DreINT0005744 @ danRer10
Intron Retention
Gene
ENSDARG00000055338 | CAPN1 (2 of 2)
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:HGNC:1476]
Coordinates
chr21:27447355-27447604:-
Coord C1 exon
chr21:27447547-27447604
Coord A exon
chr21:27447420-27447546
Coord C2 exon
chr21:27447355-27447419
Length
127 bp
Sequences
Splice sites
5' ss Seq
AACGTTAGT
5' ss Score
1.4
3' ss Seq
GACTGTTATTTGTTTTACAGATA
3' ss Score
9.55
Exon sequences
Seq C1 exon
GAAATGGAAATCAATGTGGCAAAACTTGAGATGATTCTGAATCGGGTTGTCAGCAAAC
Seq A exon
GTTAGTATGCTTATGTCAAGCACATTTCACAATGATTTGTTTTTAAATTTTCTAAAACACAAATTCCCACATACATTTCCTAAAATAAGCCAGTTAAATAAGCCCATGACTGTTATTTGTTTTACAG
Seq C2 exon
ATAAAGATATAAAAACAGATGGATTTGGCAAAGAGACTTGCAGAGGCATGATAAATCTCATGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000055338:ENSDART00000077657:15
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=0.000
Domain overlap (PFAM):
C1:
PF138331=EF-hand_8=FE(31.1=100)
A:
NA
C2:
PF138331=EF-hand_8=FE(34.4=100)
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:
GAAATGGAAATCAATGTGGCAAAACT
R:
TGCCTCTGCAAGTCTCTTTGC
Band lengths:
106-233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]