HsaINT0027450 @ hg19
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]
Coordinates
chr1:223934699-223936824:+
Coord C1 exon
chr1:223934699-223934867
Coord A exon
chr1:223934868-223936740
Coord C2 exon
chr1:223936741-223936824
Length
1873 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
GACGGTTGCTGTGTTTGCAGATC
3' ss Score
7.33
Exon sequences
Seq C1 exon
GATCAACGGATGCTATGAAGCGCTATCAGGGGGTGCCACCACTGAGGGCTTCGAAGACTTCACCGGAGGCATTGCTGAGTGGTATGAGTTGAAGAAGCCCCCTCCCAACCTGTTCAAGATCATCCAGAAAGCTCTGCAAAAAGGCTCTCTCCTTGGCTGCTCCATCGAC
Seq A exon
GTAAGTCCAGGCTGCCTTCCCTAGCCTCACCCCATCTGCTCTTGCTGAAGGGAGGCTCCCACAGTGCCCAAGGGAACCCACTGCTCCTGTGTACAACGTAATGCAGCCCTCGTCCACGTAGGGGCCAAAGGAAAACCTCCCTCCACCCTCTGAAGGTCCGCTGAAAATCAACTGGCAAAAGGAAGACTAATACAAGAAATGGCATACAAATGTATGAATGTGGACAGGGGAGAATCACAAGAGATTTCCCTACCACGCATTGGGATACAGAGGGTTATATTCCCTTCCTCTTAGGGGAAGGGAGATGGGGAGGTGCGGATGATTTTAGGGATGTCGTAAATGATTTTTAGGGGAATTCATTGGGCTTAAAGAACATAAATGGTCTGGGATAAAGTCTGTTGGGCCTGCAGAGCAGACAGTGGTTTGTGACAAGTCTGTCTAGCCATGTTGACAGACTTGTCTTTCTTCCTGCAATATGAGTTCAGTTCATAATAACTCATGGAAAGGACCAGACGTCATTGTTTTCATCTTTGGCAGGTCCAGACTTTAGGCAGGTGAGGGAACTTCAGAGAATAGCTTCCTCCTGTGCTTTGGGGGAGAGTGGATCGAGAGACAGAAGGAAAGGGGAGGTCAGAGAGATCTTGAGGCTTCTTCAGTTTAGCATTTCAAAGTGCCATCTCTTAGAGGTATTGGTTTCTGAGCACCCCAGTGTCTACCATTATTGCTCATCACCTGGAAGCCAAGGGTTGCTAGGCAAAAGTCAAGCTGTCTGGGGTGTAATGGATGGGGTGATGGTGCCTCCAGCCCTTCTGTCTTCAGTCCACTTCCCACTCTTAGCCTGCTCTGAATCACCCCCACCCCTCTGACCACAGGTTCCCTGGGAGCCCCTGCCACCTGCTGCCCCTGCCACCTTCCCCTCCATCTGCAGTGCTGTGCAGCCTTCCCCTGCACTCTTGCAGAGCTAATAGGCCCGTGGGAGACTTCGGAAGGAAGAGGAGGAAAGATTTCCTCATAATAGCCTTGCTGGCAACGCTCACCAGGGGATGGGAGGTGGGCACTGTGCCCAGGAGCCTTGGAGCAAAGGCTGTGCCCAACCTCTGAGCCCTGTCCCATCCAGGTTCTGGTCTCTGCGGGGGACAGAGATAAGAAGCCCTGGCTTTTGGAGCCAAAATCTAGGTCAGACTCCCTAGGCAGGAATTCTCAAAGTTTATCAGCAGAACACGTTGAGGCAGAAGACCCTTTCTGCTCCAGCCCTTCTTCCCAGGCTCAACCTTCATCAGAATAGATAGGGGAAAGGAGAGGCTGTGAGGCGTTCTTAAAACAGAAGCAAATTCTGACTCAGACCGGAATAAACAACCGTCCTAGTATAAACCCTACAGCTGGGCTGGGCCAGACCACGGAGCATGGGCTGGTGGTGGGGCGAGGGTGTGCTCAGTGTCCCTGGGCCACTCAAGGCTGTCTGGGTATCAGCCCTGCGCCATCGAGGACCCCCTCCGGCCCTCTCTCGGCCGTGCGCCCTTTCCCTGCGCCATCGAGGACCCCCTCCAGCCCTCTCTCGGCCGTGCGCCCTTTCCCGCCCTTCCCAGCCTGCAGAAATCCGTGGATGCGCTATTCACACGGGAATGCCTGTGCTCGTTCCGCGAGAGGGTTGCATTCCGCCTTTTCTCTGGTATTCTCGGCGTTCAAGCATTTGAACGGGGTAGGAAAGGTTCTCCAAGTGCAAGAAAGCGCAGCCCTGAGCCTCCCACCCCAGGCCTCGGCCGCTGCGCTAGTGCGTCCGGCGGTCCCGCCCGGCAGTAGGACAGAGGGAGCGAGGGAGTCCGGGAGGAAGGGAGAGCGGGTGCGGCCAGTCTGACGGTTGCTGTGTTTGCAG
Seq C2 exon
ATCACCAGCGCCGCGGACTCGGAGGCCATCACGTTTCAGAAGCTGGTGAAGGGGCACGCGTACTCGGTCACCGGAGCCGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909-CAPN2:NM_001146068:5
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(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(10.2=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:
TATGAAGCGCTATCAGGGGGT
R:
CTCCTCGGCTCCGGTGAC
Band lengths:
240-2113
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)