HsaINT0026533 @ hg19
Intron Retention
Gene
ENSG00000151062 | CACNA2D4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:HGNC Symbol;Acc:20202]
Coordinates
chr12:1904465-1904946:-
Coord C1 exon
chr12:1904832-1904946
Coord A exon
chr12:1904546-1904831
Coord C2 exon
chr12:1904465-1904545
Length
286 bp
Sequences
Splice sites
5' ss Seq
TATATCCTG
5' ss Score
-28.05
3' ss Seq
TAACAGTGGCTTCTGCACATAAT
3' ss Score
-5.87
Exon sequences
Seq C1 exon
GGTATTTGTGGTGCAGCAGATTCCCAACAGTAACCTCCTCCTCCTGGTGACAGACCCCACCTGTGACTGCAGCATCTTCCCACCAGTGCTGCAGGAGGCGACAGAAGTCAAATAT
Seq A exon
ATCCTGCAATGCTCGGGGATGTGTGCGGTGGGGGCGGGGGCTGTAGGAGGTGTCTGTAGGGCTCAGATTTTGAGCAGCGGGGCCAGCCTCCTTCACCGCCCGTGTCCTCCACAGGGCTCCGTTATTTGTTCTCTAACCCTTCCCTGGGCCCCGGTGCTGCCTCCTGACCCTAAAGCTGCTTGCAGGGCAACTGGTGGCACCAGAGCAGGTTCTTCCAGACCTTTTTCCAGTCTGCAGAATGGGCTCCGGTCCTGAGATATTGACCTTAACAGTGGCTTCTGCACAT
Seq C2 exon
AATGCCTCTGTCAAATGTGACCGGATGCGCTCCCAGAAGCTCCGCCGGCGACCAGACTCCTGCCACGCCTTCCATCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000151062-CACNA2D4:NM_172364:36
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.111
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTATTTGTGGTGCAGCAGAT
R:
CTCTGGATGGAAGGCGTGG
Band lengths:
196-482
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)