DreINT0040136 @ danRer10
Intron Retention
Gene
ENSDARG00000002167 | cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:ZFIN;Acc:ZDB-GENE-040718-399]
Coordinates
chr3:16021731-16022079:-
Coord C1 exon
chr3:16022021-16022079
Coord A exon
chr3:16021841-16022020
Coord C2 exon
chr3:16021731-16021840
Length
180 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TGAATTATTGTTTGTTCCAGAAT
3' ss Score
7.93
Exon sequences
Seq C1 exon
GTCACAGATATGATGCAGAAAGCTCTCTTCGACTTTCTAAAACACAAATTTGAGGGCAG
Seq A exon
GTGGGTACCATAATGTGCATGCCATGATTATAATGAATAATAGACTTCTTCTCATCACTATGGCATTGATAAACATTTAGGTAACATTACAGCTCTGTGCAGATCATTCATGATGGAAATATCACAGCGCACTCATGCTATAATTGGAATAGCGTGGTTATGAATTATTGTTTGTTCCAG
Seq C2 exon
AATATCCATCACCCGGGTGACAGCCGACATCTCACTTGCCAAACGCTCCGTCCTTAACAACCCCAGCAAACACACCATCATCGAGCGCTCCAGCACCAGATCCAGCCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002167:ENSDART00000111707:9
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=0.154
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(10.3=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(20.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCACAGATATGATGCAGAAAGCT
R:
CAGGCTGGATCTGGTGCTG
Band lengths:
168-348
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]