HsaINT0027331 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64950599-64951063:+
Coord C1 exon
chr11:64950599-64950668
Coord A exon
chr11:64950669-64950944
Coord C2 exon
chr11:64950945-64951063
Length
276 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGC
5' ss Score
6.03
3' ss Seq
GTGCATCCCTCCTGCCCCAGGGG
3' ss Score
7.77
Exon sequences
Seq C1 exon
GAACTGCTGTCAAACCCCCAGTTCATTGTGGATGGAGCTACCCGCACAGACATCTGCCAGGGAGCACTGG
Seq A exon
GTAGGCCCCCAGGGCGTCGGGTCCCGGGTATTTTTTCCACAGTAGTTCCCCATTCCCGCTCCTTCAGGCTCTGCCCCAACCCCTCCCTCTTGCAAGCCCAGGCAGGATCTGGCTATCAGCGCTGGGGCTGGTTTGCCCAGATTCCTGGGTCTTTTCTGCAAGCTGAGGGGAGTTAAGTGGCACCCTGGCCAAGGAACCCCAGATTCTCCCTAGCACCCGCTTCCCCCCCCGGGGCAGGTTGGTAGAGCAGGCTAATGTGCATCCCTCCTGCCCCAG
Seq C2 exon
GGGACTGCTGGCTCTTGGCGGCCATCGCCTCCCTCACTCTCAACGACACCCTCCTGCACCGAGTGGTTCCGCACGGCCAGAGCTTCCAGAATGGCTATGCCGGCATCTTCCATTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:3
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(19.8=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(13.2=81.8)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTGCTGTCAAACCCCCAG
R:
CTGGAAATGGAAGATGCCGGC
Band lengths:
189-465
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)