HsaINT0027317 @ hg19
Intron Retention
Gene
ENSG00000014216 | CAPN1
Description
calpain 1, (mu/I) large subunit [Source:HGNC Symbol;Acc:1476]
Coordinates
chr11:64949343-64950439:+
Coord C1 exon
chr11:64949343-64949484
Coord A exon
chr11:64949485-64950171
Coord C2 exon
chr11:64950172-64950439
Length
687 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CAGGCCCATCTGTCCGGCAGGAT
3' ss Score
6.29
Exon sequences
Seq C1 exon
AAGGAGAGAGGGAGGGCGGAGGGCGGAGGGGCGGCGGGAGGAGGGCGGGGAGGAGCGCTCTTCCTGGTTGGGCCCTGCCCTGAGCTGCCACCGGGAAGCCAGCCTCAGGGACTGCAGCGACCCCCAAACACCCCTCCCCCAG
Seq A exon
GTAAGAAGCTGGGTAGCCGAGCCGGGATTCCTTGACCCTGGCCACTGCTCCTGGGCTGAGGGGCTGCCCCAGCACGGTCCCTTCTCGGGGGCCTCTGCGTTCCTGGAGCAGGGGTGGGGGCTGGCGGAGCGGCACAGCCCAGGCGCCTGTCCCAGCCTGGCTCACCGCTGTCCCCAGGGGCTGGGCTAGGGCCCACCAGCTCTGATATCGAGCCTGCTGCGGGGGCCTGAGGAGGGGGACCCCGACCGTCTGGGGTTTTCAGCCCACGGCAAGGGGCCGGTGCACCAGGAGCTTGGTTAGTTTGGGGAGGGGGTTGCAGGCCTGTGAACAGGATCAAAGAGGCCTTCCCTGCTGTGTCCCACCTGCCCAGTTCCTTGTGCTGTCTGGAGGCTCCGCCCTGCCCCACCTGACCTGCTGGCTCACTACAGAGCTGCAAGCCCCTGACAATGGGATCCGGGAAAGGAGAGGTGGCCGGCACGCCTGGGAACTGGGAAATCCCTTTCCTGGATTCACTGGGAGCACCGGGAGGTGGCTGAGAACCCTACTTCTGTGAGGGGAGCAGTGAGGCAGGGAAACCCTAGGTTTGGGGATGGATAAGCAGGGGCAGGAGAGCAGAGCTTGCAGGCAGGAGCCCAGGTTCTAGTCTTGGGAAGGCCTGGGTTCTGAGCAGGCCCATCTGTCCGGCAG
Seq C2 exon
GATGTCGGAGGAGATCATCACGCCGGTGTACTGCACTGGGGTGTCAGCCCAAGTGCAGAAGCAGCGGGCCAGGGAGCTGGGCCTGGGCCGCCATGAGAATGCCATCAAGTACCTGGGCCAGGATTATGAGCAGCTGCGGGTGCGATGCCTGCAGAGTGGGACCCTCTTCCGTGATGAGGCCTTCCCCCCGGTACCCCAGAGCCTGGGTTACAAGGACCTGGGTCCCAATTCCTCCAAGACCTATGGCATCAAGTGGAAGCGTCCCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000014216-CAPN1:NM_005186:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0064816=Peptidase_C2=PU(11.3=38.2)
Main Skipping Isoform:
NA
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:
GAGGAGCGCTCTTCCTGGTT
R:
GACGCTTCCACTTGATGCCAT
Band lengths:
356-1043
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)