DreINT0090021 @ danRer10
Intron Retention
Gene
ENSDARG00000044010 | loxl2a
Description
lysyl oxidase-like 2a [Source:ZFIN;Acc:ZDB-GENE-070818-1]
Coordinates
chr10:20456156-20457183:-
Coord C1 exon
chr10:20457018-20457183
Coord A exon
chr10:20456390-20457017
Coord C2 exon
chr10:20456156-20456389
Length
628 bp
Sequences
Splice sites
5' ss Seq
ATAGTGAGT
5' ss Score
6.97
3' ss Seq
TCTGACGGCATCCATCACAGCGG
3' ss Score
5.05
Exon sequences
Seq C1 exon
GAGACCTGGTACTGGGCTGGAGATGCGAATGCAGATAATGTTGTGATGAGTGGAGTCAGATGCTCAGGAACTGAGATGAGTCTTCCTCAGTGTCTTCATCACGGAAAACACATCAACTGCCCCAAAGGAGGAGGACGCTTTGCCGCTGGAGTCTCCTGCTCTGATA
Seq A exon
GTGAGTCTCTCACCTCATATTGAAGAAACATAAAAAATTAATGATTTATTGGTGTCAAAACTTATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATACTGTATGTATCATTTTTTTTAAACAGACAATATATTGTAATGTTTGCTGTGTATACAGAAAACAGTATCCTGAGCTATTATTCCTTTTTAAACATAAGCAAAGTGTGAAAATACTGAAGATTTTCTATTAACTTAAAGGAATTGTTCACTCAAAAATCTAAACTTACTCTCATTATACTCACCCTCAAGTTGTTCCAAACTTGTATGAGTTACTTTTTCTGTTTAACACACACACACACACACACACACACACACAAAAAGATATGGTGGTAAAGTTGATACCACATTCCCCACTGACTTCAATAGTTGGAGTGAATGAGTAAATGATGACTGAGTTGTCATTTTGGATTAATTAGCCCTTTAATAAACTCACAATGGGTGATCTTCAGAAGCAGCTAAAAGCCTAGTGGTCCAGACTAATTTGCGGAGGAATTTGTTTCTGTCTGACTTCTGACCTCTGACGGCATCCATCACAG
Seq C2 exon
CGGCCCCTGACCTGGTGCTCAACGCTCAGTTGGTGGAGCAGACCACCTATCTGGAGGACCGGCCCATGTATGCTCTTCAGTGTGCTCTAGAGGAGAACTGCTTGTCCAGCACTGCCCGAAAGAATGACCACAGCTCCTACCGCCGCCTGCTCCGTTTCTCCTCACAGATACACAACGTGGGCCAATCCGACTTCAGACCCAAACTGGGATACCACGCCTGGACTTGGCACGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044010:ENSDART00000064613:8
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(49.5=94.6)
A:
NA
C2:
PF0118612=Lysyl_oxidase=PU(37.4=96.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGGGCTGGAGATGCGAAT
R:
GGATTGGCCCACGTTGTGTAT
Band lengths:
345-973
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]