HsaINT0027491 @ hg19
Intron Retention
Gene
ENSG00000149260 | CAPN5
Description
calpain 5 [Source:HGNC Symbol;Acc:1482]
Coordinates
chr11:76832980-76833758:+
Coord C1 exon
chr11:76832980-76833095
Coord A exon
chr11:76833096-76833621
Coord C2 exon
chr11:76833622-76833758
Length
526 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTCCCACTCCCTCTCCCTAGGGG
3' ss Score
12.48
Exon sequences
Seq C1 exon
GGAGCTGCGCCTGGATGAGCCCCCACACACCTGCTGGAGCTCCCTCTGTGGCTACCCCCAGCTGGTGACCCAGGTACATGTCCTGGGAGCTGCTGGCCTCAAGGACTCCCCAACAG
Seq A exon
GTGAGCTCTCCCAGGGAGAGTCCCCCGGCCCTCCTGCCAGTTGTCCCATGGCCTCTCTCCACCAGCACGGATACCAGCCTCAGAGCTCTCCTGCTCTCAGAGGCACTGCAGGCCTGGCCATTTCTGGGGTGATGCCTGATGCTGGGCACATAGAGAGGAAAAGGTTTACCTTCTGCTCTCAGGAGGCTTCCAGCTGGGAGGGAGGCCTCAGGAAAGGCTTCCTGGAGGGAGTGGCCTTTTTCTAGGCTGAGAAGGTATTAAGATACAAAGCCTGATGAAAGGGGGTAAGGGAGAAAGGTGCTCCGGGCAGAGGGAGCAGTGTGGGTAAAGCTCTGGAGGCTGGAGATGGCCAGTGTGCCCCTGCTGGCCGGCCTGTCTCTGGAAACGAAGGGGCCCTGAGGTGGGTCAGGCTCCAGTCTCTCCATCTGAATAACTGAGCCGGGTGGGCATCTCACCTGTAGATATCTGTGGCCCTGCCACAGCCCCCACCCCCACCCTCACCCCATCTCCCACTCCCTCTCCCTAG
Seq C2 exon
GGGCTAACTCTTATGTGATCATCAAGTGTGAGGGAGACAAAGTCCGCTCGGCTGTGCAGAAGGGCACCTCCACACCAGAGTACAATGTGAAAGGCATCTTCTACCGCAAGAAGCTGAGCCAGCCCATCACTGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000149260-CAPN5:NM_004055:11
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=0.065
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=PD(0.1=0.0),PF0016825=C2=PU(20.5=40.0)
A:
NA
C2:
PF0016825=C2=FE(57.7=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:
GAGCTGCGCCTGGATGAG
R:
TACAGTGATGGGCTGGCTCAG
Band lengths:
249-775
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)