DreINT0090023 @ danRer10
Intron Retention
Gene
ENSDARG00000044074 | loxl2b
Description
lysyl oxidase-like 2b [Source:ZFIN;Acc:ZDB-GENE-050208-29]
Coordinates
chr5:26880695-26882956:+
Coord C1 exon
chr5:26880695-26880935
Coord A exon
chr5:26880936-26882840
Coord C2 exon
chr5:26882841-26882956
Length
1905 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TTTCCATATTAATGCTACAGGCA
3' ss Score
6.56
Exon sequences
Seq C1 exon
CTGCTCCAGATCTGGTGCTCAACCCGCAGGTGGTGGAACAGACCACATATTTGGAGGACCGTCCTATGTTCATGTTACAGTGTGCTTATGAGGAGAACTGCCTGGCCAGCACCTCCAGTGCCACTCCTGCCAACTCCCCTCGCCGGCTCCTCCGTTTCTCCTCCCAGATCCACAACAACGGACAATCTGACTTCAGGCCCAAAATCTCCAGAGAGAACTGGGTTTGGCATGACTGTCACAG
Seq A exon
GTAGGGCTGCACAATATGACGTATGATGATCATCAGTGTGGGACAAAATTACTTTTGAAAGTAGTGCATTACCATATTGAGTTACATCCCCAAAAAAGTAACTAATTGCTAGTTACTTTTTATGGAAAGCAATGCATTATATTACTTTTCAGTTACTTTTGTGTTACTTTTCCTTACCTGACTGAGGTTTGATCTCTTTCAGAACTTGCAGGTGTTTTTTCACGTTTTATATAGAGAAGCTCTGCATTTAACAACCACTTATAAACCTACACCTTTATTTTCCTTTAAAAAATGTAGGATAATATTATATTTTGAGAACTTTCTGATCCCAGAGCTAGACATGATGTATATACAGATAAGTGACAGCATGCAATGTGTTTGCTACTTTTGAATGTTTTGTGTTATTAAATAAATTCACTGTTTTTAAATAAAGCAAATTTTTAATAAAAAAAAAAAACAGATTTTAAACCTTTAAAATATTTAATAACAAAATGAATAGCAAGACGAAAAAAAACAGCCCCAAATCAAAATAAATCTTTGAGCTTTATACATTGAATACTTTTCTTCACATGGCCTTAACAAATGTGTAAATCGTTTGCCACAAGAAAAAAAATCTTAGTATATTACAAAACATAGTCACTTCTACAATAATGTTGGACAGTGGCTGCATCTCCTCAAATAATAAAAGCAATAACCATTTTTAATTTAGTCTAATTAATTGTTTTACCTGGAGAACATGAACTGATGTCAATCATTGGTTGTTTAGCTGGAAGGGGTGCGGGTGCAGTGCTTCACATCCAGTTTTTTTTTTTTTTTTCCCAATGTTGTGTTTCTTGCAGTTGTCGAGAGTTTTACTTAATAAGTTAATAATCTACACTTAACAACAATCCACTTCTTTTCTTCAATGAGTTCAAAAAAACAAGAATCCATTGCAAAAATGTAAGTCTTCGGCCTGCCATTCTGACTGTCTGTAGTGATGATGGGCGATTTGCGAATGAATTGAATGAATTTTTCAAACCGGATCTTCTGAACCGGTCGAATTGTCGTGAAACGGTTTGCGTCTTCAATAAGTACTAACATATCGGATACTCCCTCTGACTTGAAATAAACCAATATCCTAAGATATTCAGTTACTAGAACAGTACACTGACTCATCTGCTGTGAAAAAACCTGACCATGATGATGAGTGCGAGCCGACTGTCTGTTCACTCGCAGCACACAAGTCTCTAATTGAGTGCGTGATTCAACCTGACTAGGGTACTTTTCATTCTGCAATATGTTTTGTAAAAACCAATTGAGCAAGGTAAAAAGTAAGTTGAGGAACAATCTTGAATGCAGAAGCCACATTTTGACCAAATTTGGGTCTTGTAGCATGAACGGCCTATGAGGAGATACGTTTTTGAGGACAGAGTAGTATATGAGCAAGCATAGGAGCTTCCATCTAAAAGTATTAGTCAATTATCTCTGTTTAATAATCAAAACTGACAAGAATGTGACTGTGAGGGGCTCCATCAGCGATTCCTCTGAGCGACATGAGCAACCGAATGAACAAGTGTAATAGTTACAAGTGAAGACAAAAGGTTTTTCGATATTGCAGTATTATTTCAATTCAAGATATGAAAGTGTTTATTTTTAACCAAAAGATTGCAACCTTAGCTTAAAAATTCATGAAGTGAAAGTCACTAGCATCACTGGCACTTGACGGTCAACAAAATACAGACATAACAAAAATATACGTGCCTCCTGATGACACATTGAGGTCTTAAGAAGTGAAAAGATCAAGCTGTTCAAGATTAGTCTGGAGCATAGCCTCTTGTCTCACGATGACAGGCGCAGATGCAAACTCAAGTGTGAGCTGACACCTGACTTATAATTTTCTAATTCATTTCCATATTAATGCTACAG
Seq C2 exon
GCACTATCATAGCATGGAAGTGTTCACCCATTATGATCTACTCAGCACCAATGGCACTAAGGTTGCAGAAGGACACAAAGCAAGCTTCTGTCTGGAGGACTCAGAGTGTGATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044074:ENSDART00000144013:10
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:
PF0118612=Lysyl_oxidase=PU(38.4=96.3)
A:
NA
C2:
PF0118612=Lysyl_oxidase=FE(19.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCAGGTGGTGGAACAGAC
R:
TCACACTCTGAGTCCTCCAGAC
Band lengths:
328-2233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]