RnoINT0028935 @ rn6
Intron Retention
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221352012-221352340:-
Coord C1 exon
chr1:221352132-221352340
Coord A exon
chr1:221352052-221352131
Coord C2 exon
chr1:221352012-221352051
Length
80 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CCCTCTTCTCCACTCTGCAGGGA
3' ss Score
10.48
Exon sequences
Seq C1 exon
TTGGCGGGTCAGCCTGTGCACTTGAAGCGTGACTTCTTCCTGGCCAATGCTTCTCGGGCACAATCAGAGCACTTTATCAACCTTCGAGAGGTCAGTAACCGCATCCGCCTGCCGCCGGGGGAGTATATAGTGGTGCCCTCCACCTTCGAGCCCAACAAAGAGGGTGACTTTCTGCTGCGCTTCTTTTCAGAGAAGAAGGCTGGGACCCA
Seq A exon
GTGAGTAGCCGACTCCCCCCATGCTCCCACCTCCCCTACCCCCCAGGCCCCTCTGACTGACCCTCTTCTCCACTCTGCAG
Seq C2 exon
GGAACTAGATGACCAGATCCAGGCCAACCTCCCCGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935:ENSRNOT00000028431:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.005 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(43.9=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
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:
CGGGCACAATCAGAGCACTTT
R:
TTGGCCTGGATCTGGTCATCT
Band lengths:
182-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]