DreINT0090011 @ danRer10
Intron Retention
Gene
ENSDARG00000044010 | loxl2a
Description
lysyl oxidase-like 2a [Source:ZFIN;Acc:ZDB-GENE-070818-1]
Coordinates
chr10:20486440-20488168:-
Coord C1 exon
chr10:20487901-20488168
Coord A exon
chr10:20486616-20487900
Coord C2 exon
chr10:20486440-20486615
Length
1285 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
AATTGTTCTTTGTTCCCCAGGTC
3' ss Score
10.37
Exon sequences
Seq C1 exon
ATGGCGGTGTCTTCTGCATTGTGCATCTTCAGTCTGTTGGTTCTAGCTCAGGCCCAATCTGAACTCCAGCAACCCAAGATTGAACTCCGTCTAGCCGGTGACAAACGCAAGCATTACGAGGGTCGTCTGGAGGTCTTCTACAACAATGAATGGGGAACTGTGTGTGATGATGACTTCTCGATTGAAGCCGCTCACGTGGCATGCAGGCAACTTGGCTTCTTGGGCGCTGTCGCTTGGTCTCCGTCTGCAAAGTTTGGACAAGGAGAAG
Seq A exon
GTAGGCCAAAAGCTTATTGAAGATCCACTATGTACATATGTTCTTGGATTACATTGGTAATCCATCATGTTTTAGTCATTAGGGGTAAATGATAGCCATCAGACTGTTGTTACCTTTAGGAAAAAAGTATGGAAATAAGATTGAAAGTCAAGAGCAGACATAATGTCATCTTTCTGTCTCTTTATTATAGAAACATGCTGATTTGTCTCAATAAATCTGTCTAAAGATTGTAAATCAAACTCTACTGTTCAGTGGGTGGTTATGACTGAGCCCAATGGAAGAATAACCACTGGTTATTCCACTCTTATCCTCATTTCCACAGAGTTAGCAAAATCATATGAAGAATGTAATGCATCGAAAGAGAACATTTGGGAAGTGTTTGTCATTGGTAACTTGAATTTAAAAAACAATGATGATATAAATTAAAAATTATGTCACCATTTGCTTTAAATCTGCATTTTTTAATCAGAATTAGTATACAAGAATAATGGAAACTAGCACTTTTGAGCCTTGAAATGAATCAGAATTTTTAAGTGAGGTGTCTGAAAAGCTCTGTTGAGAACCGGTGTTCTTTCAGTTTGCGTTGGCGACCCAAGAGTGTTTCAGACTGTACCAAAAAGCTCAAAAGCGTATGTGGGGGAGGCGGATTGGTGCTGAAATACAGTAGTTTTCCAGGAGAAATAACTAAACGGTAGGGTGGCGGTAGATAGGTCTGAAATGAATGTAATGGGAAAAAATTTGAGTGTTGGCAGGTATGGGCTAACGACCCACCTTGTAAATATTTGATGTTATGAAACACCAGTATGGTGCAGCTAAATATCAAATTTGCCCTGGGAGTAAGTAAGTATTATCAGTTATTCAGGTGTGATTTAAATAATATTCTTCTGAAACTAATCTTTTACAAATGTCATACAAGTTTATAATTATATAAGGTACAGTTAAAGCCCTAATATACAGTATACTTCAAGTGAAAAAGAAGAATGTAATCTTATAATCTGAAGTTTGAAATGAGTGAAGTTTCCAGGACAATTTGCTTTTGCTGGTAAATAGCGTCAAACTACCTGCGAAGGTAGGCATGACAAACTTCTCCCATAAATGTAGTCTGTTCAGTCCACTGAGCTAGACATCTTGTTTCCTTTATGGTAGAAACTATAATGTAATTCAACTGGAAAGCAGTTGGGAGTAAACTTTTTCTTTATGTGAGCCTGGTAGTAGTAGTCATACCATTAAAAAGCCACCATCTGCTGGTGATTGACAAAACCAACAATTGTTCTTTGTTCCCCAG
Seq C2 exon
GTCGCATCTGGCTCGACAATGTCCACTGCACAGGCAGAGAAAACTCTTTAGCTGCATGCCCCTCCAATGGCTTTGGTGTGTCGGACTGCAGGCACAGTGAGGATGTCGGGGTGATTTGCAATCAAAAGCGAATTCCTGGTCACAGGTTCATCAATATCATGAACAACAATGTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044010:ENSDART00000064613:1
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(58.2=63.3)
A:
NA
C2:
PF0053013=SRCR=PD(40.8=67.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCAGGCCCAATCTGAACTC
R:
TTGCAAATCACCCCGACATCC
Band lengths:
344-1629
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]