HsaINT0027326 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64977320-64977567:+
Coord C1 exon
chr11:64977320-64977388
Coord A exon
chr11:64977389-64977488
Coord C2 exon
chr11:64977489-64977567
Length
100 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
ACCCTCTGCCGCCACCTCAGTCC
3' ss Score
3.54
Exon sequences
Seq C1 exon
CGTGATGGCAATGGGAAGCTGGGCCTGGTGGAGTTCAACATCCTGTGGAACCGCATCCGGAATTACCTG
Seq A exon
GTAGGTTGTCCCCACTCACCTCAGTCATGCAGGTGCGGGCCGGGCAGGTGGGAAGGGCCGGGTGACTCAGCCTGGCCCTCACCCTCTGCCGCCACCTCAG
Seq C2 exon
TCCATCTTCCGGAAGTTTGACCTGGACAAGTCGGGCAGCATGAGTGCCTACGAGATGCGGATGGCCATTGAGTCGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:18
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:
PF138331=EF-hand_8=PD(29.5=78.3),PF134991=EF-hand_7=PU(5.5=21.7)
A:
NA
C2:
PF134991=EF-hand_7=FE(28.6=100)
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:
GTGATGGCAATGGGAAGCTGG
R:
CTGCCGACTCAATGGCCATC
Band lengths:
147-247
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)