BtaINT0086273 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020895 | LOXL4
Description
Bos taurus lysyl oxidase-like 4 (LOXL4), mRNA. [Source:RefSeq mRNA;Acc:NM_174384]
Coordinates
chr26:19213931-19214350:-
Coord C1 exon
chr26:19214310-19214350
Coord A exon
chr26:19214151-19214309
Coord C2 exon
chr26:19213931-19214150
Length
159 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
CAGTCTAGCTTGTCTTCCAGACT
3' ss Score
3.16
Exon sequences
Seq C1 exon
AGGAAAGTCTGGGATTCAAAGATGAAGGACCCCAACTCTAG
Seq A exon
GTAAGGAGTAGTGCCCTCATGGGAGGGTGCAAACGAGGTGGCATGAAGGGCCTCCTTCCTCCCCCTTCCCCTCCTCCAGGCCCCTCTCCCCTCCCCGGTGCCTTGCCTCCCAGAGTCCTGAGCACCCCTTCTGCGCCCTCAGTCTAGCTTGTCTTCCAG
Seq C2 exon
ACTGAAGAGCCTAACGAAGAAGAATTCCTTCTGGATCCACCGTGTCAACTGCCTGGGCACAGAGCCCCACATGGCCAACTGCCAGGTGCAGGTGGCGCCAGCCCAGGGCAAGCTGCGGCCAGCCTGCCCGGGTGGCATGCATGCTGTGGTCAGCTGTGTGGCAGGGCCCCGCTTCCGTCCTCCGAAGGCGAAGCCAGGGCGCAAGGAGTCCAGGGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020895:ENSBTAT00000027838:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.311
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(15.6=71.4)
A:
NA
C2:
PF0053013=SRCR=PD(82.8=71.6)
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:
AAGATGAAGGACCCCAACTCT
R:
CTCTGCCCTGGACTCCTTGC
Band lengths:
243-402
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]