BtaINT0085437 @ bosTau6
Intron Retention
Gene
ENSBTAG00000011124 | LHX3
Description
Bos taurus LIM homeobox 3 (LHX3), mRNA. [Source:RefSeq mRNA;Acc:NM_001038620]
Coordinates
chr11:103738289-103739228:-
Coord C1 exon
chr11:103739057-103739228
Coord A exon
chr11:103738492-103739056
Coord C2 exon
chr11:103738289-103738491
Length
565 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGC
5' ss Score
6.39
3' ss Seq
GCGCCCTGTGCGTCCCGCAGGCG
3' ss Score
9.16
Exon sequences
Seq C1 exon
AGATCCCGCTGTGTGCCGGCTGCGACCAGCACATCCTGGACCGCTTCATCCTCAAGGCTCTGGACCGCCACTGGCACAGCAAGTGCCTCAAGTGCAGCGACTGCCACGCGCCGCTGGCCGAGCGCTGCTTCAGCCGTGGGGAGAGCGTGTACTGCAAGGACGACTTCTTCAA
Seq A exon
GTGAGCCCGCCAGCTGCCTGGGGCGGGCGGCGCACCCAGGGGAGCCCCGGGGCCCTCACCGTAACCAAGTCTGGAGCCCTGAAAACCCCCATCTCCACACCCTTCCTTTTCCCCAAACAGGGCACCCCCGGGGCCTCTCTGTTGGCGGCTGGGCTGGCCCACTAACAATCTTTTAAAGTAATTAATTTTGTGAGTCATTGAAGCAGTAGTTAAAAGGATAACCCCAAATTTGTAACGCTCTACTGGACGTGCTCCCTCTTCGTTTTGGTCTTGTATTCGTGCTTAATGGTGGGGATGGGGCTCCTACTGCACGTCGGCCCCGGTGGCCAAGGCCCTGCCCTTCCGAATTCACCTCCCCCATCCGGGCACAGAGGACAGCTGTGTGCCCCAGAGCATCTGGATCCCCTTCTCGGTAGTCCCTGAGGGTAGTCTCTGCGACCAGGGGCAGGGCCCGGGACGCCTTCCTCCAGGAACCACCCTGCGCCAAACCGCGTTAGCGGTTCTCCGACCCGCTCCGGGCGAAGGAGCGGCGGCCGCTCTGAGCCGCGCCCTGTGCGTCCCGCAG
Seq C2 exon
GCGCTTCGGGACCAAGTGCGCCGCGTGCCAGCTGGGCATCCCGCCCACGCAGGTGGTGCGCCGCGCCCAGGATTTCGTGTACCACCTGCACTGCTTCGCCTGCGTCGTGTGCAAGCGGCAGCTGGCCACGGGCGACGAGTTCTATCTCATGGAGGACAGCCGGCTCGTGTGCAAGGCAGACTACGAGACAGCCAAGCAGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000011124:ENSBTAT00000055580:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0041217=LIM=PU(94.6=91.4)
A:
NA
C2:
PF0041217=LIM=PD(3.6=2.9),PF0041217=LIM=WD(100=87.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACATCCTGGACCGCTTCATC
R:
CTGCTTGGCTGTCTCGTAGTC
Band lengths:
342-907
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development