DreINT0090013 @ danRer10
Intron Retention
Gene
ENSDARG00000044010 | loxl2a
Description
lysyl oxidase-like 2a [Source:ZFIN;Acc:ZDB-GENE-070818-1]
Coordinates
chr10:20452010-20453096:-
Coord C1 exon
chr10:20452960-20453096
Coord A exon
chr10:20452122-20452959
Coord C2 exon
chr10:20452010-20452121
Length
838 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
CGTCTCTTTCTGACACACAGGTG
3' ss Score
7.79
Exon sequences
Seq C1 exon
GTATTTCGAAGCGTTACCATTGTGCTAACTTTGGTGAACAGGGCATCACTGTTGGCTGCTGGGACACTTACAGACATGACATTGATTGTCAGTGGATTGATGTCACGGATGTCAAACCAGGAGACTACATTTTCCAG
Seq A exon
GTACAGTTTCAAATCACTGTTGGTGTGAAGTTTAGACAATGAGTTTTTGAGGGAATTCTCTTATGTTCACCGTAGGTGGATTTATTAAGTTAAGACATTCAATTCAATCAGTTGTAATTTACAAGTTGGATTAAGTGTATTCTATATATATATATATATATATATATATATATATATTAACTTTATTTCTTCCTGTCATGCAAAGCTTTTCCTGCATCTAGTCCTCACATGATCATCGAGAAATCATTTATGCTAATTTGGTGCTCAAGAAACATATTATTATTATTATTATTATTATTATTACTATTATTATTATTATTTTTATAAATTTTAGAAACTCTGCTTTTTTATATATTTTGTAAACTGATACATGCCATTTTAAACTGGGAAGGTATGATTTAAAAAAACCAAGAAATTAAAATTTTATACAACAAGAGTGCATCAAAAGTCACAGCAATATTTATTATGTCACAAAAGATTTTTTACATCACATAAATGTTCTAGTCTTTAGATTCCTGATAATCCAAAAATAGCTGCTAAAAAAAACGTTTTGTAAGATATAAGATATTTTAAAAAAAATGGAAATAGAAAACAGGTATTTTTTATTGTAATAATATTTAATACCAACTCGTTTTTTCCTCTATTTTTAATTGGTATTTGACAAAAGTAGTATAAAATACAGAATAAGAAAAATCACAGACTGTCTTAGTTTTACTATTTTGCTTTACTTTTTGATTAAAGAACTGCAGCCTTGCATAAAGAGACTTTTTAAAACTTTTGACCGAAAGTCAATATCAAAAATGTTATTTCACCTGACACGTCTCTTTCTGACACACAG
Seq C2 exon
GTGGTAATCAATCCAAACTATGACGTCGCTGAATCAGATTACACCAACAACGTCATGAAGTGCAAGTGCCGCTATGATGGATACAGGATATGGACATACAGCTGTCATATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044010:ENSDART00000064613:12
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:
PF0118612=Lysyl_oxidase=FE(22.2=100)
A:
NA
C2:
PF0118612=Lysyl_oxidase=FE(18.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTTCGAAGCGTTACCATTGTGC
R:
ATATGACAGCTGTATGTCCATATCCT
Band lengths:
246-1084
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]