DreINT0040157 @ danRer10
Intron Retention
Gene
ENSDARG00000001881 | cacnb3a
Description
calcium channel, voltage-dependent, beta 3a [Source:ZFIN;Acc:ZDB-GENE-060221-2]
Coordinates
chr23:14402700-14403252:+
Coord C1 exon
chr23:14402700-14402800
Coord A exon
chr23:14402801-14403100
Coord C2 exon
chr23:14403101-14403252
Length
300 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
GTGTCTGTTTGTGCCCTCAGCGG
3' ss Score
9.33
Exon sequences
Seq C1 exon
GATTTCAATAACCCGAGTAACTGCTGACCTTTCACTGGCCAAGAGATCAGTTCTCAACAAGAGACCCATCATGGAGAGGTCAAACACACGGACCAGTTTGG
Seq A exon
GTGAGGACATCACACAATAAAGCTACACTGCTATACAGAAAACCCTCCAAAGCTCACAAAAAAATCCCCATTTGCTGATCTTGCACACTTTTTTGTGTTTTACATATTTTATTGCTTACGTAAATGATTATCAAGCTGGTTACCAAGATCTTTTTTCAAAACTGTGAGAACACTTTAGAGGCATCTGCCAGAAAAGGTGCAAAACATAAAAACCAGAACAAAAATCAGACAAATATGTAATAAACCCTTTCTTTCAGTATGTTCTCGGGCTTCATCTTTTGTGTCTGTTTGTGCCCTCAG
Seq C2 exon
CGGAAGTACAGAGTGAGATTGAGAGAATATTTGAGTTGGCCAAAACCCTTCAGCTGGTGATTCTGGATGCAGACACCATTAACCATCCAGCACAGCTAGCTAAAACCTCACTAGCACCTATTATTGTATATGTAAAGGTCACGTCTCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001881:ENSDART00000087280:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.286 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(19.1=100)
A:
NA
C2:
PF0062516=Guanylate_kin=FE(28.1=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:
ATAACCCGAGTAACTGCTGACCT
R:
CTTTGGAGACGTGACCTTTACA
Band lengths:
246-546
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]