DreINT0090063 @ danRer10
Intron Retention
Gene
ENSDARG00000025089 | loxl4
Description
lysyl oxidase-like 4 [Source:ZFIN;Acc:ZDB-GENE-080722-19]
Coordinates
chr13:40090336-40092687:-
Coord C1 exon
chr13:40092474-40092687
Coord A exon
chr13:40090517-40092473
Coord C2 exon
chr13:40090336-40090516
Length
1957 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATC
5' ss Score
6.99
3' ss Seq
TTTCATTTCTTCACTCATAGCTG
3' ss Score
7.79
Exon sequences
Seq C1 exon
ATTGAGTCAGATGGCTAAGAAGAAGGGATTCTGGGTTGAGAAACTTCATTGTTTGGGCACAGAGCCCAGTCTGGCTGAGTGCCACACCCAGCTATCAATCCCTCGAAGCCCCGCCCCCTGCAAGAATGGTCGCTATGCTGTGGCCCGCTGTGTCCCAGGACCACAGTTTGCCCGTATGTCCTCTGGCAGACCGCAGGCACCTCATCCTGTCCAG
Seq A exon
GTAATCTTTGAGACATTTAAGTATTTTAGATAAATTTATAAATTTGTTATTAAGAGACAATTATAAAACACAATTATAAAACAGTGATTCTTGATTCCGATTGGTTGAGACGCATTAGAAGCTGTTGTAAATTGCTCTACAAGCATATACCCATGACTGTTGGCAACCATTAAACCATCAATATACTGAGCCAGAGAAACTCAATTCATCTTTATTTATATAACACTTTTACAATGTAGGTTGTGTCAAAGCAGCTTAACATAGAAGTTCTAGTATAGTAAGTTCTAGAAACTTTTTAATTTGCTTTGTTTTGTGAGACCTTGCTGCAAAAGTTGAATAACCCAGCAATTAGTAAACACGTGAATCTGTAGTATACAGTGAATTACTAACAGCTAAGGGGCTTTGTTATACACAAAGTGGAGTAAACCATTTTATTTCACGGCTGTCTGGAATACTCAATATTGACTGGTCATTTGCAACATTCAAAGGTATGTTATCCCAAGACAACAACCGTTAAATAATGCAGGCTGATCAGGAAGTTTTGAATCGCCTTAAATGTCAGGGATACATTCATATATTTATATCTACATATATTCATATATTTACATACACATTCATATGCATCTGCTTGTCTATCACAGTGTGGTTTTGGACTAGTTTTGGCTGTTTGTTGCCTTTTTGTGAAGGAATACGTTGATTCAGACTCTGTCCTGGAGGGTTGGTGTCTTGCATAGTTTGCCTCTAAGCCCAATCAGACAAACCTGAGCCAGGTAATAAAGCTCTTACTGGGCTTGCTAGAAACATCCTGGGAGGTTTGTTGAGGCAAGTTGGAGCTAAACTCTGCAGGACACCAGCCCTCCAGGACTGAGTTTGGGCACCCCTGCTTTCTTTTCTGGTTTCATCTCTGTCAGATTTGCGTTATTGACTGTTTGTCGCCATCTTATGGCAGAATAATGCAGAAGTTAGTGTATATTCTATCAGCTGTTTCCTTTATTTCCTTCCTATTGAGCTTTGCTCTGCAATAACAATCTCCTGCATGTACTTCATGTATCCATGGCTTTTTTGGGGCATATTGTTTTATTCTACACAAAGCAGTTAGCATTGTTAAAGCATTTTAGTGTGCAGTGATTTTTATCTTTGCACCATCTATTTTTCTTAAAAGCAATGAATGTCTTATTTCAACAAGTAATCATTAAAAAATGTTAACAATACAGACTGTCACTTTGAAAGGTAGGTGTGAGGGAGCGAATTGAGGGACAACAAAGGTAATTATCCAAGTGCAGTTTAATACTGTAAGACTAGTCTTACAGGCAAGCAATGGTCAATACAAGAGTAAAATAGGAACATACTGGTCATCCAAATTGTAGTAATTAAATGTAAGGCTGCGAAAAAGCATACAACAAAAAACACAAGGCTTAGGTCAAAACCACGGCTGGTAAAGCAAAGCACTAGAAACACTCGCTATAAACACTTAACAATGAACTAATGTGTGTAGTGTATTATTAGTCCAAATGATCTGCCAGACACTGTACTTATTCAACCTAAAGTATATTTCAATCAGGATTTCCACAAAAAAAAAAAAAAAAATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAAGTAGCATAAAAGTTTTTACCATTGATGCTAACCATAAATGTTTCTTTATTAGTAGACCAGCATATAGAAAGATCTAGAAGAAATGATGCTAAAAAATCCAGCTTTTCCATCATTGGAATAAATTACATTTACGGGATAATATGTATAAATCAATGTTAAACAAACCATATTTGTTGACCACTTATATGAAGATTGTAGTCCTTAAATGTGTGTTGTGGCTAAAACCCAGGCCAGAAGTGGGAAAATATGATTACATGAAAGAAACCTCATCAATTTCATTTCTTCACTCATAG
Seq C2 exon
CTGTCAGTGCGTCTGAAGGCAGGGCCGCGTCTGGGAGAAGGCCGAGTCGAGGTTCTGCGTGAGGGAAAGTGGGGAACCGTGGTTGACCACCTGTGGGACCGTATTTCAGCCAGCGTGGTGTGCAGAGAGCTGGGCTTCGGCACTGCCAAAGAGGCTCTGACTGGAGCTTACATGGGTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025089:ENSDART00000044963:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.203 A=NA C2=0.074
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(44.3=70.8)
A:
NA
C2:
PF0053013=SRCR=PU(56.1=90.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCATTGTTTGGGCACAGAGC
R:
TGACCCATGTAAGCTCCAGTCA
Band lengths:
349-2306
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]