HsaINT0027449 @ hg38
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2 [Source:HGNC Symbol;Acc:HGNC:1479]
Coordinates
chr1:223745306-223747165:+
Coord C1 exon
chr1:223745306-223745439
Coord A exon
chr1:223745440-223746996
Coord C2 exon
chr1:223746997-223747165
Length
1557 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
CGTCTAATCCCCTCTTGTAGGAT
3' ss Score
9.32
Exon sequences
Seq C1 exon
TTCTGGCAATACGGCGAGTGGGTGGAGGTGGTGGTGGATGACAGGCTGCCCACCAAGGACGGGGAGCTGCTCTTTGTGCATTCAGCCGAAGGGAGCGAGTTCTGGAGCGCCCTGCTGGAGAAGGCATACGCCAA
Seq A exon
GTAAGTTGCCATCCTCCCCTGGCCCCATGGCCTTCCCCCAATGCCCTGGATTCCAAAAAATTCACTCATGCCTGTAATCTCAGCACTTTGGGAGGCCGAGGTGGGTGGATCATTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCGTCTCTACTAAAAATATAAAAATCAGTAGAACTACTCCAGGACTACTTTGAGTGGGAAGTCCTTTTCTATAGAAGGACTTCTTTGGCCAAAATTAGGCTCTAAATGCAAGGAGATAGTGCATGCAGGGTGCCTGGCTGCACTGTACGCTGATAAATGATGTCTATCACCATCTTTAACCAAATGCACAGGAACAAGTTATGGTACTGATTGTGCTGGACTTGAGAAGGAGCTCTACTTCCTTGACAGGACACATTTGTATCAACTTAAAAAAGCAGAATTTTTGCCAATGGGCAGAACTATTCATTGCAGAGGTAGGAAACTTGCCCAGAATAGATGATGTCACTGATTAGCAATGGCTTCCCCATCTCCGCACAGCTGCTTCCCACCCAGGTTGCCCACAGTTGAGTTTGTCCAGTGCTCAGGGCTGCCCACTCTCAGTAAGAAGCCCCACACCAGCCCCTCTCCACAATGGCCCCATGTTGGCTGTGCCGCCCGGCTCCTTCCATTAAAGTGACCCCACTTTAGAGCAGCAAGTGGATTTCTGTTTCTTACAGTCCCAATCCAGGAAGGAGGAGTCAGCTGTGAGAACCTGGAGCCTGACGGATGCTTCTAAGTCCCACTGCTCAATACTGGGGTCAGGGAAGCCACCGGACTCCAGCATCAGCAGTCAGGAGCACTAAGCCCTTGCCAACACCGTGCCTGTTTCTCAGAGAAACTGCTTCCATTATTGAATGGTTGTCCTTTTTTAAGCTATCAATGCCAAACGACCCATTAGTAGACCTCCCCTTTCTTGTCAGGATGTAGAAGGAATCAATACAGGAGGTTCATCCAGAAAATCACTAAGGTCCTTCCGACTCTAAGGTTCTACGAGAATCTTTTTTTTTTTTTTTTTTTTTAATACGGAGCCTCATTCTGTCACCCAGGCTGGAGTGAGCGGCATGATCTCAGCTCACTGCAATTTCCACGTTCTGAGTTTCAGCAATTCTTTTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATGCACCACCATGCCCAGCTAATTTTTTTGTATTTTTAGTAGAGATGGTGTTTTGCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAAGTGATCCGCCCACCTCGGCCTCCCAGAGTGCTGGGATTACAGGCATGAGCTACCGCGCCCGGCCTGAGATTTTCTTTAAAACACAAAATACCAGGGAAATGGTAACTGTGGACATTATACCTTGCCTTCCTGAGCACCCCGAGCTGGGAACAAGGCCAAGGAGAATGTGAGCAGGGGGTCCCTGGAGCATCAAATCTAGACGGTACTAGGGGGTGGCTGTTTGAGAGATTATAGCATCAGTAGTGTCAAGGGTAGCGGCAGCGTCTAATCCCCTCTTGTAG
Seq C2 exon
GATCAACGGATGCTATGAAGCGCTATCAGGGGGTGCCACCACTGAGGGCTTCGAAGACTTCACCGGAGGCATTGCTGAGTGGTATGAGTTGAAGAAGCCCCCTCCCAACCTGTTCAAGATCATCCAGAAAGCTCTGCAAAAAGGCTCTCTCCTTGGCTGCTCCATCGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909:ENST00000295006:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.002
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(14.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(18.7=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:
TTCTGGCAATACGGCGAGTG
R:
TGGAGCAGCCAAGGAGAGAG
Band lengths:
298-1855
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