HsaINT0027469 @ hg19
Intron Retention
Gene
ENSG00000092529 | CAPN3
Description
calpain 3, (p94) [Source:HGNC Symbol;Acc:1480]
Coordinates
chr15:42676681-42678483:+
Coord C1 exon
chr15:42676681-42676750
Coord A exon
chr15:42676751-42678364
Coord C2 exon
chr15:42678365-42678483
Length
1614 bp
Sequences
Splice sites
5' ss Seq
TAGGTAGGA
5' ss Score
7
3' ss Seq
TGCCCTGTGTCTGCCTGCAGGGG
3' ss Score
11.68
Exon sequences
Seq C1 exon
GAAATTTGCGAGAATCCCCGATTTATCATTGATGGAGCCAACAGAACTGACATCTGTCAAGGAGAGCTAG
Seq A exon
GTAGGAAAGTGCCTCAGGTCAGATCCTGCCAGATGATCAAGGGGTGATTACAAGGTGTGATCCCCTTCCAGGAGGTAAAGGGACAATCTGTGCTTGCTTCCAGTAACTTTTTGGAAGATTTTTTATAACAGTTGCTTTATGGTCGTTTATCTACATGCTGGCGATTGCTTCATTTCCTCCTACATGCCTCTTTAGCACTCTGCCATGCATCACAGGGGGTATCTGCATCCTGTGGCCTCCTCTCCAGTATCTCAAGGACACTTACATACCCCACTCAGCATGACAAAAGCCCTGCTTTTCACTGTATCGTCTTTCTTGGAAGACAGCTCTGTGACTGTGCACCAAGCATGCCCCTTGGGCATGGAGATTCTAGATACACACACAAAAGGCATCGCCAAGGAAAGCACTTGTAACTGGAACCCTTGTTTAAATTGCCCCAGCATAGCTCCATCTTAAAAGAGTCTTTCCACAAAGATGGCATCCGCCATGTGGATGAGCATCCAATTTTCTCTTTGATTGGTTAGCTTGACTGCTCCATCTGATCTTCCTCTCTCTCGACCTCTTGTTCAGAAAGTATTGTCTTTGGTGTGGACTATAAGCAAGCTCTGTGAAGTAAAATTGGAGAGAACACCAACAGAAACAATTTAAATTTGAGGAAAAGGGGGCACCTAAGACCAAAGGAATTTGGCTTATTTCATTCCAGAAGGGGAGGCTGAGAATAAATCAGATGAATATCTGGGTTCCTGCACCTGAGGGAAGGCTTCCTGCAGAGCCCTGGGCATAATAATCTGGGACCTTCAAACCAATAACCTCTTTCCAAGGAAAGACTGGCTGCTTCCAAGGAGGGTAGGGGAGAGTGGCTGCAGGCAGCTCTCAGTCTCCCCTGCACACTCTCAGTTGCATTTCACTTAACCCATCCTCCTTAGAAGGCAGCTCTGTGACCAGGTACACCCCCTATTATATATATATATACACACACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGCAAAGTGTTACCTCCAACTACATACAGTACTCTGTCAGAAAAGAGGTTCAGAGAATAAGAAAACGTCCCGAGCTCATTCCGTTGCCAGCAATGTCTTACTGCCCCCTATAGACGGGTTCCAGGGCAGCTGCCTACCTGGCCTTCCTTCCAATACAAATCATCTTGGTGGATGGTTCTCTGAGGCTCAGTCTTCGCTGAAGTCAGAAGAGGAATTGGACTCACATTGCAAAGGCACAGGGCAGGGCAGATTTCCTACAGGTGTTAGGAAGAACAACCCAGTTATGATCACCTACTGCTCTGTCTCCATTGAGGCCTAAAAAGGAAGTGAGTTTATACTGCAGTTGGAGGAACTGCCTGCAGCCTTGAGGAAAATGTCTAGTCACAAGGGAGTAAGTTACCTGTTGATCATATTGTCAAGGAATTCCTGTCCAATTCTCCTTCCCTGGGTTGACACCTCTGTAAGGTCAGATCTGGAAGTAGGAGAGTGGGCACCAAGGGAGTCCCCGTTCAGGGAAGTGGAGTGGCTGGCTGGGATTGGGGCTTTTTCTTCCCAGGAGGAGCAGGAGTGCTCACGATCTGTGCCCTGTGTCTGCCTGCAG
Seq C2 exon
GGGACTGCTGGTTTCTCGCAGCCATTGCCTGCCTGACCCTGAACCAGCACCTTCTTTTCCGAGTCATACCCCATGATCAAAGTTTCATCGAAAACTACGCAGGGATCTTCCACTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092529-CAPN3:NM_024344:2
Average complexity
IR-C
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(11.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(19.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAATTTGCGAGAATCCCCGA
R:
AGTGGAAGATCCCTGCGTAGT
Band lengths:
184-1798
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)