HsaINT0027538 @ hg19
Intron Retention
Gene
ENSG00000203697 | CAPN8
Description
calpain 8 [Source:HGNC Symbol;Acc:1485]
Coordinates
chr1:223717429-223718212:-
Coord C1 exon
chr1:223718134-223718212
Coord A exon
chr1:223717546-223718133
Coord C2 exon
chr1:223717429-223717545
Length
588 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CAGGCTCCCTCTGCCCTCAGGTT
3' ss Score
10.75
Exon sequences
Seq C1 exon
GAGATCTATTGGGAAACTGATTATAACCACTCGGGCACCATCGATGCCCACGAGATGAGGACAGCCCTCAGGAAGGCAG
Seq A exon
GTGAGGACACATCCTGTAGACAGGGTCTTGGGATCCAGGTGTGCACATTGTAAATATTTATTCTCATGATGATGATTGCTAATGATCATCATTTGTAGCTTTCTTATATGGGATATCAAGGCAACAACAGAGCTTTGTTGAGTACCTTCCCTGTCCAGGAAGGGGAGAATATTGCTCGATTCCATATAGCATAATATTTTAGAATTTTTCCAAGATCTCTGCCTGTTACTGGGAAGGTGACAGCAATTACAGAGGAAGGGGCTATGAAGGAGACAGACAGGAACTGGCCAGACAGGCAGCCCCCTCACCTTCTCTGCTTTTGCTTGCTGATGTGACCCATGGCTGAGTTGGTGCTGGTACTAGCGCTGGACCTGGAATTAGGCTGATCTTGGTGAGGAGTAGCTACAAGGAGAGGGATGGATGGCAGGACACCTTCTGGGATCCCCTGGAGAAGGCAGAGTCAGGCCTGGTTTGCAGATTGATACAGAACCACAGAGGGGCCCCTGGGATGTCAGCTCCTTGAGTGTTTATGGGAGACAGTGCTGAGTCCTCCACTCTACCTGTGACCCAGGCTCCCTCTGCCCTCAG
Seq C2 exon
GTTTCACCCTCAACAGCCAGGTGCAGCAGACCATTGCCCTGCGGTATGCGTGCAGCAAGCTCGGCATCAACTTTGACAGCTTCGTGGCTTGTATGATCCGCCTGGAGACCCTCTTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000203697-CAPN8:NM_001143962:14
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:
PF134991=EF-hand_7=FE(28.0=100)
A:
NA
C2:
PF134991=EF-hand_7=FE(41.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTGGGAAACTGATTATAACCACTC
R:
TGAAGAGGGTCTCCAGGCG
Band lengths:
190-778
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)