DreINT0052619 @ danRer10
Intron Retention
Gene
ENSDARG00000001559 | csmd2
Description
CUB and Sushi multiple domains 2 [Source:ZFIN;Acc:ZDB-GENE-030616-39]
Coordinates
chr19:36640094-36642520:-
Coord C1 exon
chr19:36642404-36642520
Coord A exon
chr19:36640304-36642403
Coord C2 exon
chr19:36640094-36640303
Length
2100 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGG
5' ss Score
9.2
3' ss Seq
CTGTTTTATCCTGCCAACAGGGG
3' ss Score
9.49
Exon sequences
Seq C1 exon
CTCAGTGTGGAGGGATCAGAGAGGAGATGGAAGGCACCATCCTCAGCCCTGGTTTCCCAGGAAACTACCCTAGCAACGGCGACTGCACCTGGAGGATTTACTTGCCAGTCGGTTACG
Seq A exon
GTGAGGAAAACACTGAATGAACAGATGCTGTTTTTTAAGAGTTCACTGCTAATTTGTGGAGTTCTGATTTAGCAACTGAAAATGCTAAACATTATTTATGTGGATTGGTTATTAAAAATTACTGTAGACAGAAGGAGGAGAAAAAAAATGAAGAGGGATAATATCAGTATATGAGTCATAGTTTCACTTTTTAGTTATAAGATCCTTCTTCGGTGCATATATAACATGATATTAATGATTAAATGAATTGACATATATTTGAAATCTCAAGTTTGTGTTGTCATGTTTTTATTATAATTTATTTTAAATTATGTAAGTATTTATTTGTTTATTTATATAGTTATTATTGTTATTTTTATTATTATTATTAGTAGTAGCAGTAGTAGGAGGAGGAGCAGGATTATTATTATTATTATTATTATTATTATTTATTTATTTATTTTTTATTTATTGTGGTGATTCTTATTTATTTCTCACAAATATTATCTTATTATATTATCATTGATATTATTTTATCATTGATGTGTCAATATAGTTTTTATTTATTTTTTAAATATTATTTATTTTATTTCTGTTATTTATTATTATTGATTTTGTTGTTGTTGTTTTATTTTATTTATTTTATTTTATTTTATTATTTTATTATTATTATTATTTTATTGTGTTTTTTAATGCTTCTCATTTAATTCTCTCAAATATTATATCTTTTTTTAAAACTAATATTTATAAGTATTAATTGATATGTCAATACATTTTAATATATTCATTTTTTCATATTTTTCAATTATTATGTATTTTATTTATTTATTTATTTATTTTTATTTTTGTTTAGAGATTCTCATCCATTTCTCTCAAATAATATATTTTTTTTCAAACCAATATTTATAAATATAATGCCATCGATATGTCAATACAGTTTTTATATATGAGTTTGTTTTCATGTTTTAATTATTATTATTATTATTATTATTATTATTATATTATTTTATATTATAAATTTTAATTTTATTTTAGAGATTCTCATCTATTTCTCTCAAATATTATCTTTTTCAAACCATTTTTTTATAAATGTAATGTCATTGCTGTCAATATAGTTTTTATATATGAATTTGTGTTTTCATCTTTTGTAAATATTATTTAATTAAATTTTTTTTTGCGATTCTCATTTATTTCTCTCAAATATTATATATATATATTTTTAACAATTTATTTGTAAATGTAATGTCATTGATATGTTAATATAGTTTTTTTATTTATGAATTTGTATTTTATATTGTATTTTTAATTATTAATTATTTTATTAGTCCCTTTATCAATCAAGAGTCGCCACAGTGGAATGAACCACCAACTTATTCAGCATATGTTTTATGCAGTGGATGACCTTCCAACTGCAACCCATTACTGGGAAATATCCATACACACTCATACACTATGGCCAATTTAGCTTACCCAATTCACCTTGGACTGAGGGAGAAACCGGAGCACCCGGAGGAACCTCACGTGAACACTGGGAAAACATGCAAACTCTACACAGAAATGGCAACTGACACAGCCAAGGCTCGAACCAGCAACCTTCTTGCTGTGAGGCAATCGTGTATAGTAATATATATATATATATATATATATATATATATATATATATATGCATATATTATATTATATTATTTTTATTTATTTATGTTTTATTTTTTTATGTAATTTTAGTGTATTTACTTTTATTTATTTATTTTTATTTTGTTCTGAACCATTTTCTCTCAAATATAATCTTGTTTTTTTCAAACCAATATTCAAAGTCCCCTGCATATACAGTAGTCTGCTAAGTTATTTTTTCAAGTTTTTCTGTAATTATGACAAGGTTTTCTAATCTTTTTTTTCATGTATACATTGAATTCATCACTGCTGATTAATGAAATATATTGTATTGTAATTCAAAAATCTATATTTTTCATGTTTAGTTATAGTTAGCACTGAATTGAACTTGATCAAACAGTTTGTTCCGTTTATCCATGTCAATGGCATCAGTAATTGTATGCCTGTTGCCTTTGCAGATCTCTAAGACTTTGATGTTACTAAGCACATTCTGTTTTATCCTGCCAACAG
Seq C2 exon
GGGCTCATGTGCAGTTTTTGAACTTTTCCACCGAGGCCAACCATGATTTCCTGGAAATAAGGAACGGACCTTTTGACACTAGCACAGTGATTGGCAGGTTCAGCGGACAGGAATTACCATCATCTCTCCTAACCACTTCCCACGAGACCACAGTATACTTCCACAGCGACCACTCTCAGAATAAACCTGGCTTCAGATTTGATTATCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001559:ENSDART00000132471:40
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.050 A=NA C2=0.014
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(34.9=92.5)
A:
NA
C2:
PF0043115=CUB=PD(64.2=95.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]