HsaINT0027453 @ hg38
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2 [Source:HGNC Symbol;Acc:HGNC:1479]
Coordinates
chr1:223751997-223752956:+
Coord C1 exon
chr1:223751997-223752071
Coord A exon
chr1:223752072-223752795
Coord C2 exon
chr1:223752796-223752956
Length
724 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
ATTGTCTCTGCTTTTGCCAGGAT
3' ss Score
7.43
Exon sequences
Seq C1 exon
CTGCCCAAGCTGGAACACTATAGACCCAGAGGAGAGGGAAAGGCTGACCAGACGGCATGAAGATGGAGAATTCTG
Seq A exon
GTAAGATTAGTGGAGGCTTCAGGGAAAGCTCTGTCTGCCCCAATGTTCTTTACTAGAAAACTGCTAATTAGAAAGAGTGTCGGCCAAAGTGAGTTTACCATGTCGAGGACACAAGCGTGTGGGATCCTGGTTTTGTTATTTTAAGTTCACTATAAGAGCCTGAATAAAGAAATTCTTAAGCCCCTTCAACGGTCCATCTTGACAATGGGGTTTATAAGCTGAGCAGCTTCAGAAAAAGGCTAAGAGGAATTCCTTTGGTAATGTTCAGATCCCAGGAAACAAGGGAAAGATGGGGCCTTTCTCCCCCAGGTTCCGGAGACTCATCCCAGCCCCTTAAGAAACTGGTCCCTTAGTGAGCAGCAATGGACCCACATGTCTGTGTGTCTGCGCCACTCTATAACCACCTGCACCTGGACACAACATGCTCTTTATCAAATGGGGCCCATATATTGTCACATTTGATGGGCACGGCTCCCATTTTTGCAGGTGAGAGTTCTGAGCTTCAGAGAAGTTTAAGTAACCTGCTCAAAGTCACCCAGCTAGAAAGTTGCAGCGCCAGGACTGGAATCTGGGCCTTCTGATTCTGAACCTGGTGCCCATCCACTCAGTTCTAATGAGCTGCTCTGCCTGGCTTTGGGTGGCTCCTGGTCTGGTGTTGGTGGAAAGTCAAGGCTTACCAGTGTGTCTTCTTATCACCTGTGATGATTGTCTCTGCTTTTGCCAG
Seq C2 exon
GATGTCTTTCAGTGACTTCCTGAGGCACTATTCCCGCCTGGAGATCTGTAACCTGACCCCAGACACTCTCACCAGCGATACCTACAAGAAGTGGAAACTCACCAAAATGGATGGGAACTGGAGGCGGGGCTCCACCGCGGGAGGTTGCAGGAACTACCCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909:ENST00000295006:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.346 A=NA C2=0.029
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(8.3=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
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:
CTGCCCAAGCTGGAACACTAT
R:
TCGGGTAGTTCCTGCAACCTC
Band lengths:
236-960
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