HsaINT0027566 @ hg19
Intron Retention
Gene
ENSG00000135773 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:1486]
Coordinates
chr1:230914719-230916082:+
Coord C1 exon
chr1:230914719-230914879
Coord A exon
chr1:230914880-230915924
Coord C2 exon
chr1:230915925-230916082
Length
1045 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CTACCTCTCCCAAATGACAGATA
3' ss Score
6.22
Exon sequences
Seq C1 exon
GATGGCATTTAAGGACTTCAAGGCCCACTTTGATAAAGTGGAGATCTGCAACCTCACTCCCGATGCCCTGGAGGAAGACGCGATCCACAAATGGGAGGTGACGGTCCATCAGGGAAGCTGGGTTCGCGGCTCCACGGCTGGGGGCTGCCGCAATTTCCTGG
Seq A exon
GTAGGTAGGCTGCCTGTCACTCTCTCTGCCACTCCCAAGTGTCCCTTCCAACTCAGGACACCAAAGGATAAGGGCCGGGTCCTCAGAGAAAGCCTGAAACATAGTAAGGTTTCAAAAGTGACTGGGGAAAAAAGGCTGCAAAGATTTAGTTGGATAAGAATTGTTTGGGGAAACCTCCTTTGTTTTACCACTTAGGTTATTTTCCATTACAAGTAATGGAAAGCATGACTCATGCCAGTTTAGCAATAGAAAGGATTTGTTATCTCACATAATTGAAGAGCTCAGAGGAAAAGTAGGGTGGGCTTCAGGCACAGTTCTATCAGGGCCCTGGTTCCATTTGCTTGTAATTCACTGTTCTGCCCTCTTTTATGTGTTGACTTCTTTCTCTGTCTGGCTTTCTTTATAATCACAGGAGGGCTGGCAGCAGTATCCAGGGCTTCCTGAGCCCTCATTCACACGAACAGCAAGAGCTCCTGGGGGTATCAAAAAAAAGCCCTCAACTTCCCTCTAATTGGAAATTCCTTGAACTAATATTGTCCAGTGAATGCTATGCATTGATTGGCTTTGTCCAATCCTCGGTGGCAAAAAGGACTGGCACAGACCAATCAGAATTCATGCTGGAGCAGTGCTCGAGGTCAATCCTACTCAAACGGCCCACCATCAAGTAGATGCCAGGGGGACAACCAGAAGTCCACTGCACTCTCCTTTGAAATACTAAGTGGAAAAAAAACTGATAGAACAAGCTTTAGCAGACTAGACCCAGAAGAATGTCCTTAAGAAACTGCATAGGAAATGGTTGAAGAGAAGGTGGAAATGAAAGAGAGGATATTTTGCATTCCCGTTGGGGATTATCAAAAGTAGGGTAGGAGGACTTATTGAACAGGGAGAGAAGGTATTACTTTCTCATGTTTGGTAGGACATATAATGAGGGCAGATAGGTGTATGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTCTTTGTGGGTTGTTTTTTAAAAGGGGAAAATAATCTACCTCTCCCAAATGACAG
Seq C2 exon
ATACCTTTTGGACCAATCCACAAATAAAATTGTCTCTGACTGAGAAAGATGAGGGGCAGGAGGAGTGTAGTTTCCTTGTAGCCCTGATGCAGAAAGATAGAAGGAAACTCAAGAGATTTGGTGCCAATGTGCTGACAATCGGCTATGCCATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135773-CAPN9:NM_016452:8
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(6.4=34.5),PF0106717=Calpain_III=PU(16.3=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.4=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:
GATGGCATTTAAGGACTTCAAGGC
R:
GGCATAGCCGATTGTCAGCAC
Band lengths:
310-1355
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)