HsaINT0027448 @ hg38
Intron Retention
Gene
ENSG00000162909 | CAPN2
Description
calpain 2 [Source:HGNC Symbol;Acc:HGNC:1479]
Coordinates
chr1:223744100-223745439:+
Coord C1 exon
chr1:223744100-223744218
Coord A exon
chr1:223744219-223745305
Coord C2 exon
chr1:223745306-223745439
Length
1087 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
CCACCTCTCTTGTTCTGCAGTTC
3' ss Score
9.49
Exon sequences
Seq C1 exon
GTGACTGCTGGCTGCTGGCAGCCATTGCCTCCCTCACCTTGAATGAAGAAATCCTGGCTCGAGTCGTCCCCCTAAACCAGAGCTTCCAGGAAAACTATGCAGGGATCTTTCACTTCCAG
Seq A exon
GTAACTTAATGGTTGGCTCAGGTGGTTCCTCAACAGGTCCAGGGGGCTAGGAACAGTCTTCTGGCTTGGCTGGGTTCATCAGTCCCTGGTGTTTGCAGACTCCCAAGACCAATACTGTTCTACAAAGGACATTGGGCGAGAGCAGGAAGCTTCCTGGCTTACCCGTGGCCAGGATGTGAGACCCGGCTGGGATGGCCCTGGGTGGTTTCTTGGGACATGTAAAAGGGAGGTAGAGCAAGGTGTTCAGGAACTAATTCCCAAGTTTAAAAAAAAAAACTGTATTATTTGATGTTTGAGACAAAAACGTTGAAGTTCTCCTCCTTTTATGCCGGTAAATGAGAAATAATACTTGAAAAAGCTGGCTGGGCACGGTAGCTCATGCCCGTAATCTCAGCACTTTGGGAGGCCGAGGTGGGCAGATCATTTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGATGAAACCCCATCTCTACTAAAAGTACAAAAATCAGTTGGGCGTAGTAGTGCAGGCCTGTAATCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTTAACCTGGGAGGCAGAGGTTGGGAGGCCAAGGTGGGTGGATCACTTGAGCCCAGGAGTTCGAGACCAGCTGGGGCAACATGCTGAAACTCCGTCTCTACTAAAAACACAAAAAAAATTAGCCGGGTGTGGTGGCACGTGCCCTTAATCCCAGCTACTCGGGAGGCTGAGGCAAGAGAATCACTTGCATCCAGGAGGCAGAGGTTGCAGTGAGCCGAGATCGTGCCACTGCACTCCAGCCTGGGCAGAGCAAGACTTGGTCTCAAAAAAAAAAAAAAACAGCCTAAGGTACAGGGCAGAATGCTAAAGAGGCGGGTGTGGATTTGAAAGGATGGACATGCGCCTCTGTCTTCGCTTTTTTAGTGAGGACTTGGCCTGCATAGGAGAGTTAAGGGAGCACCTCCTCCCAGGATGCGCTCATGGAACCTATCCCAGGGGATCAGGGCAAGGGGAGCCAGAGGCAGCTGAGGCTCAGAGTCCCAGTGCTGCCACCAGCTCCTCCTGCAGCCCACCTCTCTTGTTCTGCAG
Seq C2 exon
TTCTGGCAATACGGCGAGTGGGTGGAGGTGGTGGTGGATGACAGGCTGCCCACCAAGGACGGGGAGCTGCTCTTTGTGCATTCAGCCGAAGGGAGCGAGTTCTGGAGCGCCCTGCTGGAGAAGGCATACGCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162909:ENST00000295006:3
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(13.0=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.7=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:
GTGACTGCTGGCTGCTGG
R:
GCGTATGCCTTCTCCAGCAG
Band lengths:
250-1337
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