RnoINT0028986 @ rn6
Intron Retention
Gene
ENSRNOG00000020389 | Capn12
Description
calpain 12 [Source:RGD Symbol;Acc:1307341]
Coordinates
chr1:87073256-87073759:+
Coord C1 exon
chr1:87073256-87073464
Coord A exon
chr1:87073465-87073716
Coord C2 exon
chr1:87073717-87073759
Length
252 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGC
5' ss Score
3.73
3' ss Seq
CTTTCTTCCGTAATTTGCAGGGA
3' ss Score
11.17
Exon sequences
Seq C1 exon
CTGCTGGGCCTCTGGGACTCTCCGCGCAGCCGCGCGCTCTTACCGGGACTGCTGCGCGCCGACCGCTCGGTTTTCTGTGCCCGCCGCGACGTGAGCCGACGCTGCCGCCTGCCGCCCGGCCACTACCTGGTGGTGCCCAGCGCCTCGCGCGTGGGCGATGAAGCCGACTTCACGCTGCGCATCTTCTCGGAGCGCAGCCACACCGCAGT
Seq A exon
GTGAGCCGGTGCCCCCCTCGCCAAGCCTTACCAGGGGGAACCCTGACCCCCACCCAGGAACCTCAATCTAGAATCATAGAATCCCTGGCACCAAACCCCGCCCAGGGATCGCAAATTCCCGCCTCTGCATCCCCAGCCCCGCCCTACCCGGGTATTCCCCCCCTTTCCCCAAAACGCCACTTTCCTTTGACTGTACCCACGTCCTCTGCTGAGACCCCCGCCTGAACGCTTCCTTTCTTCCGTAATTTGCAG
Seq C2 exon
GGAGATCGATGACGTGATCAGCGCGGACCTGGACGCCCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020389:ENSRNOT00000027645:12
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:
PF0106717=Calpain_III=FE(39.2=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
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGGCCTCTGGGACTCTC
R:
CAGGTCCGCGCTGATCAC
Band lengths:
237-489
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]