HsaINT0027400 @ hg19
Intron Retention
Gene
ENSG00000162949 | CAPN13
Description
calpain 13 [Source:HGNC Symbol;Acc:16663]
Coordinates
chr2:30959369-30961159:-
Coord C1 exon
chr2:30961101-30961159
Coord A exon
chr2:30959438-30961100
Coord C2 exon
chr2:30959369-30959437
Length
1663 bp
Sequences
Splice sites
5' ss Seq
GAAGTATCC
5' ss Score
-0.29
3' ss Seq
ACTCTTAACTCCTTACCCAGCTG
3' ss Score
4.52
Exon sequences
Seq C1 exon
GACCTCCAGGGGACATGTTCTCCTTAGATGAGTGCCGCAGCTTGGTGGCTCTGATGGAA
Seq A exon
GTATCCTTTGCGGTCATCCCTCCCATGCTCTGAGCACCCCTCAGCTCTGTGGGCTTCCCCAGAGACCTAATTAGGACAGTAGGGAACCCTTTTCCCACTCAGTATTTTCTCTTCTTCCCTGTCCTTGAGTTTCTGGGGATTCTCTACTAACTCACTAACATACCACAGCAACAATGATAATAGTTACCATCTATCAAGCACCTACTATGTGCTGATCAGTGTACTGGGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCCTTATAATTCTTGAAGCAATCCCTCTGATACAAAAAAGTATCATCTCATAATACAGTAGAAGAAACAGGAGTTCAGAGAGGTTAAGTAATTTGCCCAGATCACACAGCTAGTCAGGACTCATGCTCAGATTTGAAGTTGGAGCTTTCAGCCTCCAAAGTCGATGCTCTAACCTTATCCTAAACCGCCCCTTTATAGCACCGTTGGGAACTATTTTCCCTTTTACCCATTCACTTCCCACTGGAGGAGTCTCCATTATTTAAATTTCTTACTTCAACAAGTCCCCAATTCAATCAAGATAACTACCACCAAAACATGGAAAACTGCCTGGTCTACACAGCAGTTGCACCCCAGCATTGCTATGCTGCATTCACAGCGGGAGACGCTGGGCAGAGGCAGTTCAGAGACTCACTCCAGGCCCGTGGCTACAAGTGTAGGACCAAGAATTGAACCCCAGACTCCTGACCCTCCTCCTGATTTCCATTCCCCAGTGAGCCATCCTCTTCCTGCGTACCCCTGGCTTGGCAAGCAGAAGAGGCTGACTCCATGAGTGTAGACCCCCAGATGCTGCCCTGCCAGCCCCTCACTCGGCAGTGTGCTGTCTCCTGAGACGCATTGCCCCGCTCCTGCACCGTTGACAAGGCTGAATTGGGACTGTGAAGCCGGCCATTGTGAAACAAGAGGGCTTTTTTGATGAAATCATAAATCAGGCCCTGTCTCTGCTGGCTGTGCTTTGGAATCTATCAGAGACACAGCCCATCTCCCACAGAGGAATCCAAATGGTCCTCACAGTGCCACGGCCCGGGGTGAGTAACCCGAGGGGAGGTCACATTTGCTGGACCCCTGCAAAGCGGACAGGTCTCTTTCAGCCTTCTTCCTACTCATGGCTCCCCTTCCAGTTCTCAGAGGTTAATGCTTTTCCCTTCATTAGTCATCACTGAACCCATCATACGGCATGGCCAGGGCTGGCTTTAACATGCCCACGAGATGCATTCCCTCTACACTTGTGCACGCAGGACTCTATGTGCTCGCCTGTGGCTGCTGCTTCTGGGGTTGCCATGACCCTTCGTGCTCCTCCCCAACTTCTGGAGCCAGAGGGCCCACTCCAACTGGTGAAGGCCGTGTTCTAGACCCCTCTCTTCCCTCAGATGCAAGTGATATTGGCCTCCTTTCCTCAGGGCTTCCTTCTTCCAATTGCCCATTTTTCTTTGTAAAACAAATCTAAGCCAGGTCCCTTTCAGACACAGCGGGAGCCAGCTGGCATGGGGCCACATCCAGGTGACAATGGACCAGCTGTGTTGCTAGTGATGAATGGGCCTGCTCTGGCTTTGTTGGCAGGATGGCAGCCCCTCTGCACCTTGCACGCTGGCTGGTTCACTCTTAACTCCTTACCCAG
Seq C2 exon
CTGAAAGTGAATGGGCGGCTAGACCAAGAGGAGTTTGCGCGACTGTGGAAGCGCCTTGTTCACTACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162949-CAPN13:NM_144575:17
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:
PF138331=EF-hand_8=FE(34.5=100)
A:
NA
C2:
PF138331=EF-hand_8=PD(32.7=78.3)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)