HsaINT0026538 @ hg19
Intron Retention
Gene
ENSG00000151062 | CACNA2D4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:HGNC Symbol;Acc:20202]
Coordinates
chr12:1995389-1996235:-
Coord C1 exon
chr12:1996175-1996235
Coord A exon
chr12:1995540-1996174
Coord C2 exon
chr12:1995389-1995539
Length
635 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
ATGTCCCTTTCTTCCTTCAGGTA
3' ss Score
12.9
Exon sequences
Seq C1 exon
GTATAAAATGGACACCTGATGAGAATGGAGTCATTACTTTTGACTGCCGAAACCGCGGCTG
Seq A exon
GTAAGAGCTCACAGGGGAAAGGTTTGCGGCCCGGGTATTTATCTCATAGCTTTTGGGTTTTGCCTCATCCTCCTCCACTTCCGCCCCTTCCCCCACCGCCACTCAAGGGCCTTGGGTGTGTAGAACCCTAGCCCGACACAAGAGCAGGAAGAGGGCCAGCATTCCTCCCTTCCCTCTACAATTGCCTTGCTCCAGGACTGATCATGTTTGTCTTTCCCAACCTAAACCTCCTGCCAGGACACTGAGCTGTCTCCACGTCAACCTTTTGTTAGGCTCTCCTCTCCTTCCACACCCCTTTTGTGGCAAGTTGGTAACAGAATCTGAAGCCCAGCTCTCTCCCTTTCTGCTGCCAGCCCCTCAGGGACCCCGGTTGGTCTAAATCAAAAGGAACAAGCGTTACCTCCAGGGCTTGACCTGGCCTGTTAGGTGGCACATCCCCAACCACTGCCACCCCAGATGGCTTCAGCACTGTGTCAAGTGGTTATGGAACATGTGAAACCTGGCATAGATGGGTTGCCCTGAACTTTGGGTGGGCTCGAGCCAGCATCTGAACAGAAATAACTGCAGACCCCTTGGTCAGGTATTGGTTCCGGCTTTGGTTTTCCCATCTTGGGCATGTCCCTTTCTTCCTTCAG
Seq C2 exon
GTACATTCAAGCTGCTACTTCTCCCAAGGACATAGTGATTTTGGTGGACGTGAGCGGCAGTATGAAGGGGCTGAGGATGACTATTGCCAAGCACACCATCACCACCATCTTGGACACCCTGGGGGAGAATGACTTCATTAATATCATAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000151062-CACNA2D4:NM_172364:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF083996=VWA_N=PD(2.6=14.3)
A:
NA
C2:
PF137681=VWA_3=PU(24.7=80.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATAAAATGGACACCTGATGAGAATG
R:
TGATATTAATGAAGTCATTCTCCCCC
Band lengths:
206-841
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)