DreINT0090040 @ danRer10
Intron Retention
Gene
ENSDARG00000076306 | loxl3a
Description
lysyl oxidase-like 3a [Source:ZFIN;Acc:ZDB-GENE-070818-2]
Coordinates
chr14:5603818-5605884:-
Coord C1 exon
chr14:5605588-5605884
Coord A exon
chr14:5603982-5605587
Coord C2 exon
chr14:5603818-5603981
Length
1606 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGA
5' ss Score
7.4
3' ss Seq
AAAAATCTATGTTTCTGCAGGTA
3' ss Score
8.87
Exon sequences
Seq C1 exon
CCATGCTGAGAAGTGAACTTAGGGATATGGTGGTTGCAATGGTGCTTTGGGGCATCTTGTTGCCCTTTTGTCTCAGCCAGACCACCTCACCATCTCAGGATGGGAAAATAAAGTTTCGTCTGGCCGGATACCCTCGCAAGCACAATGAAGGGAGGATAGAGGTGTTTTACAATCGAGAGTGGGGCACTATCTGTGACGACGACTTCACACTGGCCAACGCTCATGTGCTGTGTCGCCAACTAGGGTTCGTGGAGGCACTAAGCTGGTCCCACAGTGCCAAATATGGACCGGGCAGCG
Seq A exon
GTGAGAATCAGTCTTATTTGCATATGGGCAGTTGACGGTAACACTTTACTAGAAGGGGTTTTTATTAGATGGACATTAAACCTTTATAATCATGATATGACACATTTCATGAATGACTTTATGCATGCTTTTAAAATCTGTCATTAAGTGTCATTGGCTCAGTTATGACATTTTTAATGCAACGTTGACATTGTTTGTTATGAGGGGTGTTCATTAGACTGTCATTAAACCTTTATAATCATGACATGACACATTTCATGAATGAGGTTATGCATGCTTATAACAACTGTACTTAATTGCCATTGGCTCAGTTATGACATTTTTAAAGCAAAGATGACATTGTTTGTTATGACAATGATGGGGTGTTCATTAGACTGTCCTTAAACTTTTATAATCATGACATGACACATGTCATGTATGTGAATGATTTTTTGCATGGTTATAACAACTCATTAACTGTCATTGGCTGAGTTTTGGTATTCTTAATGCAAAGGTGACATTGTTATGAGGGGTGTTCATTAGACTATCCTTAAACCTGTATAATCATGACATGACACATTTCATGAATATAAATGAGGTTATGCATGCTTATAGCAAGTATCATTAATTGTCATTGGCTCAATTATGATATTTGTAAAGAAAAGAGTTGTTTGCTCAGACAATGATGGGGTGTTCATTCATTAGACTGTCCTTAAACCTTTATAATCATAACATGACAAATTTCATGAATGCGAATGAGGTTATGCATGCTTATAACAACTGTCATTAATTGTCATTGGTGCAGTTATAATATTTTTAAATCAAAGATCACATTGTTTGCTCAGACAATGAAGGGGTGTTTATTAGACTGTCCTTAAACCTTTATAATCATGACATGACACATTTTATGAATGTGAATGAGGTTATGCATGCTTATAACAACTGTCATTAATTGTCACTGTCTCAGTTATGACATTTTTAAATCAAAGATGACATTGTTTGCTCAGACAATGAAGGGGTGTTCATTAGACTGTCATTAAACCTTTATAATAATAACATGACTCATTTCATGAATGTGCATGATTTTATGCATGCTTATAGCAGCTGTCATTAAGTGTCATTGACTCAGTTATGACATTCTCAATGCAATTGTTTGTTATAAAAACACATCACAAAATAAGTAAAACTGTTAATTATCATTCATTCATTCAATTTTGGCTTAGTCCCTTTATTAATCGGGACTCACCACAGTGGAATGAACCGCTAACTTATCCAGCACATGTTTCACGCAGCGGATGCCCTTCCAGCTGCAACCCATCTCTGGGAAACAAACCATTAATTAATTAACAGATAGTCATTTCAATGTGAAATCACTTCAATCATTTGCATAAAATGATCTGAAACGACGATAATATTGCTTATCGCAACAATTTCTGTGACAATATATCACACAACAAAAAATCTTCATCATGACAAGCCTAGTTGGTGTGACCGATAAAATAAGGTCAAGTCAAAAACTCATTTACATTTTAGTCTGTGCTGTTTGGATGCTTTCACATATCTGCAAATAAGCTTGCACTTTATGAAAGTTTTGTTGTAAGCTGGGTAAAAATCTATGTTTCTGCAG
Seq C2 exon
GTAAAATCTGGCTGGATAATGTGATTTGTGGAGGAAGTGAAAACAGCATTGAGAAATGTGTGTCCCGTGGCTGGGGGAACAGTGACTGCACGCACCAGGAAGATGCAGGGGTCATCTGCAAAGATGAGAGACTTCCAGGCTTTGCAGAGTCTAACATCATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076306:ENSDART00000054866:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(57.3=55.6)
A:
NA
C2:
PF0053013=SRCR=PD(41.7=72.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGCCCTTTTGTCTCAGCCAG
R:
AGATGACCCCTGCATCTTCCT
Band lengths:
355-1961
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]