HsaINT0027459 @ hg19
Intron Retention
Gene
ENSG00000092529 | CAPN3
Description
calpain 3, (p94) [Source:HGNC Symbol;Acc:1480]
Coordinates
chr15:42691690-42694008:+
Coord C1 exon
chr15:42691690-42691850
Coord A exon
chr15:42691851-42693838
Coord C2 exon
chr15:42693839-42694008
Length
1988 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
CTTCCTTTCTGGGGGTGCAGATA
3' ss Score
6.03
Exon sequences
Seq C1 exon
GATGTCCTATGAGGATTTCATCTACCATTTCACAAAGTTGGAGATCTGCAACCTCACGGCCGATGCTCTGCAGTCTGACAAGCTTCAGACCTGGACAGTGTCTGTGAACGAGGGCCGCTGGGTACGGGGTTGCTCTGCCGGAGGCTGCCGCAACTTCCCAG
Seq A exon
GTGGGAGATGCTCTTGATGGGGGGAGGGTCTAAGCCGAAAAAGTTCCAGGCAGAAGAAGCCTAACTAGTGCTTATTAAGTCTCTCTGTTCCAGACGTCCACTATCTTATTAAACCTTCCCTGTTTTACTGAGAAGGAAACCACCATGCTGAGAAGTTTGCAATAGGGAGCTGGTAGCAACTTTGAAGCAGGAAACTGTGGGAACAATGCAGATGCTGCTTGACTTACGATGAGGTTATGTCCAGATAAGCCCATCCATCTTTGAAAATACCCTAAGTGAAAAGTGCATTCAATATGCCTAACCCACCAAACATCATAGCTTAGCCTGGCCTACCTTAAACATGCTCGGAACACTGACCTTAGCCTAAAGTTGGGCAAAATCATCTAACTCAAAGCCTATTTTACAAGAAAGTGTTGAATATCTCATGTAACTTACTTAATACTGTACTAAAAGTGAAAAACAGAATGGTTGTACGGGTACTCGAAATCCAGTTTCTACTGAATGTGCATCTCTTTCACATTGTAAAGTTAAAAAATTGTAGCCGAACCATCCTAAGTCAGGGACTGTGAGTACTGTGTCAGTAACAGTAAGGGCACTATTGGAGAACCAAGTTAGCAGCTGCTGCAATAGTTCAAGTCAGAGATGATGAAAACCTAGACCAAGTCAGTAGCAGCAGAGATGGAGGGGAGACAGCAGATTTAGGGAGAGCATATTGGGTGATGTAGGGAAGGAAGAAGAATGATGTCAAGATTCCCAGTTGGGGACCTGACAACATTGCAACATAAGACACACAAGAAGATCGGGTGGGTGGCTCATGCCTATAATCCCAGCACTTTGGGAGGCAGAGCCAGGAGGATCACTTGAGCCCAGGAGTTCAAGACCAGCACAGGCAACATAGTGACACCTCATCGTTACAAAAAATAAAAAAAAAAATGAGGTGGGAGGATTGCTTGAGCTCGGGAGGTTGAGGCTACAATAAACTGTGATCATGCCACTGCACTCCTGCCTGGGTGACAGAGTGAGACCCTGCCTCAAAAAAAAAAGACACACAAGAGAAAAATATCAGCGTGTTGTTTGTTTTTGGTGGAGTTAATTGTGGGGTTCTAGGGAAAGGAATTTAGCTTGGGACATGGAAAGTTTGAGGTTCCTGTAGAGTGTCCCAGTGAAGATTTGTAATAGAGCATCGGATGCGCATATTAGATGGCACTTGGTGATATGATAAGAACTCAAAAAATATTTGAGGAATAAAGGAAAGAAGAGGCCAGACGTGGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCAGGCGGATCACTTGTGGTCAGGAGTTCGAGACCAGCTTGGCTAACATGGTGAAAACCCATCTCTACTAAAGATACAAAAATTAACCGGGGATGATGGTGGGTGCCTGTAATCCCAGCTACTTGGGAGGCTCAGTCAGAAGAATCGCTTGAACCCAGGAGGCGGAGGCTGCAGTGAGCCGAGATCGCGCCACTGCACTCTAGCCTGGGCAACAGAGCCAGACTCCGTCTCAAAAAAAAAAAAGTGAGAGAGATTGAGGCTGGGATATATGGCTCAGGCATCATGCGCGTGTAGGGGGCAGTTAAAAAGCAGAAGTAAGAAAGATTGCCTAGGGAGGCAGGAAGGGTGAGGTGAGAGGAGAAGAGGCCCAGGACCAGATTCTAGTCACCAACAGCGTTTAAGGGGCAGGTAAGGAAAACAAAACCATCAGCAAAGACTGAGAATGAAAGCCCAGAGAGGAAGGAAAAGCCACACATACAATCAGTACAGCTCCATCTGAATAAAGGTAGCGCCCCCCCCCCCCCCAAATCATTAGAGAAATGCCTGAATCGTGTTTTCTGTTGATATTTCCTAAGCACCTAGATGTAGGGAATAGAAATAAATGGCTCCCTCTGTCTCATCCCCTTCCTGCCCTCTGAGAGGCAGCTGTGAATGCGTGCTTCCTTTCTGGGGGTGCAG
Seq C2 exon
ATACTTTCTGGACCAACCCTCAGTACCGTCTGAAGCTCCTGGAGGAGGACGATGACCCTGATGACTCGGAGGTGATTTGCAGCTTCCTGGTGGCCCTGATGCAGAAGAACCGGCGGAAGGACCGGAAGCTAGGGGCCAGTCTCTTCACCATTGGCTTCGCCATCTACGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092529-CAPN3:NM_024344:10
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=PD(12.8=34.5),PF0106717=Calpain_III=PU(15.5=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(36.8=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:
TCCTATGAGGATTTCATCTACCATT
R:
CAATGGTGAAGAGACTGGCCC
Band lengths:
310-2298
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)