DreINT0090019 @ danRer10
Intron Retention
Gene
ENSDARG00000044010 | loxl2a
Description
lysyl oxidase-like 2a [Source:ZFIN;Acc:ZDB-GENE-070818-1]
Coordinates
chr10:20462263-20462690:-
Coord C1 exon
chr10:20462539-20462690
Coord A exon
chr10:20462431-20462538
Coord C2 exon
chr10:20462263-20462430
Length
108 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TTTGCTTTTGACTATAACAGATA
3' ss Score
7.57
Exon sequences
Seq C1 exon
GAATGGGTCCGGTCCACATGAATGAGGTGGAGTGCTCTGGATTTGAGAAATCTCTCACTGACTGCTACTTTAATAATGATGCTCTGGGATGCAGTCATGAGGAGGACGCAGCTGTTCGCTGTAATGTACCTGCTATGGGCTTTCAGAAAAGG
Seq A exon
GTGAGGATTTTTAAAATATAATTTACATATTAATTAGCAATAGTTTTACGCTCATGAATCGGTATGATTATGAAACATTAACATTATGTTTGCTTTTGACTATAACAG
Seq C2 exon
ATACGACTAAGTGGAGGAAGAAACCCATTTGAAGGACGTGTGGAAGTTCTCGCTGAGAAGAACGGTTCTCTCGTTTGGGGAACCGTTTGTAGTGAAAACTGGGGGATTATAGAGGCTATGGTGGTCTGCAGACAGCTGGGATTAGGCTTCGCCAGCCATGCGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044010:ENSDART00000064613:6
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(42.3=80.4)
A:
NA
C2:
PF0053013=SRCR=PU(48.6=92.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATGGGTCCGGTCCACATGA
R:
ACAAACGGTTCCCCAAACGAG
Band lengths:
242-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]