BtaINT0086269 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018578 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
chr11:10086818-10087285:+
Coord C1 exon
chr11:10086818-10086998
Coord A exon
chr11:10086999-10087130
Coord C2 exon
chr11:10087131-10087285
Length
132 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
CCTCTGACTTCTGACCTTAGGCA
3' ss Score
7.88
Exon sequences
Seq C1 exon
GCCCGAGTGCGTCTAAAGGGCGGCGCCCACCCAGGAGAGGGCCGGGTAGAAGTCCTGAAGGCTGGCACGTGGGGCACGGTCTGTGATCGCAAGTGGGACCTGCAAGCAGCCAGCGTGGTGTGTCGGGAGCTAGGCTTCGGGAGTGCTCGAGAGGCTCTGAGCGGTGCCCGCATGGGGCAGG
Seq A exon
GTGAGGCGGGCACAGGTTGGAGGGAGAGGGAGGTAGGAGGTACATACTCCTGGAGGGGTACATTCCTTAGGAAGGAGACCCCTGGGCAGACAGTAAAGTTAGAACCTCCCGACCTCTGACTTCTGACCTTAG
Seq C2 exon
GCATGGGTGCCATCCATTTAAGTGAAGTTAGATGCTCTGGACAGGAACTCTCTCTCTGGAAGTGCCCCCACAAGAACATCACAGCTGAAGACTGCTCGCATAGCCAAGATGCTGGCGTCCGATGCAACCTGCCCTACACTGGGGTAGAGACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018578:ENSBTAT00000024724:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.148 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(56.1=90.2)
A:
NA
C2:
PF0053013=SRCR=PD(42.9=80.8)
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:
TAGAAGTCCTGAAGGCTGGCA
R:
GACGCCAGCATCTTGGCTATG
Band lengths:
254-386
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development