DreINT0052629 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36583956-36584722:-
Coord C1 exon
chr19:36584537-36584722
Coord A exon
chr19:36584151-36584536
Coord C2 exon
chr19:36583956-36584150
Length
386 bp
Sequences
Splice sites
5' ss Seq
TCCGTGAGT
5' ss Score
8.93
3' ss Seq
AGCTCATTTTGATCCTCCAGCTG
3' ss Score
6.96
Exon sequences
Seq C1 exon
TCGTTTCCTGTGGGATGCCGATTGCTCCAGTCAATGGCACTGTCATCGGGCAGCACTTCACTCTCGGATCTAGAGTCACTTTCTCTTGTAATCCTGGTTTCCGATTGGCCAACACTCAGCCAGTGTCAACACTTTGTCAAGAGTCTGGGAGGTGGAGCCCAATCGAGACCCGCCCTCGCTGCGTCC
Seq A exon
GTGAGTTCTTTAGCACCAATATTGCTTGATGATTTTATTTGCTTAAATTTAAAATGTAAATATTTAACTGTATTTTAATATATATTTTAAATTTGTTCTAATCTAAATAGGCTTTCTTAAGGTTTTCCAATTTTGTATTTATTTAATTTAGTATTTTTAAAGTTATATTTAAATAAGACAAGATAAGATTTAGGTTTCATAAATATGTTAAGTTGAATGGTGATGGAACATTACTTCATTCCTATTTTGTCAATTTATTTATTTTGTTTAGATATTTGACATTTATTTATATGCATAAAAATATTAAGAACCATTTATATAATAAAAAGAAGTATATATAGCATTATTTTAGGTCTTACTAAAATAAGCTCATTTTGATCCTCCAG
Seq C2 exon
CTGTGAACTGCCCTGACATCGGCCACTCTGCAGTAGATCATGGGAGGTGGAGGCTTATTTATGGCATGCAGAATAAATATGAAGCTATGATGATGCTGACCTGTGACCCTGGATATTTCTACAAGGGTCAAAGGGTCATCCGCTGCCAAGCTAATGGCACCTGGGATTACCCTGAGCCAAGACCTTCCTGTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:50
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:
PF0008415=Sushi=WD(100=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTCAATGGCACTGTCATCGG
R:
TCACAGGAAGGTCTTGGCTCA
Band lengths:
351-737
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]