DreINT0052641 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36552616-36553969:-
Coord C1 exon
chr19:36553796-36553969
Coord A exon
chr19:36552690-36553795
Coord C2 exon
chr19:36552616-36552689
Length
1106 bp
Sequences
Splice sites
5' ss Seq
TAGGTCAGA
5' ss Score
4.42
3' ss Seq
ATTGTGGGCCTTTTTTTCAGATC
3' ss Score
8.91
Exon sequences
Seq C1 exon
CTGTATTTTGTGGAGATCCAGGGATTCCAGCCCAGGGGAAGAGGGAGGACAGAGGGTTTACCTACCTGTCCTCTGTTTCATTCTCCTGTTACCCGCCTTTGATTTTAGTTGGCTCTGCTCGACGATACTGCCAGTATGATGGAACCTGGAGTGGAACCCAGCCTTCTTGCATAG
Seq A exon
GTCAGAAGCTTGAATGTGTTCATGGTGTCAGTGTATTAAACAAGTCATTCAATCAATCGAAAATGTATTACTATTTTTTTTAAAGAGTTTTAAAAATTATATTAATTTTAAAGATTATAGATAGATATTTTATTTTAAAGAAGTAAATAGAATTTTATTTAAAGAATTATTTTATTATTATTATTTTTACTTTATTTTGTTTTATTTAATTTGATTATTTTATTTTATTTTATTTTTATTTTTTTTATTTTTTGCTTTGGTTTTTTATGTTATTTTATTTATTTATTTATTTTTTTGCTCTATTTTTATTTTATTTTATTTAGTTTTATTTTATTTTATTATTATTTATTTTATTTTATTTTATTTTAGCTCAATCAAACATCCATGGTTAATGTCATCTTCTTCCAGAATATCATCTTTTACAACCAAAACTGTTGTTTTTTAATTTTATTGTAAGAATTGCATAAAATTATATTAACTTTGTAGATTTATTTTTATTTAATTCATTATTTTATTTTATTTTGCAGAATTTATTTATTTTTTTTATACAAATTATTTGTTCCACGCTTCTAATATTTTGGTCAAAACATAATAATACATAATGTTGTGCATATATAATATTTTATTAAGAACTAGATTTGTTTGTATAGGTAGAAAATTACATACTACCATAAGAAACCTTTGATTGATTTGAAAAAAAAAATGTAAAAGCTATAAAATATGTATTTTCTGTCCACAAATACTGCATTTATTTGATTGTAAATGCAGCATTAACATTAATATTATAAATAAATGTTAGTTTAAAATAATGGGTTTCTATGTGAACGGAAATATTCCAAAAATATCCATTTCCAAATATTTATTTGACATAATTATACACACATGGTCATATATGACAATATTTACAATTTCTGTATGAGATTCCATGCTTCAGGATATGTCACAAATGAAATAGGTTATAAAAAGTGCTGCCCTTTTGCTTCTGTTATGCAGCAACCTCAAAATTGTGGAGATTGTAGGTTCTGTAATTTAGATCTCCAAATTGAGTACACACCAACACTGCAGTGGCACTGTGAATTACTTCTAATTGTGGGCCTTTTTTTCAG
Seq C2 exon
ATCCCAGTCACACCAGCTGTGTGGATCCTGGCACTCCTCTCTTCGGCCACCAGAACAACTCTCAAGGCTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:61
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=91.5)
A:
NA
C2:
PF0008415=Sushi=PU(32.7=72.0)
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:
TGGAGATCCAGGGATTCCAGC
R:
CTGGTAGCCTTGAGAGTTGTTCT
Band lengths:
238-1344
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]