HsaINT0027453 @ hg19
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]
Coordinates
chr1:223939699-223940658:+
Coord C1 exon
chr1:223939699-223939773
Coord A exon
chr1:223939774-223940497
Coord C2 exon
chr1:223940498-223940658
Length
724 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
ATTGTCTCTGCTTTTGCCAGGAT
3' ss Score
7.43
Exon sequences
Seq C1 exon
CTGCCCAAGCTGGAACACTATAGACCCAGAGGAGAGGGAAAGGCTGACCAGACGGCATGAAGATGGAGAATTCTG
Seq A exon
GTAAGATTAGTGGAGGCTTCAGGGAAAGCTCTGTCTGCCCCAATGTTCTTTACTAGAAAACTGCTAATTAGAAAGAGTGTCGGCCAAAGTGAGTTTACCATGTCGAGGACACAAGCGTGTGGGATCCTGGTTTTGTTATTTTAAGTTCACTATAAGAGCCTGAATAAAGAAATTCTTAAGCCCCTTCAACGGTCCATCTTGACAATGGGGTTTATAAGCTGAGCAGCTTCAGAAAAAGGCTAAGAGGAATTCCTTTGGTAATGTTCAGATCCCAGGAAACAAGGGAAAGATGGGGCCTTTCTCCCCCAGGTTCCGGAGACTCATCCCAGCCCCTTAAGAAACTGGTCCCTTAGTGAGCAGCAATGGACCCACATGTCTGTGTGTCTGCGCCACTCTATAACCACCTGCACCTGGACACAACATGCTCTTTATCAAATGGGGCCCATATATTGTCACATTTGATGGGCACGGCTCCCATTTTTGCAGGTGAGAGTTCTGAGCTTCAGAGAAGTTTAAGTAACCTGCTCAAAGTCACCCAGCTAGAAAGTTGCAGCGCCAGGACTGGAATCTGGGCCTTCTGATTCTGAACCTGGTGCCCATCCACTCAGTTCTAATGAGCTGCTCTGCCTGGCTTTGGGTGGCTCCTGGTCTGGTGTTGGTGGAAAGTCAAGGCTTACCAGTGTGTCTTCTTATCACCTGTGATGATTGTCTCTGCTTTTGCCAG
Seq C2 exon
GATGTCTTTCAGTGACTTCCTGAGGCACTATTCCCGCCTGGAGATCTGTAACCTGACCCCAGACACTCTCACCAGCGATACCTACAAGAAGTGGAAACTCACCAAAATGGATGGGAACTGGAGGCGGGGCTCCACCGCGGGAGGTTGCAGGAACTACCCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909-CAPN2:NM_001146068:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.346 A=NA C2=0.036
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(15.4=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:
CTGCCCAAGCTGGAACACTAT
R:
TCGGGTAGTTCCTGCAACCTC
Band lengths:
236-960
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)