BtaALTA0016514-2/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000005525 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr11:93078621-93081421:-
Coord C1 exon
chr11:93081201-93081421
Coord A exon
chr11:93078722-93078774
Coord C2 exon
chr11:93078621-93078721
Length
53 bp
Sequences
Splice sites
5' ss Seq
ACGGTACTC
5' ss Score
4.58
3' ss Seq
CCCACCCCCGTCCTTTCCAGGCT
3' ss Score
10.11
Exon sequences
Seq C1 exon
CCGATTCGGGACCAAGTGCGCTCGGTGCGGCCGACAGATCTACGCCAGCGACTGGGTCCGGCGGGCACGCGGCAATGCCTACCACCTGGCCTGTTTTGCCTGCTTCTCGTGCAAGCGCCAGCTATCCACAGGGGAGGAGTTTGGCCTGGTCGAGGAGAAGGTGCTCTGCCGTATTCACTACGACACCATGATCGAGAACCTCAAGAGGGCTGCGGAGAACG
Seq A exon
GCTGCCACTAGAAGAGATGGGGACGCGTGGTCAGCCACTTCTGTCGCCCCCAG
Seq C2 exon
GAAACGGCCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCGGCTAAGCGCGCCCGGACGTCGTTCACCGCCGAGCAGTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005525-7-5,7-4-2/2
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
Human
(hg38)
No conservation detected
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:
TTTGGCCTGGTCGAGGAGAAG
R:
CTTGGGCTGACTGTCCTGTTC
Band lengths:
138-191
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development