DreINT0040164 @ danRer10
Intron Retention
Gene
ENSDARG00000001881 | cacnb3a
Description
calcium channel, voltage-dependent, beta 3a [Source:ZFIN;Acc:ZDB-GENE-060221-2]
Coordinates
chr23:14389735-14390086:+
Coord C1 exon
chr23:14389735-14389857
Coord A exon
chr23:14389858-14389967
Coord C2 exon
chr23:14389968-14390086
Length
110 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGTATGTGTTTGTGCTGCAGAAG
3' ss Score
8.02
Exon sequences
Seq C1 exon
TCCAAACCTGTAGCATTCGCAGTGAAGACGAATGTGAATTATTGCGGGGCTCTAGATGAGGAATGTCCTGTTCAGGGTGCTGCCATAAACTTTGAAGCCAAAGACTTTCTGCACATTAAAGAG
Seq A exon
GTGAGCTGGAGTTGTGGTTCAATGCATGCACGAAAGCTTTGCAGGTCAGTTTTCTTAATAGCACAATCATAATAGCACTGAGGATGTTTTTGTATGTGTTTGTGCTGCAG
Seq C2 exon
AAGTACAATAATGACTGGTGGATTGGAAGGCTGGTGAAAGAGGGGGCAGACATCAGCTTCATTCCCAGCCCCCTCCGACTGGAGGCCATGAGAATCAAACAGGAGCAGAAACAGCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001881:ENSDART00000087280:4
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=0.250
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(43.9=43.9)
A:
NA
C2:
PF0001823=SH3_1=PD(51.2=52.5)
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:
TCCAAACCTGTAGCATTCGCA
R:
CTCTGCTGTTTCTGCTCCTGT
Band lengths:
242-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]