DreINT0052645 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36544378-36544723:-
Coord C1 exon
chr19:36544658-36544723
Coord A exon
chr19:36544540-36544657
Coord C2 exon
chr19:36544378-36544539
Length
118 bp
Sequences
Splice sites
5' ss Seq
CGGGTATGT
5' ss Score
8.79
3' ss Seq
TTTCTGTATCTCCATCTCAGTGC
3' ss Score
8.42
Exon sequences
Seq C1 exon
CTGATAACAGACCAAGTGGAAAAACCGTAGGAACAGTGCAAGAGCCACCCAACACAAAGCAACCGG
Seq A exon
GTATGTTTCATCATAAAGTAGAACCATCTTTCAATTAAAGTCAAGTTCATTAAAACCGAAATGTATAACTCTTGTCTTACTTTAGTTCTTTTCTTTTATTTCTGTATCTCCATCTCAG
Seq C2 exon
TGCCAAGTGGGGTTTTTGCGAAGAACTCTCTCTGGAGGGGTTCATACGAATATCTAGGGAAGAAGCAGCCAGCAATGCTTAGCATAACTGCGTTTGAAGCGTTCAGCAATCGGGTCAATGGCACTCTCATGGACCACAGCGGAGTTCAGCTCAATCTGGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:65
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.040
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATAACAGACCAAGTGGAAAAACCG
R:
CAGCCAGATTGAGCTGAACTCC
Band lengths:
226-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]