BtaINT0086272 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018578 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
chr11:10087834-10088442:+
Coord C1 exon
chr11:10087834-10087996
Coord A exon
chr11:10087997-10088198
Coord C2 exon
chr11:10088199-10088442
Length
202 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TCCTCCCTTGCTCGGTGCAGCCG
3' ss Score
6.63
Exon sequences
Seq C1 exon
GAGACCTGGTACTGGGATTCAGGAAATGTGACAGACGTGGTGATGAGTGGAGTGCGCTGCACAGGGGCTGAGCTGTCCCTGGACCAGTGTGCTCATCATGGCACCCATGTCACCTGCAAGAGGACAGGAAGCCGTTTTACTGCTGGAGTCATTTGTTCTGAAA
Seq A exon
GTGAGTCAAGTGTAGGGTGATGCAAGCCAGGGAGGCGAGGCTCTGGGTCACCTCTTTGCAGGAAGAGCTGCAATCTGGAGGGGTACACCTTCCCTGTGGAAAGCCAGTCTCACCCGTTTTCTGGGGGAGGGGGATGGAAGCACTCCCACCTGTCCCTGCCCCTCACCAGTGACGTCTAACTCTCCTCCCTTGCTCGGTGCAG
Seq C2 exon
CCGCGTCAGATCTGCTGTTGCACTCAGCACTGGTGCAGGAGACCGCTTACATCGAGGACCGGCCTCTGCACATGCTGTATTGTGCTGCTGAAGAGAACTGCCTGGCCAGCTCGGCCCGCTCAGCCAACTGGCCTTACGGCCACCGGCGTCTGCTCAGATTCTCCTCCCAGATCCACAACCTGGGACGTGCTGACTTCAGGCCCAAGGCTGGGCGCCACTCCTGGGTGTGGCATGAATGTCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018578:ENSBTAT00000024724:9
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=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(49.1=94.5)
A:
NA
C2:
PF0118612=Lysyl_oxidase=PU(38.7=96.3)
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:
TCACCTGCAAGAGGACAGGAA
R:
TGACATTCATGCCACACCCAG
Band lengths:
295-497
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development