HsaINT0027454 @ hg19
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2, (m/II) large subunit [Source:HGNC Symbol;Acc:1479]
Coordinates
chr1:223940498-223943351:+
Coord C1 exon
chr1:223940498-223940658
Coord A exon
chr1:223940659-223943181
Coord C2 exon
chr1:223943182-223943351
Length
2523 bp
Sequences
Splice sites
5' ss Seq
CGAGTAAGG
5' ss Score
6.93
3' ss Seq
CTGCCCCTTTCTGGCTGCAGACA
3' ss Score
9.22
Exon sequences
Seq C1 exon
GATGTCTTTCAGTGACTTCCTGAGGCACTATTCCCGCCTGGAGATCTGTAACCTGACCCCAGACACTCTCACCAGCGATACCTACAAGAAGTGGAAACTCACCAAAATGGATGGGAACTGGAGGCGGGGCTCCACCGCGGGAGGTTGCAGGAACTACCCGA
Seq A exon
GTAAGGGCTGTTGCATATAAGGGCTGTTGCAATGCGGGGCCACCAAAGGCCAAAGCTCCCCTTACCCCACCCTGTGTACCACACCCCAGCCTAGCAGCCCCAGGAGGCAGCTCCTGCTCACTGGAACCCTCTCTGTCTTCTTTCTCCCTGAGCCTTTTCTTTTCCCTGAGCCTTTTCTCCCCGAGCTCTCTTTCTCAATCCCTTACCTCCTGCCCTACCCAGGACAAACCCAAGAGCCACTGTTTCTGTGATGTCCTCTCCAGGCCCTAGATTCCCCAGCGCCCATCATGACCTTCAGCCTGACCTTCCGCCATGCTCACGGAAGCAGTGCTCAATCCCACTTCACGGCCATGAGCTGCTCTATGCACCCCACACCCAGGCAGCCGAGCCTACAAGGGAACCTTGTCCCGGCACCCAGGGAGCCCTCCACATATCAGGCCCTGTTTGTTGCCCCATACTCACTTCAATCAGCAAATGTTGACTGGGCGCTGCCCAGATGGGGTGAAGATTTCTCCTCTGGTCCAGCCTTTGTTGAGCCCCTTGATTCTTCTGCCTTCATGGCTTAGTCCGTCAGCAGTTGTCTGAACATGATGACATCTGCCAATTATGGGGCACACCTTCAGTGCTTGGAACTATCCTAAGTGTTTTGTACACAGGGTGAGGATCCATAATCTGAAAATGTGAAATCTGAAATGCTCCAAAATCCAAAACTTTTTCAGCCCCAACATGATACCACAGGTGGAAAATTCGACACTTGACCTCAGGTGACAGGTCGCAGTCAAAACACAGTCAAAACTTTGTTTCATGCACAAAATTATTTTAAATATGCTATAGAATTACCTTCAGCCTATGTGTATAAATTATATATGAAACAGAAATGAGTTTTGTCATTAGACTTGAGTTCCATCCCTAAGATATGTTATGTATATACAAATATTCCAAAATCCAAAAAAATCCAAAATAGGAAACACTTCTGGCCCCAGGAATTTCAGATAAGGGATATTCAGCCTGCATAACATTCTATCTAACCTTCCCAACAAACTTCTGAGGCAGGCACTTTCTTATCACCTCCATCTCTAAGATGAGGAAACTGAGGCTTGGAGAGGCTAGTGACTTGCTGAAGGCCACAGAGCGTGCTGGGATTTGAACCCAGGCCCCCTGACTGAGGAGTCACTGTGTAAGTACAGTGGCAGCAGATCATGGTCACATAGTGATTCTCTGTGACAGATGAGGAAGCTGAGCCTCTAAGTCGCATACCAGGGCCACAGAGCAAGTAGTCAGACTGCGGCTAGCTGGCCTACAGTTCTGGGGCTCGGACTCCTTCACCTCAAGTATGCAGCCACCAAGTGGCAGTCCCAGAGGCGCTGGGAAGGCCCTCTGCCCCCCACAAGGGACCCCTCCTACCCACTAGATCAGGAGTCGGAAAACTCCCTCTAAAGGGTCAGATAGTAAATAATTTTGGCTTTGTGGGCCACTCAGTCTCTATAACAACAACTCTATTGCTATAACCCAAAGGCAGCCATACTTAAGCGAATGGCCGTGGCTACGTTCCAATAAAACGTTATTTACAAAAACAGGCAGCGGCCTTCGGAGCCATAGCTGCCAACCCCTACACAAGATGGTGCCTGTAATTTCACAGTTAGGGTTTTATCCCATTAGGTATGGAAAGGCAATTAGCATAATTCCCCTTAAACATGAATGAATCTTAGATTTTTTAAATAAATAGGTTTTGGAAGTAAAGAGGGCAGAGACATCAGGAGCAGGGCAAGGGAATAGGCCTGAGAGGACAAGGGACGCAGAACAAGAAAGAGTCTGGAATTATACACAGGATGTTCTTGGCCTCCGGGCTCACCGAGGGGGCGGCGACCGGCAAGTGCAGGGAGCAGATCCCGGAGTCCCCCAGGCCAGCCGAGCCCCGCCCCAGGCTCCCCATCAGAGCCCAGTGAAGAGAAGGTACCATGAGGGGAAGCCACAGCTCTAACCACCCTGCGTTCCAGAGTGACAGACCAGTCCCCAAGACAAGCCAGCCTGGAGCCAGAGAGAGAACTGCAAGAGAAAGTTTCTAATTTAGGTTCCTGTTAGATTCAGACAAGTGCAGGTCATCCTCTCTCCACAGCTACCGTCACCCGTCTCCAGCCTAACAAAGCCTGCAGTCCACACTCCAACCCTGGTGTCTCCCACCTCCTAGCCTCTCCCAACATCGCCTGCCGTCTCTGACCATCTTCTGCCATCCTCTGCCATCTCCCACCATCTCCCACTGTCTCCCACAGCCTCCCACCGCCTCTTGCCAACTCCCACCATCTCCCGCCATTTTCTGACATCTCCCGCTGTCTCCCACCATCTTCTGCCATACTCTGCCATCTCCCACCATCCCCCACCACCTCTTACCATCTCCCACCACCTCCCACCATCTCCCTTTATCTCCATCCCTCTCAGAAGCCTCCAAGCCTGAGACCAGGGCCACCCCCCACCCCCATGCATTCCTGCTCAGGGCTGGGCTCCTCTGCCCCTTTCTGGCTGCAG
Seq C2 exon
ACACATTCTGGATGAACCCTCAGTACCTGATCAAGCTGGAGGAGGAGGATGAGGACGAGGAGGATGGGGAGAGCGGCTGCACCTTCCTGGTGGGGCTCATTCAGAAGCACCGACGGCGGCAGAGGAAGATGGGCGAGGACATGCACACCATCGGCTTTGGCATCTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909-CAPN2:NM_001146068:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.036 A=NA C2=0.053
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.9=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:
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)