HsaINT0026547 @ hg19
Intron Retention
Gene
ENSG00000067191 | CACNB1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:HGNC Symbol;Acc:1401]
Coordinates
chr17:37343046-37343854:-
Coord C1 exon
chr17:37343732-37343854
Coord A exon
chr17:37343183-37343731
Coord C2 exon
chr17:37343046-37343182
Length
549 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
ACCTGCCATATTCTTTGCAGAAA
3' ss Score
9.33
Exon sequences
Seq C1 exon
ACCAAGCCAGTGGCATTTGCTGTGCGGACAAATGTTGGCTACAATCCGTCTCCAGGGGATGAGGTGCCTGTGCAGGGAGTGGCCATCACCTTCGAGCCCAAAGACTTCCTGCACATCAAGGAG
Seq A exon
GTGGGTATCTGGAGGGAGGGCAGGGAAGTGGGTGCCAGGAGACAGGCAGCCAGAGTGCTAGTGGACAAAAGGCTTCTGAGCCAAGCAGAGCCAGGCTGAATCTGCTGTGTGACCTTAGACAAATCTCTCCACCTCTCTGAGCCTCTTAATTTTCTACTGGAAAAATGAGGTGGTAATGCTTAGGTCAGAAGGTTGTTGGGAGGGTTTGTTAGGGGGCCTGAACTGGCATGGCGGTGTGCCAGGGACATGTAGGTATCCGCATTTACTCCAGCGGCCTTTGTAGAGTAGGGTGGGCACATGGGGAGAAGGACTCTCAGAATTGCATTGGGCCGGTGGCAGGGTGGTCCATGGCCAGAAAGCATGCTGGTCCTGGAGTTGTCCTGAGAATTGGCAGCTCCACTCAGAGGCTGGAGCCAGGGCTGGGGATTTTTGAGGGTGCCACCCCTGGGCTGGGAGGTGAGTCTGGGCGTTTCCCCTAGAGAGTGACTGCTAGCTTGCCCCTGCAGTTTCCCTCTTGCTCTTTCCACCCACCTGCCATATTCTTTGCAG
Seq C2 exon
AAATACAATAATGACTGGTGGATCGGGCGGCTGGTGAAGGAGGGCTGTGAGGTTGGCTTCATTCCCAGCCCCGTCAAACTGGACAGCCTTCGCCTGCTGCAGGAACAGAAGCTGCGCCAGAACCGCCTCGGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000067191-CACNB1:NM_000723:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.506 A=NA C2=0.168
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)
A:
NA
C2:
PF0001823=SH3_1=PD(51.2=47.8)
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:
CAGTGGCATTTGCTGTGCG
R:
CAGCTTCTGTTCCTGCAGCAG
Band lengths:
230-779
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)