HsaINT0026579 @ hg19
Intron Retention
Gene
ENSG00000167535 | CACNB3
Description
calcium channel, voltage-dependent, beta 3 subunit [Source:HGNC Symbol;Acc:1403]
Coordinates
chr12:49217127-49217586:+
Coord C1 exon
chr12:49217127-49217249
Coord A exon
chr12:49217250-49217463
Coord C2 exon
chr12:49217464-49217586
Length
214 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAC
5' ss Score
7.64
3' ss Seq
CTAATGGGCAAATTCTCCAGCAC
3' ss Score
1.46
Exon sequences
Seq C1 exon
GGTTCAGCCGACTCCTACACCAGCCGCCCATCTCTGGACTCAGACGTCTCCCTGGAGGAGGACCGGGAGAGTGCCCGGCGTGAAGTAGAGAGCCAGGCTCAGCAGCAGCTCGAAAGGGCCAAG
Seq A exon
GTATACTTTCTGGGCATGGGGCAAGACAGGAGGCCAAGCTAGGTGGAAACCTGCACTCGGTCCTAAGTCCCAAGGGGTCCTTGGGCAGGATGTCCTTGAGTGTGAGAGGGTGTGTGTGATGGGCAGAGGCCACGGCCTTCTGCTGTTGGGGCACTGAAGCTGGAAGGGGTGCTTCGAGCCTTCTCTCACTTGCACTAATGGGCAAATTCTCCAG
Seq C2 exon
CACAAACCTGTGGCATTTGCGGTGAGGACCAATGTCAGCTACTGTGGCGTACTGGATGAGGAGTGCCCAGTCCAGGGCTCTGGAGTCAACTTTGAGGCCAAAGATTTTCTGCACATTAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167535-CACNB3:NM_000725:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.976 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PU(93.0=97.6)
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PD(2.3=2.4),PF0001823=SH3_1=PU(44.2=46.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTTCAGCCGACTCCTACACC
R:
CTTTAATGTGCAGAAAATCTTTGGCC
Band lengths:
244-458
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)