BtaINT0085455 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005525 | LHX6
Description
LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]
Coordinates
chr11:93078308-93078721:-
Coord C1 exon
chr11:93078621-93078721
Coord A exon
chr11:93078404-93078620
Coord C2 exon
chr11:93078308-93078403
Length
217 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
AGCCCCGCGGCGCCTGGCAGGTT
3' ss Score
3.83
Exon sequences
Seq C1 exon
GAAACGGCCTCACGCTGGAGGGGGCAGTGCCCTCGGAACAGGACAGTCAGCCCAAGCCGGCTAAGCGCGCCCGGACGTCGTTCACCGCCGAGCAGTTGCAG
Seq A exon
GTACCCGGGCTGGCCGCGAGTGGCCGGGTGTGGGCGGGGCCTCGGAGTGGGCGGGGCTGATAGGGCCTCCTGACTCCTCCCCTCTGCCCGACCCGCGGGTGGCGGGGAGGGGCTGTAGCTGCCTGGGGGCGTGGCCTTCGGGCCGGAGCCTCTGATTGGGCCGGGGCCTTGGCGACCTCGGGGGGCTCGTGCCTCACAGCCCCGCGGCGCCTGGCAG
Seq C2 exon
GTTATGCAGGCGCAGTTCGCGCAGGACAACAACCCCGACGCGCAGACGCTGCAGAAGCTTGCGGACATGACGGGCCTCAGCCGAAGGGTCATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005525:ENSBTAT00000007266:6
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=0.562
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:
CAGTGCCCTCGGAACAGGA
R:
CTGGATGACCCTTCGGCTGAG
Band lengths:
173-390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development