DreINT0090056 @ danRer10
Intron Retention
Gene
ENSDARG00000025089 | loxl4
Description
lysyl oxidase-like 4 [Source:ZFIN;Acc:ZDB-GENE-080722-19]
Coordinates
chr13:40063835-40064835:-
Coord C1 exon
chr13:40064720-40064835
Coord A exon
chr13:40063972-40064719
Coord C2 exon
chr13:40063835-40063971
Length
748 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
GCTTTCATCTGTTTCTTCAGGAC
3' ss Score
10.22
Exon sequences
Seq C1 exon
GCATTATCACAGCATTGAAGTGTTTACGCATTATGATCTGCTCACTCTCAATGGGAGCCGAGTAGCAGAAGGACACAAAGCCAGTTTCTGTCTGGAAGACACCTACTGTCCTGAAG
Seq A exon
GTAAAAGACTAAATATGTTAAAGGGGTGGAGCAGAGTCTATTTTTAAGGCTTATTTATGTTCATGGGGTGCAAAGCAATGTGTGCTCATGCGTCATTTGTAAAAAAAAATCACGTTATTTTTTCACATATCTTACTTTATTCTTTAATACAGGGGTCAGCAATCCTGGTCCTGGTGGGCCGGTGTCCCTGCAGGGTTTAGCTCCATCTTGCCTCAACACACCTGCCTGGATGTTTCAAGCATACCTAGTAAGACCTTGATTAGCTTGTTCAGGTGTGTTTAATTAGGGTTGGAGCTAAAATCTGTAGGACACTGGCCCTCCAGGAACAAGTTTGGTGACCACTGCTTTAATACTTTAATACTCTGCTAACATTTAAACCACATATTTTCCTGGTTCCTTCGAAGGCCTGCCCTTAACAGGCTCTGATTGGTCAGCTAACATAATGTATTGTGATACATTATTAGTGTTGGGCTACTCACAATCCACAGCTACTTCCATTTGGGTTGGAACTGCTCCTTCGAGGAGAGGTTTTAGGCCAAATCCAGCACTGAACTGTAGATTCTGAAAGCTTTTCTTTGTCAGAACAGAATATCTCTGCTATATCATTACAGTGCCTCTTAAACATTAGTATAGACTATTTGCATTTACTATGCTTTCTATGTATATAATCTGACTTTTGTCAGTGATTTGGACACCAAAATGTGAAATAATGTCTTTGAACAGCAACTGCTTTCATCTGTTTCTTCAG
Seq C2 exon
GACTTCATAAACGCTTTTCATGTTACAATTATGGCGATCAAGGCATTTCAGTAGGCTGCTGGGACACGTACAGACACGATATCGACTGCCAGTGGATAGACATCACTGACGTGAGGCCCGGAGACTACATCATGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025089:ENSDART00000044963:12
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(19.1=100)
A:
NA
C2:
PF0118612=Lysyl_oxidase=FE(22.1=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:
CACAGCATTGAAGTGTTTACGCA
R:
CTGCATGATGTAGTCTCCGGG
Band lengths:
246-994
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]