DreINT0090054 @ danRer10
Intron Retention
Gene
ENSDARG00000025089 | loxl4
Description
lysyl oxidase-like 4 [Source:ZFIN;Acc:ZDB-GENE-080722-19]
Coordinates
chr13:40069534-40071488:-
Coord C1 exon
chr13:40071326-40071488
Coord A exon
chr13:40069778-40071325
Coord C2 exon
chr13:40069534-40069777
Length
1548 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
GGATCACCCTGCTGTTTTAGCTG
3' ss Score
5.46
Exon sequences
Seq C1 exon
GAAACATACTATTGGCAAGGAGACCCAGCGGCAGAGGAAGTGGTGTTGAGTGGCGCTCATTGTGTGGGAACAGAAATGTCAATCCAGCAGTGCCGTCGCAACAGTTATGTCCACTGTCCTCGAGGAGGCGGAGCCAAAGCAGCGGGCGTCACCTGTTCCGAGA
Seq A exon
GTAAGTAAATAAATATGTAGATGCATTAGTCCTGCCCACTTTTTCAGCAGTGCTTGTTCTGGAAGGATTTTTCCCATTAATGCATCCTTTTAAAGATTTTACTAATCGCAAATCGCATACTTATGTATTATTCTATACCATTTTGTAGCATAAATAGTGTAAGTAGTGTGTTCACACTGAAAACTCAAAAAATAATAAGTGCACTTTAATTACCAGGATAATGCACTTATTCCGCCGCTAAAATGGAGTGTGGAACGATGGACACTTAACGCACTCAACGATCACAGCTTTGCCCACATAGCAAAAGGGGTGGAGCTATCGGGTGCACATGTTGGATTACTTTATTTATTTTGGGTTGTAAAAGTGAAATTCTCCTACGAGAGTGATTATTTGCCTCCTGATGGTGAATGCAGTTATACTCATGGCAGATATTATTTGGTAGTTTGGTCATTTATTTCACTAAATTGGCAACCGTCAAACTTCATCTGGGAAACGGTTTTAATTTCAACTTAGTAAAAAACCATTAGTGTTCCATTTGAAGACGACACCATACATATACTATGCTGTTGAGTGTGTAAGTGCATAAGTACATAGTGCATACTGTATAGTGTGCCATTTGGGATGCAGCTAAACCTTGATTTGAAGCAAAGAGTTATATTAATTTTTTACAGAAAGATGAAGGTTCAATAATGTAGTTAACAACTTTAGTGAGAGAAAGAACTACAGTCTCATTAAGCATGGGAAATTATGGTAAAGTAACGTTAAAAAATGGTGGAAAAATATAAATCTATTAATTTTAAGTTGTTCGTTTTATCTATAGCAATGCTTTATTTGTTTTATTACTACTACTGATGTAACTTCTGATGACTTCTGGTGATTTCTTCAATATTTAAAATAAAATGTTGTCAGAGTTTGCATAAAACAGCAAAAAAGTGCCATGTTTTTCAAACATGTTAACTTTAATTTTTAGAACACAATAACAATTTTATAACTTCAGAAGAGTTATGAAGTCGATATTTACAATAAGCCTGATTTATAACCACAGCAAATGGGTTTTTCTGACTACTTCTCATTTTCTGAATGCTTTATATCACAAAAACAACATTCTGAAGTGTTATCACAACTTAGAAAGGAGAATAAGAGTAATGATTATTATCAAATATTTAGGAATTTTGAGAATATATAGGTAGAAGTTGCTCTTTTGCCACTCTCTGATTGGTGGAATTTCCTTCATAGCATCATGGGTAATGTAGTTCAGCATAAATTCAGCTAATAAACAGTGTTGTTTTAAAAAATAAATTTTCTTACAGTCTAACAAAATGCTGGGTTGTAATAACCAAATGTTGGGTGTGTCAAATATGAATAAATCCAACCGATGGGTTAAAAAGTTTAATTGGAATTTTATTAAAAATGATTGACCCAACGTTGGGATACAACGACCTGTAATTTTTTAAAGTAAATCAAGAAAATTTTTAGTTATCTCTTATCAGTGTTGTGCCCTTTTATAATGAAATCTCCACTGATTAATGGATCACCCTGCTGTTTTAG
Seq C2 exon
CTGCACCTGACCTGGTTTTGGATGCGCAGCTGGTTCAGGAGAGCTCTTATCTGGAAGACCGGCCTCTGCATCTGCTCACCTGTGCCCATGAGGAGAATTGTCTGTCCTCATCTGCCAGCCGCATGCAGTGGCCGTACGGGCATCGCCGTCTGTTGCGCTTCTCCTCCCGGATCATGAATCTGGGTAGAGCCGACTTCCGGCCACGGGCTTCAAGGGAGTCCTGGACCTGGCATCAGTGCCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025089:ENSDART00000044963:10
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:
PF0053013=SRCR=PD(49.1=94.5)
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:
CTATTGGCAAGGAGACCCAGC
R:
GGAAGTCGGCTCTACCCAGAT
Band lengths:
353-1901
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]