HsaINT0027410 @ hg19
Intron Retention
Gene
ENSG00000162949 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:16663]
Coordinates
chr2:30985948-30987172:-
Coord C1 exon
chr2:30986998-30987172
Coord A exon
chr2:30986023-30986997
Coord C2 exon
chr2:30985948-30986022
Length
975 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGT
5' ss Score
9.65
3' ss Seq
TCTGCTTTTCTGCCTTGAAGCCA
3' ss Score
7.09
Exon sequences
Seq C1 exon
GCTGCTCGGATCCTATTCCGATCTGCACTATGGCTTCCTCGAGGATGCCCTGGTGGACCTCACAGGAGGCGTGATCACCAACATCCATCTGCACTCTTCCCCTGTGGACCTGGTGAAGGCAGTGAAGACAGCGACCAAGGCAGGCTCCCTGATAACCTGTGCCACTCCAAGTGGG
Seq A exon
GTAAGTCACTGGGGAGCCCTTTTGCACCAGTTCAAGCTTTCCTCAGCCAGGAATGCTCAGCCAGGGGTCCATTCAGCTAAGGAGGATGTGGCAAGCTGCCACCATTAACGAACACTGATAGCGTGCTTTACCCGGGTCACCCCATTGAACCCTGCAGTAGCCTGCCTCTAAGACATAAATTGCAGAATTCACTTCACAGAAGAAAAGGCGGGCTCAGAGAGGCTACCTAAGGTGCTCACCAACACACAGCTCATAAGTGGCTCGACAAGTCTTCCAATGCTGCTGCGCCAGAGCCTGGACCTACTGCTACAGCTCCCAAGCAACCAGTGGGCTTTACCATGCACTGGTGAACGCAGCTTCAGCTCCTTTGTATTTTGCCTTAAGTTTACACGGAGCCCCCCAGGGCCCTCTGATGCTCACTGGCTCTAATGGCAGCACCCAAGGGCAGCATGACCCATTTTGAAAAGCTTGGGTGACCCTCCAAATTATTTGAGTCTGTTCTGAGACATCTGGTTTCTATCCATGGGGATGCTTCCTTCATCTTGAAACATGTGGGCTTTGAGTCACACATTGCTAATCCAAAATGCCACCAGAAGCCCAAGATGCAGTTTAAACTCCAGTTACTCCCAATGTGGGGGTCAAGTGATTCCTGACTCCTGTGAATGTCCCAGCAGACATATTTGTGCCGTGTCTCACTGATGACATGTGGTTGGTGGAGAGAGTAACCCAGGCCCTCGGGACTCCACGGGGTTCTATCACTCATGGGGGTGGTGCCCTGAGGCATGAAATCCCTGGGGCCTCAGACACCCAATGGCCTTCCAACTCTGCTGCTCTAGAAAAGAGTTCCAGGCCATATACCAGTCCCAAGTGAGTCAGTGAGGCCCAGATGGCTCAGTGGCTGTTTGGACTGTGTTTTTCTATTTCTTTGAAGAACCTGTAGATGTCTAATGTTTGATCTGCTTTTCTGCCTTGAAG
Seq C2 exon
CCAACAGATACAGCACAGGCGATGGAGAATGGGCTGGTGAGTCTCCATGCCTACACTGTGACTGGGGCTGAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162949-CAPN13:NM_144575:6
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=0.120
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=FE(19.4=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(8.0=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:
GCTGCTCGGATCCTATTCC
R:
TCAGCCCCAGTCACAGTGTAG
Band lengths:
246-1221
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)