DreINT0008169 @ danRer10
Intron Retention
Gene
ENSDARG00000077920 | CSMD3
Description
CUB and Sushi multiple domains 3 [Source:HGNC Symbol;Acc:HGNC:19291]
Coordinates
chr19:44785834-44786551:-
Coord C1 exon
chr19:44786438-44786551
Coord A exon
chr19:44785930-44786437
Coord C2 exon
chr19:44785834-44785929
Length
508 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TGTGTGTGTGTGTTTTGCAGGGG
3' ss Score
11.74
Exon sequences
Seq C1 exon
TTCTATTCGGACAGTTCGTCCTGTTCCAGACGTCTCTGAATGATGTGGTGGACATTTATGATGGGCCGACACAACAGTCTTCTCTGCTGTCCTCTCTCTCCGGCTCGCACTCAG
Seq A exon
GTAAAGCTCAAGCTTAATATCCTATTTCTGGACTTCACATAATTAATCCATGACTATTATTCATCTCAAGCCTATGACGCGGCTTTAAAACGTTCAGATGTTATTGCAAAAAAGAGCTGTAGGACTAAGCAGCATACAGAGCATCACAAAACCAATCCTGCTATCAAATACATGGTCAATGCAAGAGCATAAAAATACCACAGAAGATGTAAACAAATCGTTGTAGTGTAAGCAAATTCAGTGTGTTTATCTCATAATGTGGTCATCACGTCTGCTATAGTAGGATCCTTCAGTGGCTTTTTAGCTGAAAGATGTTTATTGGCATTTGATGGTTCAAGGCAAACCCGAAACCTTCTATTCAGCCGCTTCCTCTGTGCAAATATACATATATCAGAAGTCATTTGAAGCCAAAAGATTCAAGAATGATGCTTACTCTTGATGTTTCATGTGCTCTATAATGCAGTTCTAAGGCGTGTGTATTTATTCTGTGTGTGTGTGTGTTTTGCAG
Seq C2 exon
GGGAGTCTCTGCCCTTGAGTACTGGAAATCAAATAACTATCAAGTTCAGTACAGTTGGACCAGAGACGGCCAAAGGCTTTCATTTTGTGTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000077920:ENSDART00000108507:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=FE(35.8=100)
A:
NA
C2:
PF0043115=CUB=PD(29.2=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTTCGTCCTGTTCCAGACG
R:
TTGATACACAAAATGAAAGCCTTTGG
Band lengths:
198-706
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]