BtaINT0086103 @ bosTau6
Intron Retention
Gene
ENSBTAG00000010228 | LMX1B
Description
LIM homeobox transcription factor 1, beta [Source:HGNC Symbol;Acc:HGNC:6654]
Coordinates
chr11:97477666-97478091:+
Coord C1 exon
chr11:97477666-97477847
Coord A exon
chr11:97477848-97478013
Coord C2 exon
chr11:97478014-97478091
Length
166 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCTTCTCCCTCTCTGGGCAGGTC
3' ss Score
12.9
Exon sequences
Seq C1 exon
TGAAGAGCGAGGATGAGGATGGGGACATGAAGCCGGCCAAGGGACAGGGCAGCCAGAGCAAGGGCAGTGGGGACGACGGGAAGGACCCTCGGAGGCCTAAGCGGCCCCGGACCATCCTCACGACGCAGCAGCGCAGAGCCTTCAAGGCCTCCTTCGAGGTCTCCTCCAAGCCCTGCCGGAAG
Seq A exon
GTGAGGGGCGGCCGGGGTGGGGCGGGGGCTGACACCCCCACACCCGCTGCCTTTCCAGACTCCTGCGGGGACCTGGGCATCCCTGCACCTCCCCGCCCAACCCCCGGACCTGCCACCTTCGGCGCCTGCCCACCCCCGGGCCTGACCCTTCTCCCTCTCTGGGCAG
Seq C2 exon
GTCCGAGAGACGCTGGCGGCGGAGACGGGCCTCAGCGTGCGTGTGGTCCAGGTCTGGTTTCAGAACCAAAGAGCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000010228:ENSBTAT00000038767:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.770 A=NA C2=0.192
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(47.4=44.3)
A:
NA
C2:
PF0004624=Homeobox=FE(43.9=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:
AAGAGCGAGGATGAGGATGGG
R:
AGACCTGGACCACACGCA
Band lengths:
235-401
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development