BtaINT0086266 @ bosTau6
Intron Retention
Gene
ENSBTAG00000018578 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
chr11:10075542-10076548:+
Coord C1 exon
chr11:10075542-10075705
Coord A exon
chr11:10075706-10076333
Coord C2 exon
chr11:10076334-10076548
Length
628 bp
Sequences
Splice sites
5' ss Seq
GAGGTCTGT
5' ss Score
5.39
3' ss Seq
GCTTGTGGCCCCCTCCCCAGGTA
3' ss Score
8.22
Exon sequences
Seq C1 exon
GCCGCATCTGGCTGGACAACCTGAGCTGCAGTGGGACTGAGCGGAGTGTGACTGAATGTGCCTCCCGGGGTTGGGGGAACAGTGACTGTACCCACGATGAGGATGCTGGGGTCATCTGCAAGGACGAGCGCCTCCCTGGCTTCTCAGATTCCAATGTCATTGAG
Seq A exon
GTCTGTAGTTCATAAACACACACACACACATACACACACACACACACACCACCCAGGACGGCAAGACAGAAAGGGCTGTGGGGTGGTTATATGTGGAGATACTAGAATGTAGGGGATCCCATGTGCCCAATGGGATAATTGGGGTCAGTGGGAGACTGGGGGAGTGGGCAAAATGATAGAGCTCTGAGACACTGCATAGTCCAGGTTTATTTTAGCATTAGCATTCAAGTTACTAAGCCTGGCATGAACCTCTCCAACTTCATCCCTGGTCCCCAGGGCACCTGTGCTCTCTCTCAGCTCAGATATTCCTGAGGGAACATTTCACTCTTACTTTCTCTTACTTCTTCAGTGCCACTTCCTCCGTAAGTGTTCCCTCAGGCTCCAAGCAGAGTTAGATGCTCCTTCCCCAGCTTCTTCTGGACCCTTAGTCATTTCTCAGAGCCCAGCAAGTCCTCACACTCTGGTGGCTGCACCACAGTCAGTACCTCACAGAGCGCAGGCCTGCCTCTCAGCCCCATCTCGCCACTGGGTTCACAGCAAGTACACTCAATCAGGGTTTCTTTAGAGTGGCCAGACGTGTGAAAGGTGCCACTGGGATGCCTTCCTCTGCTTGTGGCCCCCTCCCCAG
Seq C2 exon
GTAGAGCATCACCTGCAAGTGGAGGAGGTGCGACTTCGGCCAGCTGTTGGAAGGGGCAGACGGCCCCTGCCTGTGACTGAGGGACTGGTCGAAGTCAGGCTTCCGGATGGCTGGTCGCAAGTGTGTGACAAAGGCTGGAGTGCGCACAACAGCCATGTGATCTGCGGGATGCTGGGCTTCCCGAGCGAAAAGCGGGTCAACGTGGGCTTCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000018578:ENSBTAT00000024724:3
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=0.037
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(41.7=72.7)
A:
NA
C2:
PF0053013=SRCR=PU(50.0=72.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTGAGCGGAGTGTGACTGAA
R:
CTGTAGAAGCCCACGTTGACC
Band lengths:
344-972
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development