BtaINT0085438 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011124 | LHX3
Description
Bos taurus LIM homeobox 3 (LHX3), mRNA. [Source:RefSeq mRNA;Acc:NM_001038620]
Coordinates
chr11:103737401-103738491:-
Coord C1 exon
chr11:103738289-103738491
Coord A exon
chr11:103737553-103738288
Coord C2 exon
chr11:103737401-103737552
Length
736 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
ACGCCTCCCCCGCGGTGCAGAGG
3' ss Score
5.4
Exon sequences
Seq C1 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGATTTCGTGTACCACCTGCACTGCTTCGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTATCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCAGACTACGAGACAGCCAAGCAGCGAG
Seq A exon
GTCAGTGGGAGGGGGCGACGGTCACGGGGCTCGGCCTGGGCACGGCCCACCCTCCCCTTTCCTTCCCTGCAAAGAGGGGCTAAGGCCCGTCCGGGTCGGGTGTGGAGGGATCCTTCCCTCCAGCGTCCCCGGCGAAGCGCTCACAAAGCGGCGAGAACTTAAGCGTCTTCTCTCTGGGCGGAGGCGTTGGGGAGCCCCCGCCTCCAGGTCTGGGAGCCCGGGACAGTTAGCAGACCCGCTCTGAGAAAGCCGGGTCTGGGGTCTTAGCAGCCGTCTTCTTCCCGGGCGCAGGGAGATTGGCCTGAATTACGTGGATTAGCTCTGCGGGTCTGAATTATCGTCCTAAATCCTTGACCGTGAAGATCCGATCCTACCCGCGCCCTTAGAACAAAGAGGAGCGAGGGAGGGTTGGGGGCGGGCAGCGCTTGTCAGTAGGGGGCCAAGGCTGGAAGCGCCTGCACCCGGATCCAGGGCGGCTGGGTCCTTAAAGAAGGCCGCCGCAGGGCCGCCCCTGGCTGGGCCGGAGCACCGCCCAGCGCGTTTCCTCCATCGCTCCGGGCACCCGCGTCCCGCAAAACCCTTTGGCCTTCCCGCCGCGGCGGCGAGGCTGGCGGTCGCAGCGGCGGCGGCGGCGGCACCGGCACCTCTGGCCCCGACGTGCGCGCGCCCCGAGGGAGGTGGGAGCGCCGAGCGGCCGGAGGAGCAGGCCCAGCCTCACGCCTCCCCCGCGGTGCAG
Seq C2 exon
AGGCCGAGGCCACGGCCAAGAGGCCGCGCACGACTATCACAGCCAAGCAGCTGGAGACTCTGAAGAGCGCCTACAACACCTCGCCCAAGCCCGCGCGCCACGTGCGGGAGCAGCTCTCCTCCGAGACCGGCCTGGACATGCGCGTCGTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011124:ENSBTAT00000055580:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.706
Domain overlap (PFAM):
C1:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=86.3)
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:
GCGCTTCGGGACCAAGTG
R:
ATGTCCAGGCCGGTCTCG
Band lengths:
342-1078
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development