HsaINT0027563 @ hg19
Intron Retention
Gene
ENSG00000135773 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:1486]
Coordinates
chr1:230903287-230905009:+
Coord C1 exon
chr1:230903287-230903455
Coord A exon
chr1:230903456-230904925
Coord C2 exon
chr1:230904926-230905009
Length
1470 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
CTGCTCTTTCCATGTTTTAGACC
3' ss Score
9.14
Exon sequences
Seq C1 exon
GCTAAATGGGAGCTATGAAGCTCTGAAGGGAGGCAGCGCCATCGAGGCCATGGAAGACTTCACTGGGGGTGTGGCAGAGACCTTCCAAACTAAAGAGGCCCCCGAGAACTTCTATGAGATTCTAGAGAAGGCTTTGAAGAGAGGCTCCCTGCTGGGCTGCTTCATTGAT
Seq A exon
GTAAGTTGCTCATGGGCTCCCATTCCAGGCACTATGCTGGGGCTGCATAGTGCATTCCAGGCACTATGCTGGGGCTGTACCAGGTACCCCAGCCACACCCAAGGAGGGGCATAACTCTTGGGGGCAGTGTTTATTCCTGCTAATTAAAACACAAGTTTTGGGGGGAGGTGGGAGGGATAGCATTAGGAGATATACCTAGTGCTAAATGACTAGTTAATGGGTGCAGCACACCAACATGGCACAGGTATACATATGTAACAAACCTGCACGTTGTGCACATGTACCCTAAAACTTAAAGTATAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAATAAAAAATAAAATAAAATAAAATAAAAATAAATAAATAAAACACAAGTTTTAACCAAGCATGGTGGTGTGTGTCTGGAGTCTGAGGCAGGAGGATCCCTTGAGCCCAGGAGTTTGAGGCCGCAGTGAACTATGATCGTGTCACTGCTCTCCAGGCTGGGTGACAGATCAAGACCCTGTCTCTAATAAATAAATAACAAATAAAACACAAGTTTTTATTTAATAGTCGTCAAATAACAAAGGTAAGATGTACTTGCTGTATCAGATGGAACAATCTTGAGGCCCATACAGGCGCATTTTTACCTCCCTCCCACCCGTTTCTCAGCTGCCTCTGTTCTCCAGCTCCACCCTGGGACTGGGATCACCTGGCCTGTATCCTTCCCAGCTCTCTATCTGCTCGTACAAACAGGCACACACTTCCACACACAAACATCAAGGTCAGTTGGTTTGATTTTACTGAAACGGGATCTTCCTATCTAGTTTTCTGAAATTTGTTTTTTTTTTTTCATTTCATGTACTATGAAAAAAATAGCAGATAGAAGTCTAATGATATTTTTTAAAATTTTCTCTATGCATACAAACACACACACTTATAATTTTATCTCATCTTTTTAAAACTTTTTGTTGTTTTTTATGGACTGCTATGACACTATGTATTTTTTTTAATCAATTCTAGTTTTCTGTTTCCTCTTAGATTAGCCTTGGGGTCTGTTTTTTGCTAATGAATTAGCCAGTTCCTCTGCACTTTCAGGTTTGTGACGCAGAGCTGTGTGTCCTGTTGTTATATTCTTCTTTTCGTCTCTGGGATGTATGTGATTGTGTCTTCTCTCTCACACTATACTACATGAAGGTGACAAGTTGTTCTGTTTGGGGACAAAATAGTGAACTGTTCTTTGGAGTCCACACTGGAAGCGAGCGCCTCCCCATCCTGGGAAGAGACTGGAACTTGCTTCATGTCACTGCTAAACATCCTAGGGGAGCCCCGTGCATAGCCCACGCACATGGCCTGCACCTGGGGCAGCAGAAGGGGCTGGAGGTTGTGACCGGGCCAGGCATGTAGCTGGGTCTGATCCAGCAGGGGAGGCTTGACTTAGACGGTGGGTGTGACTCTGCTCTTTCCATGTTTTAG
Seq C2 exon
ACCAGAAGTGCTGCAGAATCTGAGGCCCGGACGCCGTTTGGTCTTATTAAGGGTCATGCCTACAGTGTAACGGGAATTGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135773-CAPN9:NM_016452:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(18.9=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(10.7=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:
ATGAAGCTCTGAAGGGAGGCA
R:
TGGTCAATTCCCGTTACACTGT
Band lengths:
238-1708
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)