HsaINT0027438 @ hg19
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]
Coordinates
chr1:223946972-223949319:+
Coord C1 exon
chr1:223946972-223947183
Coord A exon
chr1:223947184-223949282
Coord C2 exon
chr1:223949283-223949319
Length
2099 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGC
5' ss Score
2.23
3' ss Seq
TAATTTCCTTCTATTTCCAGAGC
3' ss Score
8.55
Exon sequences
Seq C1 exon
TTAAGTGGGCAGACCAACATCCACCTCAGCAAAAACTTCTTCCTGACGAATCGCGCCAGGGAGCGCTCAGACACCTTCATCAACCTCCGGGAGGTGCTCAACCGCTTCAAGCTGCCGCCAGGAGAGTACATTCTCGTGCCTTCCACCTTCGAACCCAACAAGGATGGGGATTTCTGCATCCGGGTCTTTTCTGAAAAGAAAGCTGACTACCA
Seq A exon
GTAGGCGGTTTGGTCCCTTCCTCTCCCCACCCTTCCCTGTCCCTCCCCACTGGTCTGTTCCTCGGCCCCTAGAGGGCTCTTTCATCCTCTGAATGTCAGTTACTTTTTCTGTAACACCTGCCCACCTCGAAGGACTAGTGTGGGGATTTGATGGATTGAGGAAGTTCTAGTGTTATAGTAAGGTAAACAATGGAAAAAGCCACTGTGGATATTTTTGGTTGGAAAGGGGTGGCTGTACAGTGAATTGCAGGGTCTAATTTCATAAGCGTGTCTCTGAATTCTCAAGTTGGTACTTTAATGTTAAACTACGAATCCAGTCTCGTCATTTGAAGAAAGCTGAGCAGTGCTGGTGTAATCCTTGATTTTCCAGGCCACCTGGCCTAGCAGAGCCACCAAGGGTGTAAGGTGGGAACCATCTCAACGGTTCCCACCTCCAGAACCTCTCCCTATTATAGTTGTCATGTCACCAGCTCTCTCTCCCCTTCCTCATGGGATCCCACGTTTGGGAACCCTTTGTGGCTGACATCACCATTTCCTGCCACTGTCCAGGTGGCCTCAATTCACAATGGCTTCTGCCACTTTGACTTCTGCCTCAACCATGTATGTTCAGCTGGGCACTTGATTGGCAAAGGCAGAATCTACCCTGGGTGATTTAAGCTAAAGGGAATTCATCGAAAGGCCATTGGAGACTCCAGAACTGATGGGAGGTAGGGGGTCAGGCTAGGAAGAACAGGAGCCAAGGATGTGTTGGAGGACCAGGGTGTGAGATGACCCCTTGGACTCTGGGTCATGTGCTGAGGTCTAAAGATCTTGTGGAGTGTGTCTGAGGTGCTGGGCTTGGGTCAGCCACCTGGCCTGCTGGTTCCTGTAGAGGAAGAGCCAATGGGAGGTAGAGGCAGGGAACTGCCCTTGCCCCAAGATAATGCATGATGCAGAAATAATTTCCCATGGCGAAGGGAGACAAAGCAATGCCAGGCAGCTGCATACCAATGAATGCCACCATAGCACGGCTGTAGCCCCCCTGCCACTGACAGGCTGTCTTCATTTGCTAAAGCCTACCATGGGGGAAGGGACCTTTCCTCTCAGCTCTGAGGATGCTTAGAGGAAGACTGGTGTGTTCAGTTTAGTCCTCACTGACAAGAAAATAGGAGCATGACCTGGTGGCATTAGAATAACAGTGTCCTTTGTCAAACTCATTACTCTCCCTGCCAGCCACAAGTCACTCTCCCAGGGAAGCCTCAACCCCTCAACTCTCTCTAGGGTGAGCTCCCTACCCCAAGAGGACACCCCACCTCTCAAAGGTTTCTGACTTCCTTGTCCCAAAATATTAATCCTTCTGCTCCAGATTCCAATGATCAGCACCAAGAGGTCCCCTTTTCCTTCTGCCAGGCATTGGCCCTGCTGATAGGACTCTTGGTCACTTAGTTAAAATCACAGTGGCCCAAGGAAGAACCTCCTGAGCTTGATTACCCTCACTATGGAGCAGAAGGACCTGGCCCTGGACACAGGGGCGGTGCACAGTATAAACTAACCACTGCCTGACCTGAGCTTTGGCTGAAATGACACACAGGCCTCTGCACTGCCCACCTCTCCAACCTGAGGCAGAACAAGTAGGCGATGATTTGCACTGCATGATTCTCAGTGTGAAAGTCTATGTTGGCAAAGGATATTTCAAGTGGAACTTAGAAGCTATTCCTTAAGGCTAGGACGAACACCACGCTACACGCGAAGGCTATCCTATTTGATAAAGATCAAAAACTAGCAAACAAAAATCTCCAGCTGCCCACGTTGCTTTGGTCATGACCCTTCCTTCAGATCACTTCTGCCTTTATTTTTGCTGTTTAGGGGATGTGTTATCACAGAAACTTGGAATGCAGAGAAATGTTATCACAGAAACTTGGAATGCAGAAAAATTTTTGCTTTTTAGGGGAGGTGTTATCACAGAAACTTGGAATACAAAGACCTCCCCCCACCGCAGCCCTGCCCCACCCCACCTACCCCCTGCTGGATTTAGCACTGCACTTCCATTTTAGCAGTGATTTCCTTCCTTTTTGCCCTCGCCTGCCTTCCAGTAACACATAATTTCCTTCTATTTCCAG
Seq C2 exon
AGCTGTCGATGATGAAATCGAGGCCAATCTTGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909-CAPN2:NM_001146068:12
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:
PF0106717=Calpain_III=FE(44.9=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)