BtaINT0085444 @ bosTau6
Intron Retention
Gene
ENSBTAG00000003992 | LHX4
Description
Bos taurus LIM homeobox 4 (LHX4), mRNA. [Source:RefSeq mRNA;Acc:NM_001192785]
Coordinates
chr16:62912008-62912723:+
Coord C1 exon
chr16:62912008-62912162
Coord A exon
chr16:62912163-62912551
Coord C2 exon
chr16:62912552-62912723
Length
389 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CCCTTTGCTTGTTGTGGCAGGTT
3' ss Score
9.08
Exon sequences
Seq C1 exon
ATGACTCAGAGGCTGGAGCTAAGCGGCCCAGGACCACCATCACAGCAAAGCAGCTGGAGACATTGAAGAACGCCTATAAGAACTCCCCTAAGCCCGCCCGGCATGTGAGGGAGCAGCTGTCCTCGGAGACAGGCCTGGACATGAGGGTTGTACAG
Seq A exon
GTGAGGCTCCAGCCACCCCAACCCGTGGGGGCACCTTTGCTGACCGGAGATCCCAGGCCGGGCACCATGCGGTGCCGGGGCTGGCGTGGGGGTGGAGGGTGTCCTGTGGGTCCCCACATCCGCGCGTCCACAGGACGGCTCCAGGTAGCCATGGCGCTTCATCTGTGCGGTCCCTGATCCCCTTGGGGTGCTGGGCTCAGGACCACAGCCCCAGGAAATCTGCTGAACCAGAGAGATGTCTGAGGCCCAGGCCAGGGGAAGCGATGGGCACAACCCGTTCCTCACCCATCTGCTGCGGCTTCAGTCTTTGTCTCTGGTCTCGAGGACCCTGGGGGCTTTGGGCTCGTGGTGGACACCCCCAAAGTATGTCCCTTTGCTTGTTGTGGCAG
Seq C2 exon
GTTTGGTTTCAGAACAGAAGGGCCAAGGAGAAGCGACTGAAGAAGGACGCGGGGCGGCACCGCTGGGGGCAGTTCTACAAGAGCGTCAAGAGGAGCCGGGGAGGCAGCAAGCAGGAGAAGGAGAGCTCTGCGGAGGACTGTGGGGTTAGTGACAGTGAGCTGAGCTTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003992:ENSBTAT00000005216:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.712 A=NA C2=0.500
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(77.2=84.6)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=19.0)
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:
TGACTCAGAGGCTGGAGCTAA
R:
CTCGGAAGCTCAGCTCACTGT
Band lengths:
326-715
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development