DreINT0090043 @ danRer10
Intron Retention
Gene
ENSDARG00000076306 | loxl3a
Description
lysyl oxidase-like 3a [Source:ZFIN;Acc:ZDB-GENE-070818-2]
Coordinates
chr14:5584616-5585500:-
Coord C1 exon
chr14:5585308-5585500
Coord A exon
chr14:5584797-5585307
Coord C2 exon
chr14:5584616-5584796
Length
511 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
TGCTCTTACATGTTCTGCAGCCT
3' ss Score
7.62
Exon sequences
Seq C1 exon
TCTGAAGAGCGCTTACCGTATCCATTCAGTGACCTGCTCAGGGAACGAGGCTCATCTTTCTGCATGCACGATGGAGTTCAGCAGGGCCAACTCTAGCGCCCCCTGTCCTGGTGGAGGAGCTGCTGTAGTCAGCTGTGTGCCCGGGCTGCAGTTCACACAGGGTAGAGTACGCAAAGCCAAGCTCAATCCAGTG
Seq A exon
GTGAGCACATAATGCCATTCTTTTTAAAATCCGTTAATTTTATATTGTCATTTAGGATTTCTGATTGCACTGCAACAAAACCTTCTAAATGCGAAAGAACACATGGAATCAAAACTAACTATATTGATTTTGTTCGCTCACATTGCTAGTTTTGTGGTGAATGATTCCTCTGTGCTTGTCATTAAGAATAAAAATGTTTGCCCTTTCTAAAACTGAAATCTGAAAATGCAAGACTGGTCTTAAATTATGTCTCTGATTGTAACTAAGCTGCAGGTAAAAGGTTTAAGTTTAAGTAAAACAAATCATCTTAAACAATCATAATAATCTTACGCAGTCTGATCTTGCGTGGTATTTTATTCCTAAAACAAGATCAAGATGGTTGTCTTTGTGTAGAAATCAGATAATAACCCTTTACTAGACAAGGAGTTTTTGTGTATAGGAAATATCAGCAGCATTTCTATGAATATCTGTATTGTTGCTTGTATTGATGGTGCTCTTACATGTTCTGCAG
Seq C2 exon
CCTCAGATGCGGCTGAAGGGTGGTGCAAGGGCAGGAGAGGGCCGTGTGGAGGTCCTGAAGGGCAGCGAGTGGGGTACAGTGTGTGACGACCACTGGAACCTGCAGTCTGCCAGTGTGGTGTGCAGAGAGCTGGGCTTCGGTACTGCTAAAGAGGCTCTGACCGGAGCACGAATGGGCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076306:ENSDART00000054866:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.046 A=NA C2=0.119
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(46.5=70.8)
A:
NA
C2:
PF0053013=SRCR=PU(56.1=90.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGAGCGCTTACCGTATCCA
R:
CGGTCAGAGCCTCTTTAGCAG
Band lengths:
353-864
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]