HsaINT0027544 @ hg19
Intron Retention
Gene
ENSG00000203697 | CAPN8
Description
calpain 8 [Source:HGNC Symbol;Acc:1485]
Coordinates
chr1:223813507-223814859:-
Coord C1 exon
chr1:223814691-223814859
Coord A exon
chr1:223813591-223814690
Coord C2 exon
chr1:223813507-223813590
Length
1100 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGG
5' ss Score
4.17
3' ss Seq
GGACTTTCTTCTCTACGCAGGTC
3' ss Score
9.21
Exon sequences
Seq C1 exon
GCTTAATGGTTGTTATGAGGCTCTCGCTGGAGGTTCCACAGTGGAGGGGTTTGAGGATTTCACAGGTGGCATCTCTGAGTTTTATGACCTGAAGAAACCACCAGCCAATCTATATCAGATCATCCGGAAGGCCCTCTGTGCGGGGTCTCTGCTGGGCTGCTCCATTGAT
Seq A exon
GTGAGGCATATGGCTTCTCTACTGCCCCACCTCCCCCCACCGCCACCCCTTGTGTGGTAGGGAAGGGATGAGACAGCGGGAGAGAGGCCTAGGAAGGCTTTGGGTCAGAGCAGAGTCTGGAGCTTAGTGGGCAAGTCTAGTGACACAAAGGCCTGAACATATAGGGGCTGGTGAAGACCTAATTAGTGGGTAGGAACTGGGGTTAGTTGCATTGCAGGAGCCCCAATTTCCCTCTCGTTGTTAGAGCCCCTTCAGTACTGCTGGAGTGGCCCTAAGAACATAGTCTAGGATCCCTGGATCCTAGGCCCCCCATTTGCTACCTCCTTTTTGCTAAATAATCTTGAGGTTTTGGAAAACAAATGTGATGATTGATGATACCTGATGGATCTTGAGATCCCTGAAGAAAAGACAAGTTCTGAAACCAGAGGCTGTGGCTGGACAGGAGGCTGAGCTGTGTGGATTTCCAAGGTGGCTGTGGAAACAGAGGCTGGAGGCCCCCAGCCCTGAGGTCCTGTCACCACCTCGGGCTCCTGTGACCAGCTGCCCTCTGGCTGCCCTGTCTTCCTCTCTTGTCCTTACCTGGTGATTTTAGAAATGTGAACGACAAAGTGAGAAGATCCTCCCTTTTTCCTCTCTCTGCAAACCCCAGCAGGAGATGTGGTTTTTGGTGGAGGGGTGGTATGGGGCATGGGAGAGGGGGTGCTGAGGAAATGGGAAGGGTAATGAGGAGTCCACTCAGGGAGAACCTTGGAGGACTGGGACCTGTCCAGAGCCATCAGCATGGAGAATTAGCCTTCTTCAGGCAGCTGGGGGTCACTCTCAGAGAATAAATGACTTCCCAGTTTCTTGGTGGCATTTTGAAGGCTGGTAAATTGTCTTCCAGGCTTGGCAGGCACCTGCACTGGCCCGGAACTACAGGCCTAATTAAAGAGGGAGTCTGGATGGAGATGACTCTTTACCTGAGGTTCATAGCCATGCCTACACCCCTAGTCCCACACTGAAGCCCCCAGTGGCTGTGTAGTGTGTCCTTGGAAAGCATTCTACGGCCGGCCCCTGAGAGGTCAGGGTCAGCCACTGAGTGGACTTTCTTCTCTACGCAG
Seq C2 exon
GTCTCCAGTGCAGCCGAAGCCGAAGCCATCACCAGCCAGAAGCTGGTTAAGAGTCATGCGTACTCTGTCACTGGAGTCGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000203697-CAPN8:NM_001143962:5
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(16.2=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:
TGGTTGTTATGAGGCTCTCGC
R:
TCTTCGACTCCAGTGACAGAGT
Band lengths:
246-1346
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)