HsaINT0027334 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64953641-64954769:+
Coord C1 exon
chr11:64953641-64953809
Coord A exon
chr11:64953810-64954685
Coord C2 exon
chr11:64954686-64954769
Length
876 bp
Sequences
Splice sites
5' ss Seq
GACGTGAGT
5' ss Score
9.22
3' ss Seq
GTGTGTGCCTCTTTCTGCAGATC
3' ss Score
12.09
Exon sequences
Seq C1 exon
GGTAAATGGCAGCTACGAGGCCCTGTCAGGGGGCAGCACCTCAGAGGGCTTTGAGGACTTCACAGGCGGGGTTACCGAGTGGTACGAGTTGCGCAAGGCTCCCAGTGACCTCTACCAGATCATCCTCAAGGCGCTGGAGCGGGGCTCCCTGCTGGGCTGCTCCATAGAC
Seq A exon
GTGAGTGTGCCCGGCCCCGATGCTTTGGTACCCTGGAACCCTGGTATCCTGACCTGTCACATTTTCTAAAATCCCCACCCAGGCTCCGCTCCAGACCCTGTCCTGCACTTAAGCTTCATCTCTGGATGCATACCCTGCCTCATCCATCACTTCCACCCCCCATGCCTGGTGTCGCTCCTGTCCTCACCTACCCACTCCTCCCCCAAAACTTCACACCTCAGCTCTTTCCTGTGCTTGTTTTCCCGTCTACCATGCTGTTTCCCTCATTCCTGTCATCTCAATCCATGCCATCCTCTGTCCAGTTCACCAGCCTCAGATTTCATCTCCTGGTCTCAGTTCCCACCCATCCCTAGCCTCAATCCCACACTCACTCCATTCCCACCCTTCCCTGCTCCTCTGTTCCCACACTCAACTCCGCTCCCCAGTCCTCAACGCCAGACTTGACCCCAGTATCACTGCCATCCGCAGCTCTAACCCCAGCTCCCATTCCCATTTCTAACTGACTCTTCTGTCCTCACGTCCTTCTCCGTGAGGCCCACTGAGGGCTGTGTGGCTCTGGTGGGCTGTGCACGGCTGTGTGTGTGCACATGCATGTTCGCACAGGTTCTGGTCAGCCCTGGCCAGTAGCAGTGTCAGCGGAGTGCCTGGGCTCCCCTGTCCCAGTGGCAGCATTGGTGGGGTACCCAGGCTACCCCTCTCCAAAAGAGCAGCATCTATATGTGGGGGTGTCTATAGGTGGGATCGGGGTCCCTGCTTGCTTCTCCTAGCAACTGTTGTATGTGCAAGTGGGAACGTCCAAGACCCTGAGTGCTGGGGGCTCATCTGATAGGGCGGGGGGACCTAGCCACTGACCACAGTGTGTGCCTCTTTCTGCAG
Seq C2 exon
ATCTCCAGCGTTCTAGACATGGAGGCCATCACTTTCAAGAAGTTGGTGAAGGGCCATGCCTACTCTGTGACCGGGGCCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:6
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:
PF0064816=Peptidase_C2=FE(18.7=100)
A:
NA
C2:
PF0064816=Peptidase_C2=FE(14.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTAAATGGCAGCTACGAGGCC
R:
GGCCCCGGTCACAGAGTAG
Band lengths:
246-1122
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)