HsaINT0027387 @ hg19
Intron Retention
Gene
ENSG00000182472 | CAPN12
Description
calpain 12 [Source:HGNC Symbol;Acc:13249]
Coordinates
chr19:39229214-39230859:-
Coord C1 exon
chr19:39230691-39230859
Coord A exon
chr19:39229289-39230690
Coord C2 exon
chr19:39229214-39229288
Length
1402 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
CCATCCCATCCCCTGCCCAGAGT
3' ss Score
5.49
Exon sequences
Seq C1 exon
GCTCCACGGCTCCTATGAGGTGATGCGGGGCGGCCACATGAATGAGGCTTTTGTGGATTTCACAGGCGGCGTGGGCGAGGTGCTCTATCTGAGACAAAACAGCATGGGGCTGTTCTCTGCCCTGCGCCATGCCCTGGCCAAGGAGTCCCTCGTGGGCGCCACTGCCCTG
Seq A exon
GTAAGAGACCTGGACTCGCATGCGGAACCCCCACCAGGACCAGAGCACAGTCAGGGGTGTGGTGGGGTGGGCGGAGTGCTTCCTCTGTTCTCTGCTTCCGTTACTGGCTTAGGCTCGCTCATAAATCTAACTAGTCAAAAATAAATTCATTTGCTCTCATGAATCAGGGGCTTCAGGCACAGCTGGATCCAGATGCTGAGGGTGTTGCAACTATGTTTATTTCTCATTCTGTGTTAGTGTCACTCTCAGCCAGGCTCTCCCCTCATGGGCATAAAAGGATCCCCCATAGCTGCAGGTATCTCCTACCACCCTAGGGTTTATTTAAAAAAAAAAAAAAAAAGTGCCTCTTTCTGAGAATTTCAGTAAAAGTCCCAGGATTGATTCTCGTGGGCTTAGCTTGGGTCATGTGTTCATCTGTGACCCCATGACACACTCATTCATTCACTGAGTTGGTCTAACTCCTTCACTCATTCATTTACTTAAATCCTCTGAGTTACTGCTTCTCTTTTTCTTTTGTGTCTGTTTCTCTCTTCTGTATCTTTCTTTGTCTCTGTCTCTGTCTCTCTACTCTTTCCATCTTTTTTTTTTTTTTTTTTTTTTTTGAGACGGAATCTTGCTCTGTCACCCAGGCTGGAGTGCAGTGGCACGACCTTGGCTCACTGTAACCTCTGTCACCCAAGTTCAAGCAATTCTCCTGCTTTGCCTCCCGAGTAGCTGGGACTACAGGCGCCCGCCACCATGCCCAGCTAGTTTTTTGTATTTTTAGTAGAGATGGGGTTTCACTGTGTTAGCCAGGATGGTCTCAATCTCCTGACCTTGTGATCTGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACCACAACAGGCCTCTTTCCATCTATTTTGTTTGTTTTTGTTTTTGGAGGCAGGGTCTCATCTCACTCTGTCACCCAGGCCAGAGTGCAGTAGTGTCATCATAGCTCACTATAGCCTTGACCTCTGGGCTCAAGGGATCCTCCTGCCTCAGCCTCCAGAGTAGCTGGGACCACTGGTGTGCACCACCACGCCTGTTGAATTTTTAAAATTTTTGTAGACTTGGGGTCTTGCTATGTTGCCCAGGCTGGTCTTGGACTCCTGGCCTCAAGTAGTCCTTCCACCTCGACCTCCCTAAGTGCTGGGATTACAGGCGTGAGCCCGTACCTCCATCTCCTTTTGTCTCGTTTCCATCTCCCTTCCTCTCCTTTTCTCTTTCGCCTTCAGTCACTAACCCTGACATGGTCTCTGAGCTGCGTGCCATTCAGTTCAGTGCTCTGGTTGGCTCCTGCCTTGGTGGCAGGAGGTTGGGGGCAGGGAGGAGCAGCTGCCCTCCTGTCCCCTACCTTGGCCTCACCATCCCATCCCCTGCCCAG
Seq C2 exon
AGTGATCGGGGTGAGTACCGCACAGAAGAGGGCCTGGTAAAGGGACACGCGTATTCCATCACGGGCACACACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000182472-CAPN12:NM_144691:5
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=0.000
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(18.9=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(12.5=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:
CCACGGCTCCTATGAGGTGAT
R:
GTGTGTGCCCGTGATGGAATA
Band lengths:
238-1640
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
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)