RnoINT0028937 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221351301-221351510:-
Coord C1 exon
chr1:221351445-221351510
Coord A exon
chr1:221351359-221351444
Coord C2 exon
chr1:221351301-221351358
Length
86 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
GCCATCCTTCTCTTCCCTAGGAC
3' ss Score
11.54
Exon sequences
Seq C1 exon
AAAGTGCTCTCTGAAGAGGAGATCGATGACAACTTCAAAACCCTGTTCAGCAAGTTAGCAGGGGAT
Seq A exon
GTATGTCAGGGACTGGCAGGGATGGTAAGATGGGGAACCCCTGTGTGAAGTGGGGAAACCCCAGCTGCCATCCTTCTCTTCCCTAG
Seq C2 exon
GACATGGAGATCAGTGTCAAGGAGTTACAGACCATCTTGAACAGAATCATTAGCAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.023 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF138331=EF-hand_8=PU(0.1=0.0)
A:
NA
C2:
PF138331=EF-hand_8=FE(31.1=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:
TCTCTGAAGAGGAGATCGATGACA
R:
TGCTAATGATTCTGTTCAAGATGGT
Band lengths:
114-200
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]