HsaINT0026496 @ hg19
Intron Retention
Gene
ENSG00000157445 | CACNA2D3
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 3 [Source:HGNC Symbol;Acc:15460]
Coordinates
chr3:55107472-55107886:+
Coord C1 exon
chr3:55107472-55107584
Coord A exon
chr3:55107585-55107803
Coord C2 exon
chr3:55107804-55107886
Length
219 bp
Sequences
Splice sites
5' ss Seq
GGTATATCC
5' ss Score
-11.78
3' ss Seq
ATGCCTTAACTACAGTCAACATA
3' ss Score
-13.59
Exon sequences
Seq C1 exon
GTCCTTTGTCATCCAGCAAATCCCAAGCAGCAACCTGTTCATGGTGGTGGTGGACAGCAGCTGCCTCTGTGAATCTGTGGCCCCCATCACCATGGCACCCATTGAAATCAGGT
Seq A exon
ATATCCTTTTGTGTGCAGGTCCACTCACTACCACGGAAACCAGTAAGGGGTATCAGTGGTAAGGAAACCTGGGGGAGAAATATTAGAGAAGGAAAATTACATCCTTTCCACTGTTGGAGAGAGAGAGTAGTTAAGAGAGTTGTCATTGCCAAATTTTGACCTCTGAAATGCAGAGTAGAAAAAAGCAATCCTTGGAAACATGCCTTAACTACAGTCAAC
Seq C2 exon
ATAATGAATCCCTTAAGTGTGAACGTCTAAAGGCCCAGAAGATCAGAAGGCGCCCAGAATCTTGTCATGGCTTCCATCCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000157445-CACNA2D3:NM_018398:36
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=0.035
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GTCCTTTGTCATCCAGCAAATCC
R:
CTCAGGATGGAAGCCATGACA
Band lengths:
196-415
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)