DreINT0040135 @ danRer10
Intron Retention
Gene
ENSDARG00000002167 | cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:ZFIN;Acc:ZDB-GENE-040718-399]
Coordinates
chr3:16022021-16022313:-
Coord C1 exon
chr3:16022233-16022313
Coord A exon
chr3:16022080-16022232
Coord C2 exon
chr3:16022021-16022079
Length
153 bp
Sequences
Splice sites
5' ss Seq
GAGGCAAGA
5' ss Score
2.31
3' ss Seq
TGTGTGTGTGTGTGTTGCAGGTC
3' ss Score
12.6
Exon sequences
Seq C1 exon
ATGGAACATGTTCCTCCTTACGATGTGGTGCCTTCCATGAGACCCATTATTTTAGTGGGGCCGTCCCTTAAAGGCTATGAG
Seq A exon
GCAAGACTGCACTTCTCTCAGAAATTGGCAATTTATTATTGTAGTCATGTTGTTTATGCTCATATTGTGTGTGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGCAG
Seq C2 exon
GTCACAGATATGATGCAGAAAGCTCTCTTCGACTTTCTAAAACACAAATTTGAGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002167:ENSDART00000111707:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.115 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=PU(8.2=55.6)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(10.3=100)
Main Inclusion Isoform:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCCTCCTTACGATGTGGTGC
R:
CTGCCCTCAAATTTGTGTTTTAGA
Band lengths:
130-283
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]