HsaINT0027473 @ hg19
Intron Retention
Gene
ENSG00000092529 | CAPN3
Description
calpain 3, (p94) [Source:HGNC Symbol;Acc:1480]
Coordinates
chr15:42678365-42680084:+
Coord C1 exon
chr15:42678365-42678483
Coord A exon
chr15:42678484-42679950
Coord C2 exon
chr15:42679951-42680084
Length
1467 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGCGTGACGCTTCTGTGCAGTTC
3' ss Score
5.18
Exon sequences
Seq C1 exon
GGGACTGCTGGTTTCTCGCAGCCATTGCCTGCCTGACCCTGAACCAGCACCTTCTTTTCCGAGTCATACCCCATGATCAAAGTTTCATCGAAAACTACGCAGGGATCTTCCACTTCCAG
Seq A exon
GTGAGGTAATGAGAGTGTAGTTAAGAGGGCCAGCGGCAGGCCACCCACCGCTGGTCTCCTGGCCTTGACTTCCCAGAAGCTGGAGGAAACTTCCCACCCATCTACCCGCAGCGGCAACAGTCGGCATGGACCCCCTTAAGGCTTCAAGCCTGGGAGGAAGCAGTTGCTTATCTCTGGCTCCCTAATCCCTCCCCCACCACCTTCCACTATGTCCCAGAAAGACAGGAAGACATCCTGTTTACTGTGGGTCTATTTTTGTCTTTGCAGCTGTCTGGCTGCTTTTATTGCCTGCAGCCCTTCTCAAGTAGGTCCCTAAGATATTAGCACTGTGACACCACAGGACCCTTCAGGTTGTACAGGAACCCCTGTCCAGGGCTCCTGTATACTTCTTCCTCTCTAAGGCATGGCGGTACCAAGGCTATCACTCCTCTCTTCCAAGCCCTGGAAGAAGAGTCTGCTTAACCTGGGGATCAGGCTTCTTGTTTGCCCTAGAACTGAATCTGATGGTTCTAGAATCCATCCAGCTACTGGAAATTTTCTGGGTCCCAGTCACCTTGGCATAGAGCTGGTGCTAGAGCAGAACCAAACTGAATTCTACCTGTGAGGGTCTCGTAGCTTCCGGGATGCTGGGGAGTCAGCCTGTCTCCAGCTTCAAAGGCTCCCTCATGTCCCAGGATGACCCACATTATCAGTTCTTGCTCCCCGGGTCTTGCACCTCAGCACGGAAGGCCTCAGAAAAGGTCTGTCTCCAGGCTCAGACTCCCCCTCCTGCCGCCTTGGGAACATGGCATATTTAAAGGGTCTCAGATCTAAAGGGCCTTACATACAAATATCAGATAGATTTCTGTTCTCATTTCAATGAGGGAGAAAGTGCCATTGAAAAGGAGACTAAACCACATTTGGCCCTTTTCAGTTCAAACTGATTCATTCAAAAAAGAGCGACATCCAAACTTGAAATGATTGAACAATGTTCCTGCTACAGCTAGAATAGATTCTGGGTCACTTTGTTCCTCCGTTTCAATCCTTGTTCTTCAGTTTGGCATCAAGAAATACCTAAATCAGCACAGTGCCTTCACTGCATAGTTCCCAATCCTGGCCACATTGAATCAGCTGGGGGCACCTGAGAGTGCTGACACCCAGGCCCTGCCCCAGACCTGCTGAGCAGGAGAATGAAAATCTTACATCCTAAGACACTCATGGAGCACCTACTCTACCCATTACTGGGCTGGACTCTGTGGAAGACATGAAGTATATGTAACTCACTTCCAGCTCTCAAAAAGCACCCAGTCCAGTTAGAGACAGATTTACACACCCCAAACACAAAATAGGATGAACAGGCACCCAGATGCAGAGTCCAGGAAATGATGCTGCTTTGGGATTCAAGAACCCCCTGAGGAATGTGGAGGAAGGACACATTTCCTAACAGTAATTTGAGTATGTGACTCTGTGCGTGACGCTTCTGTGCAG
Seq C2 exon
TTCTGGCGCTATGGAGAGTGGGTGGACGTGGTTATAGATGACTGCCTGCCAACGTACAACAATCAACTGGTTTTCACCAAGTCCAACCACCGCAATGAGTTCTGGAGTGCTCTGCTGGAGAAGGCTTATGCTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092529-CAPN3:NM_024344:3
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(19.1=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(21.6=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:
GGACTGCTGGTTTCTCGCAG
R:
TAAGCCTTCTCCAGCAGAGCA
Band lengths:
246-1713
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)