DreINT0090038 @ danRer10
Intron Retention
Gene
ENSDARG00000076306 | loxl3a
Description
lysyl oxidase-like 3a [Source:ZFIN;Acc:ZDB-GENE-070818-2]
Coordinates
chr14:5562692-5563343:-
Coord C1 exon
chr14:5563207-5563343
Coord A exon
chr14:5562804-5563206
Coord C2 exon
chr14:5562692-5562803
Length
403 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGCT
5' ss Score
6.52
3' ss Seq
GTGTTCTCTTCCTCTCTCAGGTC
3' ss Score
12.86
Exon sequences
Seq C1 exon
GTGTTTCAAAGCGCTACGAATGTGCTAACTTCGGAGAGCAGGGCATCACAGTGGGCTGCTGGGACTTGTACAGACATGATATTGACTGCCAGTGGATTGACATCACGGACGTTTCGCCAGGAAACTACATTCTGCAG
Seq A exon
GTAGCTATATTTATTCAGCTATATTTTCATCATCTAGATAGCACACTAGCAGCAAAGACTGTTACATGAGCAGGCTTTGGTCCCGTAGGACCCCATTGTCTGGGCTTTTCACCAGTCAAACAGCTGTCTCACTTCTGTCCTCTAGTGGTGGAGTGTTTCACAGCACTCACCATCACGTCCAGGCATGCAAGAGTTAGGATACTAATAGGATTTGGTTTGATTAATGATGTAATAAACCTTAAGTACACACAGTAGGAGGTGGAAGGAAGGGTTTTACTCAGAAAAAAACCCCACCCGGATTACGATTAACAAACAAAAAGACATTGTCATGTTTACTTAAAGCCACGCTTTACTCATGTTCTGATCAAGTTTGATTATAATTAGTGTTCTCTTCCTCTCTCAG
Seq C2 exon
GTCATAATAAATCCCAACTTTGAGGTCGCTGAGAGCGACTTCACCAACAACGCCATGCGGTGCAACTGCAAATACGACGGCCATCGTGTCTGGTTGCATAAATGTCATCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076306:ENSDART00000054866:12
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(22.1=100)
A:
NA
C2:
PF0118612=Lysyl_oxidase=FE(18.1=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:
TTTCAAAGCGCTACGAATGTGC
R:
CGAGATGACATTTATGCAACCAGAC
Band lengths:
246-649
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]