HsaINT0027337 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64955885-64956217:+
Coord C1 exon
chr11:64955885-64955959
Coord A exon
chr11:64955960-64956056
Coord C2 exon
chr11:64956057-64956217
Length
97 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CTGTGTACCTCCCACCTCAGGAT
3' ss Score
7.79
Exon sequences
Seq C1 exon
CTCCTCAGAGTGGAACAACGTGGACCCATATGAACGGGACCAGCTCCGGGTCAAGATGGAGGACGGGGAGTTCTG
Seq A exon
GTGAGCGCCCCCTCCCCTTCTACCCCACCTCTCCACCCCTACACATCAGCTCTGTGCCCTGACGGGCTGTGCCTCACCTGTGTACCTCCCACCTCAG
Seq C2 exon
GATGTCATTCCGAGACTTCATGCGGGAGTTCACCCGCCTGGAGATCTGCAACCTCACACCCGACGCCCTCAAGAGCCGGACCATCCGCAAATGGAACACCACACTCTACGAAGGCACCTGGCGGCGGGGGAGCACCGCGGGGGGCTGCCGAAACTACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.2=43.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAGAGTGGAACAACGTGG
R:
TGTGGTGTTCCATTTGCGGAT
Band lengths:
176-273
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)