HsaINT0027391 @ hg19
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:13249]
Coordinates
chr19:39227796-39228278:-
Coord C1 exon
chr19:39228115-39228278
Coord A exon
chr19:39228029-39228114
Coord C2 exon
chr19:39227796-39228028
Length
86 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
CTTTTTTCCTCCTCCCTTAGAAA
3' ss Score
10.25
Exon sequences
Seq C1 exon
GATGGAGCTGCGGGACTTCCTCCTCCATTTCGACACCGTGCAGATCTGCTCGCTGAGCCCGGAGGTGCTGGGCCCCAGCCCGGAGGGGGGCGGCTGGCACGTCCACACCTTCCAAGGCCGCTGGGTGCGTGGCTTCAACTCCGGCGGGAGCCAGCCTAATGCTG
Seq A exon
GTGAGGCCTGAGGGGCCCTGAGAGGCTTCCTGGGGTGGGGGGCGCTGTGGCCGGCTAGGAAACCCCCTTTTTTCCTCCTCCCTTAG
Seq C2 exon
AAACCTTCTGGACCAATCCTCAGTTCCGTTTAACGCTGCTGGAGCCTGATGAGGAGGATGACGAGGATGAGGAAGGGCCCTGGGGGGGCTGGGGGGCTGCAGGGGCACGGGGCCCAGCGCGGGGGGGCCGCACGCCCAAGTGCACGGTCCTTCTGTCCCTCATCCAGCGCAACCGGCGGCGCCTGAGAGCCAAGGGCCTCACTTACCTCACCGTTGGCTTCCACGTGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472-CAPN12:NM_144691:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.071 A=NA C2=0.308
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.4=33.9),PF0106717=Calpain_III=PU(13.6=42.9)
A:
NA
C2:
PF0106717=Calpain_III=FE(43.8=100)
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:
TTTCGACACCGTGCAGATCTG
R:
CTCCAGCAGCGTTAAACGGAA
Band lengths:
181-267
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)