HsaINT0027553 @ hg19
Intron Retention
Gene
ENSG00000135773 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:1486]
Coordinates
chr1:230921727-230923348:+
Coord C1 exon
chr1:230921727-230921763
Coord A exon
chr1:230921764-230923267
Coord C2 exon
chr1:230923268-230923348
Length
1504 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TTTCTTTGGCTGTTTTTTAGCCT
3' ss Score
7.28
Exon sequences
Seq C1 exon
GGATATGGATGGAAATGTAGACATTGACCTTCCTGAG
Seq A exon
GTGAGTCTTCTGATGTTGCTATGGAGTATGGGATTCAGGTGATGGTTCTGGAAACCTTCCTTCTAATCACAGCATCATGTAAAACTCTGCAGTTCAGGGATGGTTACATGCAATCAAGTAAGCATCTATGATTCTAACCTCCTGGAGACCAAGATGTGTGTGTTCTAGTCTGTGCTCTTCTAGTCCACAAGGACCTGGCATGGGAGTGAGGTGGGTGCTTGGTATAAAGTTCTGTTCGATGTCATCTTCCTCTGTGCTACTGTCAACTGAAATAACAAACACAGAGACACTCTCTAAAAGAAAAGCTATTTATTTAGGGATAAAGCACTGCAATGGGAAGGTGCATGCCATAGTAAACTATGCACCTATTTGGGGAGGTAAAGGAGGACAAAGGTTTTTAAAGAAAAAATGAGAAGGATTACATAATTGTTTTGAAATAATTATCCTTGGCTACAAAGATCAATAACAAAAGTGAAGCCAGTCTGATGTTGGACAGGCAGTTGCTAGGCAGAGGTAGAAGTATTTTTGTGTATGGTTGCGAGGGCCTCTGTGAAAGGTTGTGGGTTTTGCAGCCTTTTGTGATATTTTTGTTATCAGGCAAATAAGCATGAGAACCTTCTGGCCTTCCCGAGCTCTATTTGTCAGGGTTTTCTTAACATTAGTGACTTCATTTTGACTCAATAACTTTCACACTACCAACTCCACCTGAGAGAAGGCTGCCGCTTCTGAAGTGGGTAGACTTTTAATTGTATTTTAAGAAATCTAATCAATGAAAAGAAAACCAGAGAGGCAGGGAGATGTTTTTTACTGTGGACTCAGGGGAACACATTACATCTCCCCTATGTTATGTGGTGTGGAAGGGGTGACATGGGGGTGGCTTTACCCTCGTCCAAGGGCTGGAGGACTCGCAAGAGGCCCTGAGATACTATAGCTGGAAATAGTCTGACACGTCCAGGGACAGCAGAGATCTGCTTTTAGGAGGGAATTTGCTGTTCCATGCTGGGGCACAGCTTATTAATGGTGCTAAAAAACCAAAGAAACCAAAAATCACCCAAAACATTTACTGAGCTCTTTCTATATACCAAGCCCAGAGCTTAGTGGTAGAAACAGACTCTTGCCTTCAACGATTTTACCAGCTATCAAAACAGATGATGAAGTAAGTCATTCCAGTCCAGGGTGGTAAGAAGTAAGCCAGAGGAAGGGCAGGAAGCATGAAAATCCAATGGCCAGGACCTAACTTAGGCACGGGTCAAGGTCCTTTGGCCTCCTCGTCTGTAAGGCAGAAGGGCTCCACAGGTCCAGCTAATAAAGTCCTTCTAGTCTCACCTTCTAAAAGAGCCTTCATGAGAAAATGTTCCTCACGCTACAGGACGCAGCTTGTGCACACTGCCTCAGGAGGGTGACATGGGGCTGGGCACACAGGCTCCTGGCTTCTTTCCTGCTATTTTTGTCATGTTTCTTTTTTGTGGATCATTTTGTGCAAGTTTCTTTGGCTGTTTTTTAG
Seq C2 exon
CCTCCAAAGCCAACTCCACCTGACCAGGAGACAGAGGAGGAGCAGCGGTTTCGGGCTCTGTTTGAACAAGTCGCTGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135773-CAPN9:NM_016452:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.769 A=NA C2=0.630
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=PD(0.1=0.0)
A:
NA
C2:
PF138331=EF-hand_8=PU(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)