DreINT0040109 @ danRer10
Intron Retention
Gene
ENSDARG00000023886 | cacna2d4b
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4b [Source:ZFIN;Acc:ZDB-GENE-100422-18]
Coordinates
chr25:18939744-18939977:-
Coord C1 exon
chr25:18939933-18939977
Coord A exon
chr25:18939807-18939932
Coord C2 exon
chr25:18939744-18939806
Length
126 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
CAGTTTTTTTTTCCCCACAGGAT
3' ss Score
11.47
Exon sequences
Seq C1 exon
TGCAATGATGTGGAGGGCATTTGTCCTCTCAGCTGCGAGAGCATT
Seq A exon
GTGAGTCCAGCGTCTTTGTGTTGTCTTTACATAATCTGTGAATTGTTGTTCTGATTCTGTTCATTCACGTGAACCGTTCACCAGAGTGAATTTTGATCAAGTTAAACAGTTTTTTTTTCCCCACAG
Seq C2 exon
GATCTCAACTGTTACCTTGTTGACAGTAATGGCTTCATACTGATGTCAAAGGATAGAGGAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000023886:ENSDART00000027465:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAATGATGTGGAGGGCATT
R:
TCTCCTCTATCCTTTGACATCAGT
Band lengths:
107-233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]