HsaINT0027321 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64973934-64974290:+
Coord C1 exon
chr11:64973934-64974145
Coord A exon
chr11:64974146-64974250
Coord C2 exon
chr11:64974251-64974290
Length
105 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
TTCCTCCCCACTCTCTGCAGGGA
3' ss Score
10.81
Exon sequences
Seq C1 exon
CTGGTGGGCCAGCCGGCCGTACACTTGAAGCGTGACTTCTTCCTGGCCAATGCGTCTCGGGCGCGCTCAGAGCAGTTCATCAACCTGCGAGAGGTCAGCACCCGCTTCCGCCTGCCACCCGGGGAGTATGTGGTGGTGCCCTCCACCTTCGAGCCCAACAAGGAGGGCGACTTCGTGCTGCGCTTCTTCTCAGAGAAGAGTGCTGGGACTGT
Seq A exon
GTGAGTCATGGACTGGCCCCTGCCACTCTCCCCTCTCCCAGCCTCCCCTCTCAGGCCCTCTGCTGTCCCCCTCTGACTGGCTCCTTTCCTCCCCACTCTCTGCAG
Seq C2 exon
GGAGCTGGATGACCAGATCCAGGCCAATCTCCCCGATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.143
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(44.3=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
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:
AGCCGGCCGTACACTTGAAG
R:
CTCATCGGGGAGATTGGCCT
Band lengths:
242-347
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)