HsaINT0027390 @ hg19
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:13249]
Coordinates
chr19:39228115-39228987:-
Coord C1 exon
chr19:39228913-39228987
Coord A exon
chr19:39228279-39228912
Coord C2 exon
chr19:39228115-39228278
Length
634 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGT
5' ss Score
6.6
3' ss Seq
CTGACTGGGCCACCGTGCAGGAT
3' ss Score
3.89
Exon sequences
Seq C1 exon
CTGCCCACGCTGGGACACACTCCCCACCGAGTGCCGCGATGCCCTGCTGGTGAAAAAGGAGGATGGCGAGTTCTG
Seq A exon
GTCAGTTCGTCAGGGTCCCAGCTCTGCCTCTGGGAGGGTCTCTGCCAAGGGGTTCAGGGAGGGCGAGCCCCAGTTGAAGGATGGGTCCTAATAGGGAGAAACTGTGTACATCGGTGGTAATTTTGGGGCCAGGTTCTATTTTGGGAAATCAAGGAAGAATTGGTAGTAATATTAGAGAACCTCTGATTGGAGTGGGTTTAAAAAAGTAGTAATATGAGGGGAATTTGAAGGCCTAGTTATCTGTGGAGGATTGAAAGGGATGGGCAGTATTTAGGGCAATGGAGGAAGGCTTGGTGATATTTGGGGCATTTCTTGAGATTTGGCAATGTTGAGGGGCTGAAGGGTACTTGTTGGTAATTTAGAGTCTGAGGGTCTTGCTATTTGGGGGTTGGTGGCAATTTAACGATATTTGGGGGCAGCTTGTGAATCTTGGCGATTTGTGGGGCATGTCTGAGGACTTGGAGGAATTTGGCAGAGCTAGAGGCCCAGGCATTTGGGGTTCATTTCTGGAGCCTGAAGGGTATTTGACAATATTTAAGAAATGTGAGGGGCTTTGGGATCTGGGAGTCATTTCCGGGATCTTGGGACCCCCTCGAGGTGGGGCCGGGCAGGGTCTGACTGGGCCACCGTGCAG
Seq C2 exon
GATGGAGCTGCGGGACTTCCTCCTCCATTTCGACACCGTGCAGATCTGCTCGCTGAGCCCGGAGGTGCTGGGCCCCAGCCCGGAGGGGGGCGGCTGGCACGTCCACACCTTCCAAGGCCGCTGGGTGCGTGGCTTCAACTCCGGCGGGAGCCAGCCTAATGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472-CAPN12:NM_144691:8
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=0.071
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(13.0=100)
A:
NA
C2:
PF0064816=Peptidase_C2=PD(6.4=33.9),PF0106717=Calpain_III=PU(13.6=42.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGCTGGGACACACTCC
R:
CATTAGGCTGGCTCCCGC
Band lengths:
231-865
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)