BtaINT0086270 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018578 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
chr11:10087131-10087699:+
Coord C1 exon
chr11:10087131-10087285
Coord A exon
chr11:10087286-10087531
Coord C2 exon
chr11:10087532-10087699
Length
246 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGT
5' ss Score
8.68
3' ss Seq
CTTCCATTGCGTCACTACAGATC
3' ss Score
8.15
Exon sequences
Seq C1 exon
GCATGGGTGCCATCCATTTAAGTGAAGTTAGATGCTCTGGACAGGAACTCTCTCTCTGGAAGTGCCCCCACAAGAACATCACAGCTGAAGACTGCTCGCATAGCCAAGATGCTGGCGTCCGATGCAACCTGCCCTACACTGGGGTAGAGACCAAG
Seq A exon
GTCAGTCACTCTTTCCCACCTTGGTTCAGGAGTCTCATGTCCTATCCAGCCCTGCCTGGTCGTGATGCAGTCTGATGGCCCTACTGCCCACTGCCCCAGGCCCCGATCATCCTGCAGCTCCCCCTTGACGCCACCGCTTGCTAGCCCTGTAAGTGCTTCTGAATCACCATTCAGCCACGGGCCCACTGTGGACTCCCACTACTCCACCCCAAAAGCTTCCACAGCACTTCCATTGCGTCACTACAG
Seq C2 exon
ATCCGACTCAGCGGGGGCCGCAGCCGACATGAAGGGCGAGTCGAAGTGCAAATAGGGGGACCTGGGTCCTTTCGCTGGGGCCTCATCTGTGGAGATGACTGGGGAACACTGGAGGCCATGGTTGCCTGCAGGCAGCTTGGACTGGGCTATGCCAACCACGGCCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018578:ENSBTAT00000024724:7
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=0.071
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(42.9=80.8)
A:
NA
C2:
PF0053013=SRCR=PU(49.1=92.9)
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:
GCATGGGTGCCATCCATTTAA
R:
CATAGCCCAGTCCAAGCTGC
Band lengths:
306-552
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development