HsaINT0027500 @ hg19
Intron Retention
Gene
ENSG00000149260 | CAPN5
Description
calpain 5 [Source:HGNC Symbol;Acc:1482]
Coordinates
chr11:76830076-76831955:+
Coord C1 exon
chr11:76830076-76830198
Coord A exon
chr11:76830199-76831758
Coord C2 exon
chr11:76831759-76831955
Length
1560 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCCCCTCCCGCCTCCTGCAGGTG
3' ss Score
12.5
Exon sequences
Seq C1 exon
TACATCTTCGAAGTCAAGAAGCCAGAAGATGAAGTCCTGATCTGCATCCAGCAGCGGCCAAAGCGGTCTACGCGCCGGGAGGGCAAGGGTGAGAACCTGGCCATTGGCTTTGACATCTACAAG
Seq A exon
GTGAGGCCAGCCGGGTCCCCTGCCGTGGGTGGGGAGAGGGAGGGAGCTGGAGTTTGGACTGCCCATGCCTGAGGAAGAACGCTCTAGAACACCTTGGTCACTGCCGCTGCCCTGGCTGCCGTGGCAGACATTGTGAGGATGCCGTGGCATGGGCCCCACTTGAATATTCACAGAGGGCCCAGCCTGCCCAGCCTTGGCTTCTGTGGGAGCTCTCAGCCTGATTTCTTTCTGCCTAAGACCCACAGGCCTGGGATGTTTGGTGGATGAGGAAGGGGAAGATTACTGGTGGTTGGGGCCGGGCCCTGGGAGGCTCTGGGCATCTACTGGGCCCCCACTGCTCCTCCCTCAGGCCTCAGGGCCCCTTGCAGCCCCTTAGCCTTCCTGCATTGGAGGCCTTGCTGGGCACCAGGAGGAGGCATCCTTGAGCATAGCCAGGTGGGGTCACCTATGGCCGCACCGCCTGGCCTGGAACCTGAGGCCTTCCACGTGTTGTGATGCCCAGTGTGTGGTGACAGTCAGCATGGCGGGACCCCATGTGCCTGTCAGACCTTGAGAACGGAATGAAGCCACCGGGCCCTGCAGAGGCTGGGTACATGCTGAGTCCTTGGCATCTGATGTGCCTGGCCACGCCGTGGCACTTTGTTTATACTCTTGTGCTGGTACATTCATTGCATGCTAGTGTCTTGTGACATATTGTTGTGACTTTGCCATGTGACGATCTTCACTAGTGTGACCAGAACACTTTTTTCAGGATTGTCAGGCAGGTCCTGGCAGCTGGTGATGGCATTTCGTGGACAGGTGCTGTGACCTCTGCAGATCCTGATACTTGGTTGTGCTGTTGGAGTCAGAAACCCCACTGACATTGTTACCAGGGGGATTCCTATTGCCCTCTATTTTTTTTGTTTGTTTGTTTTACAGAGGGTCTTGCTCTGTAACCCAGACCAGAGGGCAGTGGTGCTGTCATAGCTCATTACAGTCTCAAACTCCTGGACTCAAACGATCCTCCCACCTCAGTCTCCCTAGTAGTTGGGACTATAGGTGAACACCACCATGCCTGGCTAATTTTTAAGTTTTTTGTAGAGCTGGGGTCTCGCTTTGTTGCCCATGCTGACCTTGAACGTCCAGCTTCAAGTGTTCCTCCCACCTTGGCCTCCCAAAGCGCTGGGATTACAGGCATGAGCCACTGCGCCCAGCCTCCTTTAATAGTTTTTATTGAGATATAATTCACAGAGCATGCAATTCAGCCATGTAAAGTATACAATCTAATGACTTTTGTGTGATCAGAGTTTATGCAACCATCACCACAATCAACTGTAGAACATTTTCATCTCCCCAAAAGAAACCCACTCCCTTTAACCACCACCACCCATTCCCATTGACCTCTTCCCTTCAGCCCTGGGCAAACACGAATCCGCTTCTGTTATTATAGATTTGCCTGTTCCGGACATTTCATATAAAGGGATTCCATCGTCCCTTCCATGGTGGTGAGGGGGAGGCGGGGTGGGCCAGGGTGTTGTAGGGTGTGTCTCCGCGTGGCCCAGCCCCTCCCGCCTCCTGCAG
Seq C2 exon
GTGGAGGAGAACCGCCAGTACCGCATGCACAGCCTGCAGCACAAGGCCGCCAGCTCCATCTACATCAACTCACGCAGCGTCTTCCTGCGCACCGACCAGCCCGAGGGCCGCTATGTCATCATCCCCACAACCTTCGAGCCAGGCCACACTGGCGAGTTCCTGCTCCGAGTCTTCACTGATGTGCCCTCCAACTGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000149260-CAPN5:NM_004055:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.073 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF0106717=Calpain_III=FE(27.8=100)
A:
NA
C2:
PF0106717=Calpain_III=FE(45.1=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:
ACATCTTCGAAGTCAAGAAGCCA
R:
GGCAGTTGGAGGGCACATC
Band lengths:
318-1878
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)