HsaINT0027472 @ hg19
Intron Retention
Gene
ENSG00000092529 | CAPN3
Description
calpain 3, (p94) [Source:HGNC Symbol;Acc:1480]
Coordinates
chr15:42703485-42704515:+
Coord C1 exon
chr15:42703485-42703543
Coord A exon
chr15:42703544-42703944
Coord C2 exon
chr15:42703945-42704515
Length
401 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
GATCTTGGGACTTCTTTCAGTGG
3' ss Score
4.86
Exon sequences
Seq C1 exon
GAGCTTTTCATGCATTTGACAAGGATGGAGATGGTATCATCAAGCTCAACGTTCTGGAG
Seq A exon
GTAAAGCATAGGCACAGCACATTCCCCCTACACATTAAAACTCAAGGTGGAGGGGTCAACGGGGCGGACTGGACCCAGGGTGTGCTCCTCATTTCCACACAGTGGTGGAGGGAAGGGATAGGAACAGAACATGGAGGGAGGCTCAGCAGGCTCCCAGGACACATGCACTTGAGGCCCAAAAGGACCTCTGCTCCCCCAGTCACTTGATGCGGGAAAACATGCACCTTCTTAGGGAAGATCTAGGAGAAAGGAAACAGTAAGCCACTGCTTCTTGGAAAATCTTCTGGGGGTCTGACCTGCTGGGACTGTTCCCTTTCCTCTTGCCCCGTAAGATTCCTAGGGCGGGGGGGGGGGGGGTCACTCTTTTCTGATCTACATTCTGATCTTGGGACTTCTTTCAG
Seq C2 exon
TGGCTGCAGCTCACCATGTATGCCTGAACCAGGCTGGCCTCATCCAAAGCCATGCAGGATCACTCAGGATTTCAGTTTCACCCTCTATTTCCAAAGCCATTTACCTCAAAGGACCCAGCAGCTACACCCCTACAGGCTTCCAGGCACCTCATCAGTCATGCTCCTCCTCCATTTTACCCCCTACCCATCCTTGATCGGTCATGCCTAGCCTGACCCTTTAGTAAAGCAATGAGGTAGGAAGAACAAACCCTTGTCCCTTTGCCATGTGGAGGAAAGTGCCTGCCTCTGGTCCGAGCCGCCTCGGTTCTGAAGCGAGTGCTCCTGCTTACCTTGCTCTAGGCTGTCTGCAGAAGCACCTGCCGGTGGCACTCAGCACCTCCTTGTGCTAGAGCCCTCCATCACCTTCACGCTGTCCCACCATGGGCCAGGAACCAAACCAGCACTGGGTTCTACTGCTGTGGGGTAAACTAACTCAGTGGAATAGGGCTGGTTACTTTGGGCTGTCCAACTCATAAGTTTGGCTGCATTTTGAAAAAAGCTGATCTAAATAAAGGCATGTGTATGGCTGGTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092529-CAPN3:NM_024344:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0003627=EF-hand_1=PD(84.2=84.2)
A:
NA
C2:
PF134051=EF-hand_6=PD(11.1=33.3)
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:
TCATCAAGCTCAACGTTCTGGA
R:
CAAGGTAAGCAGGAGCACTCG
Band lengths:
356-757
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)