DreINT0041257 @ danRer10
Intron Retention
Gene
ENSDARG00000012341 | capn9
Description
calpain 9 [Source:ZFIN;Acc:ZDB-GENE-010724-2]
Coordinates
chr1:53231210-53231464:-
Coord C1 exon
chr1:53231428-53231464
Coord A exon
chr1:53231291-53231427
Coord C2 exon
chr1:53231210-53231290
Length
137 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTTGTGTCTACTTTTTGAAGCCA
3' ss Score
4.95
Exon sequences
Seq C1 exon
TGAGGTGGGAAACAAAATTGAAGCTGATCTGCCAGAG
Seq A exon
GTGAGTCAAATATAATCACTGGATAATTTTATTATATCCCTAGGAAGGACATATCAAAGTCAAAAGCAGATTGCTCTTAAATAGGTAAAACTGCTCCTAAAGTTACCTGTATGTATGTTTGTGTCTACTTTTTGAAG
Seq C2 exon
CCACCGAAACCAAACCCACCTGAAGAGGAGACTGATGAGGAGAAAGGCCTGAGGAAACTCTTTGAACAGGTCGCTGGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012341:ENSDART00000007732:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.769 A=NA C2=0.704
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF138331=EF-hand_8=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGGTGGGAAACAAAATTGAAGC
R:
CCAGCGACCTGTTCAAAGAGT
Band lengths:
114-251
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]