HsaINT0027448 @ hg19
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]
Coordinates
chr1:223931802-223933141:+
Coord C1 exon
chr1:223931802-223931920
Coord A exon
chr1:223931921-223933007
Coord C2 exon
chr1:223933008-223933141
Length
1087 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
CCACCTCTCTTGTTCTGCAGTTC
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTGACTGCTGGCTGCTGGCAGCCATTGCCTCCCTCACCTTGAATGAAGAAATCCTGGCTCGAGTCGTCCCCCTAAACCAGAGCTTCCAGGAAAACTATGCAGGGATCTTTCACTTCCAG
Seq A exon
GTAACTTAATGGTTGGCTCAGGTGGTTCCTCAACAGGTCCAGGGGGCTAGGAACAGTCTTCTGGCTTGGCTGGGTTCATCAGTCCCTGGTGTTTGCAGACTCCCAAGACCAATACTGTTCTACAAAGGACATTGGGCGAGAGCAGGAAGCTTCCTGGCTTACCCGTGGCCAGGATGTGAGACCCGGCTGGGATGGCCCTGGGTGGTTTCTTGGGACATGTAAAAGGGAGGTAGAGCAAGGTGTTCAGGAACTAATTCCCAAGTTTAAAAAAAAAAACTGTATTATTTGATGTTTGAGACAAAAACGTTGAAGTTCTCCTCCTTTTATGCCGGTAAATGAGAAATAATACTTGAAAAAGCTGGCTGGGCACGGTAGCTCATGCCCGTAATCTCAGCACTTTGGGAGGCCGAGGTGGGCAGATCATTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACTAAAAGTACAAAAATCAGTTGGGCGTAGTAGTGCAGGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTTAACCTGGGAGGCAGAGGTTGGGAGGCCAAGGTGGGTGGATCACTTGAGCCCAGGAGTTCGAGACCAGCTGGGGCAACATGCTGAAACTCCGTCTCTACTAAAAACACAAAAAAAATTAGCCGGGTGTGGTGGCACGTGCCCTTAATCCCAGCTACTCGGGAGGCTGAGGCAAGAGAATCACTTGCATCCAGGAGGCAGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCAGAGCAAGACTTGGTCTCAAAAAAAAAAAAAAACAGCCTAAGGTACAGGGCAGAATGCTAAAGAGGCGGGTGTGGATTTGAAAGGATGGACATGCGCCTCTGTCTTCGCTTTTTTAGTGAGGACTTGGCCTGCATAGGAGAGTTAAGGGAGCACCTCCTCCCAGGATGCGCTCATGGAACCTATCCCAGGGGATCAGGGCAAGGGGAGCCAGAGGCAGCTGAGGCTCAGAGTCCCAGTGCTGCCACCAGCTCCTCCTGCAGCCCACCTCTCTTGTTCTGCAG
Seq C2 exon
TTCTGGCAATACGGCGAGTGGGTGGAGGTGGTGGTGGATGACAGGCTGCCCACCAAGGACGGGGAGCTGCTCTTTGTGCATTCAGCCGAAGGGAGCGAGTTCTGGAGCGCCCTGCTGGAGAAGGCATACGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909-CAPN2:NM_001146068:3
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(13.0=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.7=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:
GTGACTGCTGGCTGCTGG
R:
GCGTATGCCTTCTCCAGCAG
Band lengths:
250-1337
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)