DreINT0052634 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36572009-36572503:-
Coord C1 exon
chr19:36572315-36572503
Coord A exon
chr19:36572183-36572314
Coord C2 exon
chr19:36572009-36572182
Length
132 bp
Sequences
Splice sites
5' ss Seq
TATGTGAGT
5' ss Score
5.56
3' ss Seq
TTTTTTTCTGTCTGCTGCAGTGG
3' ss Score
9.88
Exon sequences
Seq C1 exon
TTGTGAACTGCACTGATCCGGGACATGTTGAAAATGGTGTCAGACAGGTCCTGCCCAGCGGGCCTCATCGTTACAGTTTCCAGACCGCAGTTTCTTACAACTGTAACCCTGGGTACTACCTGCTGGGCAGCAGCATTTTGAGCTGTCAAGGAGACGGGACATGGGACCGTTCCCTTCCCAAGTGCCTAT
Seq A exon
GTGAGTCATTTTATCCCAATATAACATCCCTTCAATCATTCCAGAACCTACTTTACTCTGATCTGTTTATCCACGTCAGCTGACATTGTGCACTGTGGATAAGATTTGGCTGTTTTTTTCTGTCTGCTGCAG
Seq C2 exon
TGGTTCTGTGTGATCGTCCCAGCATGCCTCCGTATGCACAGATCTCAGGGGACAGGCGCACAGTGGGCTCCGTTATCCGCTTCAGCTGCATCGGCCAGCGCAGCATTGTGGGCAATACCACCCGCATGTGCCAGCTGGATGGCCAGTGGAGCGGCTCCCTGCCACATTGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:55
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.031 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0008415=Sushi=WD(100=92.2)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.5)
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:
CGGGCCTCATCGTTACAGTTT
R:
TGGTATTGCCCACAATGCTGC
Band lengths:
251-383
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]