DreINT0090060 @ danRer10
Intron Retention
Gene
ENSDARG00000025089 | loxl4
Description
lysyl oxidase-like 4 [Source:ZFIN;Acc:ZDB-GENE-080722-19]
Coordinates
chr13:40104166-40106593:-
Coord C1 exon
chr13:40106268-40106593
Coord A exon
chr13:40104381-40106267
Coord C2 exon
chr13:40104166-40104380
Length
1887 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAC
5' ss Score
4.81
3' ss Seq
AATGTTGGGTTTTCTTCTAGTCT
3' ss Score
6.62
Exon sequences
Seq C1 exon
GCCCCATTTGGATGGATAATGTGAGATGTGAAGGAACGGAGAAAGCTCTGAGAGATTGCAGGTCAAACGGATGGGGCGTTCATGACTGCAAACACTCGGAGGATCTCGGGGTGGTCTGCAGTCCAGAGAGAAGGCTGGATCAAACATATCCTGGAGTCTCCAGAAGAGGGCACACCATCGCACTCAGACCAAACCCAGTCACGTCCAACCGCTGGCAGGACATTTACTCCAACCCGAGGACACCTGCGCATCTCAGACAGGGCAATGGACACTCACAGGATCAAACCAGATGGGATCAGTTATCCAGACAGCAACTTCCTAATCCG
Seq A exon
GTAAACAGATGTCAGAAATGATTATGATCAACCCTTACTATAATATTTATATTATATAATATTCCTAATGGTATTAATGGTGTTTTCAATAGATTTCCACAACCCCAAATCAGAAAAAGTTGGAACAGTGTGAAAAATGCAAATAATAATAATAATAAAAAAGGAGCAATTTCCAAATTTACTTTGACTTCCATTTCGTTGCAGACAATATGAACACAAAATATTTCATGTTTTGTCTGGTCAACTTCATTTCATATGTAAATATACATCCTTTCCTGTCATTCAGACCTGCCACACATTACAAAAAAAAGTTGGGACTGGAGCAATTTATGGCTAGTAATCAGGTAAATTGGTTCAATAATGATGTAATTTGAAACAGGCGATGTTAACAGGTGATTGTAGTTATGATTTAGAAAAGCAGCATCCAAGAAAGGTCTAGTCCTAAGATGGGCTGAGGATTGCTAGTTTGCCAACAAATACCAAGAAAATGTTTGAATACATTGTTCCTCAAAGCAAAATAGGAGGACATTTGTGCATTTTACTTTTAATGGTGCATAACATATTTAAAAGTTTTAAGGAATCTGGAGGAATTTCAGTGCATAAAAGTTCAGGCTAAATGACCATGACCTCGCAAGCTGAACAACCGCAAGCTGAACAACCATGATCTCCTATGCCTCAGGTGGCACTGCATAAAGAATCATCATTCATCTATAAGCGACATCATTACATGAGCTCAGGATTACTTTAACAAACCAGTTTAAACTGTACTTTGCCAAATGGAATCCCTATGTTAACAGTGTCCAGAAGCACTGTCGACTTCTCTGGGCTCGGAGGCATCCGGTATGAACGATCACAGTGGAAATGTGCGCTGTGGTCAGATTAATCAGCATTTCAGGTATTTTTTTTAGGGAGAAATGGACGTATTTCAACAAGACAAGTACTGAGTGCGGAAGATGAGGATACAAGTACTTGACTGGCCTGCCTGCAGTCCTGACCTATTTCCAATAGAGAAAGCGCACAATGCAACAACCCCGTACTGTTGCTCACCTTAAGACACAATTACACCTGAAACACTTCATCACTTGGTGTCTTCAATTCCTAAACATCTTTTAAGTGTTTTGAAAAGGAATGGCAACATTACAAACTGGTAAATAATGTACTGTTCAAACTTTTTGGAAGTGTGTCGCAAGAACCAAAATTGGAATAAGTGTTTATTTAAAAAGTAATTAAATAAATAAACGTCATGAGGAACACATTAAATGGCTGGTGATCCTTGGCCCTTCTTTGCTCCTAAAGGACTAGACCTTTCTGGGATGCTGCTTTTGTATAAATCATAATTAGTTACGGTGGTTCATTCCGCTGTGGCGTCCCCAGATTAATAAAGGGACTAAGCCGACAAGAAAACGAATGAATGAAGAATTAGTCACCTGTTGACATCACATCATTATTGAACCAATTTACCTGATTACTAGCCATAAATTTCTCCTGTCCCAACTTGTTTTGTAATGTGTGGCAGGTCTGAATGACAGGAAAGGATGTATATTTACAAATGAAATGAAGTTAACCAGACAAAACATGAAATATTTTGTGTTCATATTGTCTGCAATGAAATACAGGTCAAAGTAAATTCGGAAATCACTTCTTCCTTTTGTTTATTTGAGTTTTCCATACTGTCCCAACCTTTTTTCATTTAGGTTTGCATATATAATCAGTTTATAACCTGAATTGATAGTACTGCATGGCTTTGAAGACTTGAAATGTAGCACATGAGTAGAGTTTTGCATGTTTTTGGATGCTTTCACAGTACTTTTTTTGCATTCCATGTTAAATTCAAGATTTTTCCCTCTCCAAAAGCAGCTAATGACAAAATGTTGGGTTTTCTTCTAG
Seq C2 exon
TCTGCCAGTCGGGTAAGGATTGAAGAAGTCCGTCTCAAGCCAGTCCTCATGGTTACAAAGCGCCGTGCCCTCATCACTGAGGGTGTGGTGGAAGTAAAGCATGCTGGGAGATGGAGACAGGTGTGTGATAAAGGCTGGAGTCTGAACAGCAGCAGAGTCGTGTGTGGGATGCTTGGCTTTCCTGACGCGGAGCAGCCCAACATGAACACCTACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025089:ENSDART00000044963:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.477 A=NA C2=0.083
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(41.2=36.7)
A:
NA
C2:
PF0053013=SRCR=PU(43.5=69.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGACCAAACCCAGTCACG
R:
TAGGTGTTCATGTTGGGCTGC
Band lengths:
356-2243
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]