HsaINT0027376 @ hg19
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:13249]
Coordinates
chr19:39226010-39226184:-
Coord C1 exon
chr19:39226142-39226184
Coord A exon
chr19:39226070-39226141
Coord C2 exon
chr19:39226010-39226069
Length
72 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
AAACTTCCGCCATGCGGCAGGGC
3' ss Score
2.07
Exon sequences
Seq C1 exon
GGAGATCGACGACGTGATCAGCGCAGACCTGCAGTCTCTCCAG
Seq A exon
GTGGGGACTGTTCCTGGAGGGGCGGCATGGGGCGGGGATCTTGGCCAGCGCTAAACTTCCGCCATGCGGCAG
Seq C2 exon
GGCCCCTACCTGCCCCTGGAGCTGGGGTTGGAGCAGCTGTTTCAGGAGCTGGCTGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472-CAPN12:NM_144691:13
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:
PF0106717=Calpain_III=PD(0.1=0.0)
A:
NA
C2:
PF134991=EF-hand_7=PU(11.9=66.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGATCGACGACGTGATCAG
R:
CTCTCCAGCCAGCTCCTGAAA
Band lengths:
103-175
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)