HsaINT0026552 @ hg19
Intron Retention
Gene
ENSG00000067191 | CACNB1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:HGNC Symbol;Acc:1401]
Coordinates
chr17:37340284-37340636:-
Coord C1 exon
chr17:37340578-37340636
Coord A exon
chr17:37340394-37340577
Coord C2 exon
chr17:37340284-37340393
Length
184 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CCTCTTGCCCCATTCCCCAGGAT
3' ss Score
9.27
Exon sequences
Seq C1 exon
GTTACAGACATGATGCAGAAAGCTTTATTTGACTTCTTGAAGCATCGGTTTGATGGCAG
Seq A exon
GTAAGATCCTGGGAGCTGCTCCTCGCACCTGCCGTTGCTCTCTGCTGCTGGGGATGGGCAGGATGCCTCGAATCACAATCCTGGGACTCGGACTGAGGAACAGAAGGCGGGCCTGGAACTGGGGAGTGGGCAGGGCATTCCAGCCCACCCTGACCCCTGACTCCCCTCTTGCCCCATTCCCCAG
Seq C2 exon
GATCTCCATCACTCGTGTGACGGCAGATATTTCCCTGGCTAAGCGCTCAGTTCTCAACAACCCCAGCAAACACATCATCATTGAGCGCTCCAACACACGCTCCAGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000067191-CACNB1:NM_000723:9
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=0.039
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(10.5=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(20.4=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:
ACAGACATGATGCAGAAAGCT
R:
GCTGGAGCGTGTGTTGGAG
Band lengths:
162-346
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)