCCTGCAAGCGCCAGCTATCCACGGGCGAGGAATTCGGCCTGGTTGAGGAGAAGGTGCTTTGCCGCATCCATTACGACACCATGATCGAGAACCTCAAGAGGGCCGCCGAGAACG
Seq A exon
GCTGCCACTAGAAGAGATGGGAACGCGTGGTCAGCTGCTTCTGTCGCCCCCCAG
Seq C2 exon
GGAACGGTCTCACGTTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCAGCTAAGCGCGCGCGGACGTCCTTCACGGCAGAGCAATTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005996-7-7,7-6-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.824
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.4=2.7),PF0041217=LIM=WD(100=77.3)
A:
NA
C2:
PF0004624=Homeobox=PU(21.1=35.3)
Main Inclusion 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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATTCGGCCTGGTTGAGGAG
R:
CTTGGGCTGACTGTCCTGTTC
Band lengths:
141-195
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]