HsaINT0027396 @ hg19
Intron Retention
Gene
ENSG00000162949 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:16663]
Coordinates
chr2:30965192-30966448:-
Coord C1 exon
chr2:30966249-30966448
Coord A exon
chr2:30965226-30966248
Coord C2 exon
chr2:30965192-30965225
Length
1023 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
ACTGTCCTCTGATTTTCTAGGCA
3' ss Score
10.72
Exon sequences
Seq C1 exon
CAGCGGTTCCGGGAGAAATTTCCACCCGTGTTTTTTTCCTCGTTCAGAAACACTGTCCAAAGCTCAAATAATAAATTCCGCCGCAACTTCACCATGACTTACCATCTGAGCCCTGGGAACTATGTTGTGGTTGCACAGACACGGAGAAAATCAGCGGAGTTCTTGCTCCGAATCTTCCTGAAAATGCCAGACAGTGACAG
Seq A exon
GTACAGAACCCTCTGGGATTGTAAATGTTTTATTCTACTTAACTTTATAAAAACACATTGTGTAATTATGGGCAGTTCTCTGTGCATTCGTGCAGCCTGTGCTATGTCACTGGGGACATGATATTGGCCCCACTCTAGAGCAGCTCACCATAAAGGGGGAGCGAGAAAGTCTATGAACCAAGAACCAGACCACAAACAGGATGGGTCCATTGCCAGATGGAAATGCAAAGTGGCACGGGAGGACTGAGTGGCAAGAGGGACTGAGGAAGGCTTCTTGAGGGAAATGACACGTGAGCTGGGCTTTGAAGAAAAACATAATTTAATAGTTTAAAAGGGAAGGCGATGGTAGCCATGGGAAGGTAGGTAGAAGAAAAAAGCATGAATGGCGGGAGGGAAGTGGCTGTGCACAGGGCTGCTTGGAGAGTAAGTAGCATCGGCATCCATACAGGAAGGTGGCATTTGGCCAGCATATCACATGGCCTGAAATGTGGGGTATAGCAGGGAGACAGTGAAAGATGGGCCTGAAAGAAAGAGTCCATCATGGAGGGTCTTCCATGCCAACTTGATCATTCAAGACTGGGACCAGCAAGTGCTCACCCCACTGGGCCCCTTGTCTCCTCTTGGGCCCAAGACAGACATTGCCATCATTATGGCAGTCTTTGCAGCTGAGCATTGGTGAGACCTTCTAAGTCCAGCATGCCAGGCCGCCATCATACCACCAATCAGAGATGGAACCTAAGGCAGAGCCTATCTGCCATACTGACAATGGGGGTTGCTGGAAGTGTGTATCGGGTTGTGGAAGGAACCATTTACTAAACAGTTAAAGACCAGACCATTTCCAGCCAAAAGGCTGGGCTGGTGGCCACGGTGCTGTAGCTGCTCACTTCGTGTCCTGCGGTGCTGAGGGTGCCCCATTCAGGAACTTGGCATCAATATCCAGTGCCACCTGGGTGCCCTCTATATGCAGGCCCCCTTTGAGTGGTGAGCTGGTCATCTTTGTCACACTGTCCTCTGATTTTCTAG
Seq C2 exon
GCACCTGAGCAGCCATTTCAACCTCAGAATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162949-CAPN13:NM_144575:13
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=0.667
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(47.4=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCGGTTCCGGGAGAAATTTC
R:
CATTCTGAGGTTGAAATGGCTGC
Band lengths:
230-1253
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)