DreINT0052643 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36550764-36552522:-
Coord C1 exon
chr19:36552411-36552522
Coord A exon
chr19:36550944-36552410
Coord C2 exon
chr19:36550764-36550943
Length
1467 bp
Sequences
Splice sites
5' ss Seq
TAGGTTAGT
5' ss Score
5.5
3' ss Seq
CTCTGGTTTCTTTTTCTCAGCTC
3' ss Score
8.13
Exon sequences
Seq C1 exon
ATTGGTAGTTCAGTGTACTACAGCTGCAGGAAGGGTCATCTTCTTCTGGGTTCAATCTCACGGACGTGTCTACCAAACCTCACCTGGAGCGGCATGCAGCCTGAGTGCATAG
Seq A exon
GTTAGTAACAGATTTATAAACATATGTGCCAGTTATGTTGCTTGTTTTCAAATGCATTTTAATATTAATGTACTGTAGCTGCAAACAGTAATCATTGCGTTCCAAGCTCAATCCATTAGGCAACTGATGCTGAAAAGACATCAAATTGACATGAAAATAGATATAATAAAACTGGTTAAATATGCTAATCAAACTGACTTCAAAATCTTGACATGATGTTGATTTGATGTAAATTGAATGTCAGATATTTTGGTCTACTCGAACATTAAACCAATTTCAGTTTGGAATTAACTTCTGTTACTTGTTTTCACCCAATTACGACTGAAACCACCTTTCAATACAAGTTTAACATGACTCTACAACATTGTCATCAAATATGATAAACAGATGACAAGGTGCCTGCTGCATAACTTAACGGATATAGTTATAGTAAAATGTTTAACTTTCTTTTTAAACATAATGTAAGTATTTAATTGTCTTTCAGTTGATATTATTTTTTTGTTATCAGTTGTAAATATTTTTTTCAATATATTACAATAGATCAAATCAATTTTAATTATTTAAAAACAAACAAAAAGTACTCAGAGGTAGCTCAAATATTTGGTCAGTGCTCTTTTAGTAAGGGAAAAACAACAACATAAATCAGTCCAAGGCACTCGAAAAATGTGGAAAAATTTAAAAAGCCATTATTCACATGGCTAAACTTATCAACTATCATCATTAATTTAGCAGTTAATTTAACTGACTGAACTTAGATTGTTTTCTTCTTTTTAAACTTATTAAGCTCTTAAGTTCATGTGCCTTATTTATGTGGATAATATAATTCCAGTAGGTTGTAGTCTGTCTGCCATTTTTAATTTGGTAACTACTGTAGCCTTAAACCATTTGACTAGTTCATACAAAATTTGGCTTGCGCAATCTATCGACAATAATGACAAAAACTTTCAAACTATTTTAATTATAATTATAAAACTATTATTAAAATGCTATAATATAATACAATTAAAAATTATAATATATAAACCAATTTATTGTGTAACTACACCTCAATACACTCATTAAACCATAATTTCTAGCTTAGTCAAATTTTCACTTTTTGTCATCAGGATCTCTAGATGACAAAATTTTGCACTGATTGCACAAATAATCTAGGAGGAGTACTATAAAGTATTTGGCACCACCTTGGCTGTTTTGTTGTTTATAGGACTTGCAGTTTTGACTGGTCAGATATTTTGTGGGCCGAAAATAATATTAATAATTATAAAAGGAACAAGCATATCAGAACATTTACAATATGGTTCCTGAACCTTTAATGTTTAGACACCTAATTAAGGAGTGTTTAGTAGAGAATAATACAGTAATATAGAACAAGATTTTCTAATAAGTGTGGTTAGATTTACTTAATTATTTTTTTGTTGTTGTTGTTTTGTTTTTGCACATTTTAAGACTCTGGTTTCTTTTTCTCAG
Seq C2 exon
CTCATCACTGTAATCAGCCAGAGCTGCCTGCTCAGGCAGATGTAGGTGCCATAGAGCTGCCGTCTCTGGGTTATACTCTCATCTACACCTGTCAGCCTGGTTTTTACCTCGCTGGAGGCTCTGAACATCGAACCTGCAGGGCTGATGGCAGCTGGACAGGGAAACCTCCACTGTGTGCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:63
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=0.057
Domain overlap (PFAM):
C1:
PF0008415=Sushi=PD(63.6=92.1)
A:
NA
C2:
PF0008415=Sushi=WD(100=91.8)
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:
GGTAGTTCAGTGTACTACAGCTGC
R:
CACACAGTGGAGGTTTCCCTG
Band lengths:
286-1753
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]