HsaINT0027490 @ hg19
Intron Retention
Gene
ENSG00000149260 | CAPN5
Description
calpain 5 [Source:HGNC Symbol;Acc:1482]
Coordinates
chr11:76831759-76833095:+
Coord C1 exon
chr11:76831759-76831955
Coord A exon
chr11:76831956-76832979
Coord C2 exon
chr11:76832980-76833095
Length
1024 bp
Sequences
Splice sites
5' ss Seq
CCGGTACTT
5' ss Score
5.68
3' ss Seq
CCCCTGCCGCCCCATATCAGGGA
3' ss Score
7.3
Exon sequences
Seq C1 exon
GTGGAGGAGAACCGCCAGTACCGCATGCACAGCCTGCAGCACAAGGCCGCCAGCTCCATCTACATCAACTCACGCAGCGTCTTCCTGCGCACCGACCAGCCCGAGGGCCGCTATGTCATCATCCCCACAACCTTCGAGCCAGGCCACACTGGCGAGTTCCTGCTCCGAGTCTTCACTGATGTGCCCTCCAACTGCCG
Seq A exon
GTACTTGGGGGCTGGCTTGAGGCCAGTGTGGGTGGGAGTGACATTCACACTGGGCCAACCAGGAACCTGCAGCCTCAGAGATGCTCAGTGTCTCTGGGCCTCCAGCCACTCTGGGCTGATACCAGTGCCCATCTCCTTCCCTTCTCTTCCCTTGTTCCCCTGTCCCAGCATCCCTGGCCATGACTAGGAACAGCTTCTTGTATGTGCACTGCACTCTACAGTTGACAAAGAAGCTTTCACTCATCTTGATCTTCCTGCATCCCTGAGTGGGAGGCCTGACTCCCGCACTTTACCAGTGAGATTCAGGGGCCGAGGTTAGAAGGGTTGTCTGAGGTCATGCAGCCAGCGGTGGAGATGGGCTGGGCCACCCAGCCTGCCTGGTTCCAGGGTTGGGTCTTGTCACCACAATTTCCTGTCCCATGGGGGTGGCTCTGGGCTCCAGTGGACTGCTGAAGCTCTCTCAGTCCTTGCTGGGGCATAGACCCTGTGCGTCCCGCACTGCCCTCCACTGTGATACACAGCCCAGGCTCGGTGTCCCCTGAAGGACAGGTGAGCTCTGCCCACGTGCCAGAGCCAGGAGGCAGCTTGTGGCATGTGGAGTCAGACGGCTCAGGGTCCTGCCGGCCCAGGCTCCCCAGCTTTCCAGCTGTTTGGGCAAGCCCTTCACCTGGGTGAGCCTGCTGCTTCCTCAGCTGTGACATGGGCACCATAATAGCCTTTGCGGGGCTTTGCAGGGATTAGGAATCACCCATAACGCCAGCAGGGGGCTTGGCACACAGCAGGTGCTCAGTAAGGTGCCTTTCCCCTGGGGAAGGATGGGGTACCCTTGATAGGGATAGAGAAGGCAGGAAGCCCACAGGGCTTGGAGCTGGGGACTGCCCATGGGGATTTGCTCAGGACTAAATGAAATCAAGTTTGGGCTAAATACTGCTTCTCTTCCCTTCCCACTTCCTGAACCCCCTCTTCACCCCTGTCTTCCTGGCCCTTCTCCATCACTCCCCTCTCCCCTGCCGCCCCATATCAG
Seq C2 exon
GGAGCTGCGCCTGGATGAGCCCCCACACACCTGCTGGAGCTCCCTCTGTGGCTACCCCCAGCTGGTGACCCAGGTACATGTCCTGGGAGCTGCTGGCCTCAAGGACTCCCCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000149260-CAPN5:NM_004055:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.045 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(45.1=100)
A:
NA
C2:
PF0106717=Calpain_III=PD(0.1=0.0),PF0016825=C2=PU(20.5=40.0)
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:
GAGGAGAACCGCCAGTACCG
R:
CTGTTGGGGAGTCCTTGAGGC
Band lengths:
310-1334
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)