DreINT0040076 @ danRer10
Intron Retention
Gene
ENSDARG00000026855 | cacna2d4a
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4a [Source:ZFIN;Acc:ZDB-GENE-041210-213]
Coordinates
chr4:20569276-20569588:-
Coord C1 exon
chr4:20569529-20569588
Coord A exon
chr4:20569439-20569528
Coord C2 exon
chr4:20569276-20569438
Length
90 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
TCCTGCTTTTACTTTTGCAGTTT
3' ss Score
9.73
Exon sequences
Seq C1 exon
AGAATGGCAGAGACAGCAGAAGACGCAGATTTTTATCATGAATTTAATGCCACATTAGAG
Seq A exon
GTGAGTTATCCAGCAGTCCTTCGATCGATCTCCCTCACCTCCATTCATTTATTATTATACATTTAATTTTTCCTGCTTTTACTTTTGCAG
Seq C2 exon
TTTGACTACTACAATTCCATGTTGATTAACACATTAAATGAAGATGGAAACAACATAGAGCTGGGGGGTGAATTTCCTTTGGAGGAGAATGAACACTTCAACAATCTGCCTGTCAATACGCAGCAAAGCGTCGTACAAGTGCCCACAAATGTTTATAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000026855:ENSDART00000136069:3
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=0.236
Domain overlap (PFAM):
C1:
PF083996=VWA_N=PU(12.0=66.7)
A:
NA
C2:
PF083996=VWA_N=FE(46.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGAGACAGCAGAAGACGCAG
R:
TTTGCTGCGTATTGACAGGCA
Band lengths:
180-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]