HsaINT0027563 @ hg38
Intron Retention
Gene
ENSG00000135773 | CAPN9
Description
calpain 9 [Source:HGNC Symbol;Acc:HGNC:1486]
Coordinates
chr1:230767541-230769263:+
Coord C1 exon
chr1:230767541-230767709
Coord A exon
chr1:230767710-230769179
Coord C2 exon
chr1:230769180-230769263
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:ENST00000271971:5
Average complexity
IR
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