DreINT0041271 @ danRer10
Intron Retention
Gene
ENSDARG00000012341 | capn9
Description
calpain 9 [Source:ZFIN;Acc:ZDB-GENE-010724-2]
Coordinates
chr1:53235414-53235766:-
Coord C1 exon
chr1:53235689-53235766
Coord A exon
chr1:53235575-53235688
Coord C2 exon
chr1:53235414-53235574
Length
114 bp
Sequences
Splice sites
5' ss Seq
CTGGTATGT
5' ss Score
8.14
3' ss Seq
GGTGATTTGTTGTGTTGCAGGAT
3' ss Score
8.22
Exon sequences
Seq C1 exon
TTCGAGAGAATGGACTGTCATTGACAGCTCAGAGAAGAAACGATTGCTGCAAAACTCCCTGGATGATGGAGAGTTCTG
Seq A exon
GTATGTCCAGCTATCAGATACAATAAAGATGTTTCTGTGTGCCACATTAAAACCAGTATCTAAAAAGCTCTATCTGACCAGCGGTAATAACATAGGTGATTTGTTGTGTTGCAG
Seq C2 exon
GATGGAGTTCGGAGACTTTAAATCCAACTACGATAAGGTTGAGATCTGTAACCTGTCTCCAGATGCTCTGTCCGATGACGTTTCCAAGCAGTGGGCTGTGAACCTGTTTGAAGGCAGCTGGATCAGGGGGTCCACCGCTGGCGGCTGCAGGAACTACATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000012341:ENSDART00000007732:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.8=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.4=34.5),PF0106717=Calpain_III=PU(16.4=43.6)
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:
CGAGAGAATGGACTGTCATTGACA
R:
AATGTAGTTCCTGCAGCCGC
Band lengths:
236-350
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]