HsaINT0027389 @ hg19
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:13249]
Coordinates
chr19:39228913-39229143:-
Coord C1 exon
chr19:39229058-39229143
Coord A exon
chr19:39228988-39229057
Coord C2 exon
chr19:39228913-39228987
Length
70 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TCACACCACAGTCTCTCCAGCTG
3' ss Score
0.71
Exon sequences
Seq C1 exon
GTGTTCCTGGGCTTCACCAAGGTGCGGCTGCTGCGGCTGCGGAACCCATGGGGCTGCGTGGAGTGGACGGGGGCCTGGAGCGACAG
Seq A exon
GTGGGATGGGTCTGGGGTGGGTGTGGGGCTGGACCCCACCTGCCCGCCCCTCACACCACAGTCTCTCCAG
Seq C2 exon
CTGCCCACGCTGGGACACACTCCCCACCGAGTGCCGCGATGCCCTGCTGGTGAAAAAGGAGGATGGCGAGTTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472-CAPN12:NM_144691:7
Average complexity
IR-S
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:
PF0064816=Peptidase_C2=FE(14.6=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(13.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGTTCCTGGGCTTCACCAAG
R:
CAGAACTCGCCATCCTCCTTT
Band lengths:
161-231
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)