DreINT0052615 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36651787-36652136:-
Coord C1 exon
chr19:36652032-36652136
Coord A exon
chr19:36651906-36652031
Coord C2 exon
chr19:36651787-36651905
Length
126 bp
Sequences
Splice sites
5' ss Seq
AGAGTAGGA
5' ss Score
0.81
3' ss Seq
TGTCTCATTTTCCCTCACAGCTG
3' ss Score
11.16
Exon sequences
Seq C1 exon
GTACAACAGTGCCAGCCCTTCTGAACAGCACCTCCAACCAGCTCTACCTGCACTTCTTCTCAGACATCAGCGTCTCTGCAGCCGGTTTCCGTCTGGAGTACAAGA
Seq A exon
GTAGGACATCTGTTACAATACCAGTGCATCTGGACTTCACATACTCTCTAAAAAGCCAACTATTTTTTTTTGCATTCAGCAGAATACCTCTCATTGTTTGTCATATTGTCTCATTTTCCCTCACAG
Seq C2 exon
CTGTGTCCCTCACTAGTTGTCCTGAACCGGTTGTACCCATGAATGGCTTCAGAGTGGGCGAAAGACTACAGATGAACAATGTTGTGTCCTTTCAGTGCGACCCTGGATTTACGCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:37
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PD(31.1=91.7)
A:
NA
C2:
PF0008415=Sushi=PU(58.9=82.5)
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:
GTACAACAGTGCCAGCCCTTC
R:
CGTAAATCCAGGGTCGCACTG
Band lengths:
218-344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]