DreINT0090047 @ danRer10
Intron Retention
Gene
ENSDARG00000076306 | loxl3a
Description
lysyl oxidase-like 3a [Source:ZFIN;Acc:ZDB-GENE-070818-2]
Coordinates
chr14:5573055-5574839:-
Coord C1 exon
chr14:5574680-5574839
Coord A exon
chr14:5573299-5574679
Coord C2 exon
chr14:5573055-5573298
Length
1381 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
CTTTCTTTCACAACCTATAGTGG
3' ss Score
5.66
Exon sequences
Seq C1 exon
GAAACATGGTACTGGGACAGCAGTAATGTGACGGAGATGGTGATGAGTGGAGTCAAGTGTAAGGGAGATGAGATGACCTTAACCGACTGTCAGCATCATTCTGTCGTCAGCTGCAAAAGAGCTGGAGCGCAGTTTTCCGCTGGCGTCATTTGCTCGGACA
Seq A exon
GTGAGTGCTTTGCAAGTCTTTTAAGTTTGTTGGCATAGGTATCAAGCATAGCATTAGCTAACACTGATTACGTTATAGACATCAGTAATCTAATTATTTACCTTAATCTAAATATGACAGTGATACGATTAAATTATTTACATTAGTTGCTTTTTGAATGTTCCTTTCATTTACGTGTGCATAGTTCGATTAACGTCATTACGTCATTATTTAACAATAGTATCCTTTGGCGTTTCACGCAAAAGTTCTTTTTTAATTTTGTAAATTAAAGTTCAACTGCAGGTAATTTCTCACACTATGCATGCCAACAGATGAAGGTGGATACAAACTCTCAAGCAAAAGGCCGCCATTTCATTCACTATCTTTTAATTTGTGCCCCCACAACAAACTCAGAGGTGCTGGATGAGGGCATAGTCTCATGCTGCATTCACACCAGACTCAGAACGCGCGTCAAGCGTGAGTGATTTACATGTTAAGTCAATGCAAACGTGCGAATAGACAACCTGCGGCGCGTTACACGCAAATGACACGAACTGTGCGGCGCGGATTGAGCGTTTTGCACGCTTGACACGTGTTTCGCGCGAATTGCTGGAGTTCGAAAGTCTAAACTTCAGTGGACATTCGCGCCGCGTTAACCAATCAGGAGCTTGCTCTTGTGGGGGCGTGATTGTGATGTACACCTATTGTTAAAAAAGAGTTCATCAAACTGGGCTGGGCTCAGTCTGAAGCACCGCTGAAAGCCTCCATTATCCTTTTATCCAAAGCGACTAACAAATGAGGACAAGGAAGCAATTTACACAACTATAAGAGCAACAATGAATAAGCGCTATAGGCAAGTTTCAGGTCTGTAAAGTCTAAGAAGGAAAGTATTAGTAGTATTAATTTTTTTTTTTTTTTTTTGGGTTCAGTTAGTGTGATATTCAGAGAGGCAATTGCAGATTAGGACGTGAAGTGGAGACTAAATAGTTGAGTTTTTAGTCGTTTCTTGAAAATAGCGAGTGACTCTGCTGTTCTAATGCAGTTAGGGAGTTCATTCCACCAACTTTTGTCACATGGCTGCATTTTATTAGTTTTTTTTCAACTGGTTTGGACCAAAGCAATCAGTGTGGTGTGAAAAGGACCCAAAAACGGCAGAAAAGTACTGCAGTGTTTCATTTGTTGCCCTTGGTCTACCAAATGAACAGAACCACCGATGTGAAAGCACCCTTAATTTGTTTTCTGTTTAGTTCGATTATAACTTTAGTTTGATTAAGCTAATCTAAAATCACAGTTTACATGATACAGAGTACTGTCTTAATCTTCTTAAAAAACTGTGTCCATGTAAACGTACACACTGTTCTATTTGGATGTCATTGTGGTCTCTTTCTTTCACAACCTATAG
Seq C2 exon
TGGCTTCGGATCTAGTGCTGAATGCTCCATTGGTGGAGCAGACTGTCTACATTGAGGACCGACCCCTTCACTTGCTGTACTGTGCAGCAGAGGAAAACTGCCTCGCCAAATCAGCTGCTCAAGCCAGCTGGCCATATGGCCATCGGCGCCTGCTACGCTTCTCCTCCGAGATACACAACATCGGCAAGGCTGACTTCCGGCCACGACTCGGCCGCCATTCCTGGGTGTGGCATGAATGTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000076306:ENSDART00000054866:9
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(48.1=94.4)
A:
NA
C2:
PF0118612=Lysyl_oxidase=PU(38.7=96.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACAGCAGTAATGTGACGG
R:
GAAGTCAGCCTTGCCGATGTT
Band lengths:
344-1725
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]