GgaINT1008188 @ galGal4
Intron Retention
Gene
ENSGALG00000025788 | CACNB1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1401]
Coordinates
chr27:4109999-4110744:-
Coord C1 exon
chr27:4110649-4110744
Coord A exon
chr27:4110104-4110648
Coord C2 exon
chr27:4109999-4110103
Length
545 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
ACCTCAGTCTCCCCCTCCAGGAG
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTGCTGCAGCGGTTGGTGAAGTCCCGGGGCAAATCCCAGGCCAAGCACCTCAACGTGCAGATGGTGGCCTCCGACAAGCTGGCGCAGTGCCCGCCT
Seq A exon
GTGAGTGTCCCCACCCCAACCCCTGCCACCACCCTGCGGCCATTGGCTCCGCCCCCCCAGGCAGAAGCTCCTCCCACCACCTCATCCTTACGTAGGGATTCCACCTATCCTGGCCCCGGGCTCCGCCCACCACCATATTGGGTTATGTAGGCTCCACCCCCGTGTGGCAAAGGCTCCACCCACCACCATATTTGGGTACATATGCTCCTCCCCCATGTGTCAAGCTCTGCCCAGCACCTTTTTTGGGTACATCAGCCCACCCACTACCTTATATGGGTAAATAGGCCACACCTCCACATGATACAGGCTCCGCCCACCTCCTTATTTGGTACATGTGCCCCACCCACTACCTTATATGGGTACGTAGCTCCCACCCCCGTGTGTACAAGCTCCGCCCATCGCCTTATTTGCATCCATAGGCTCCACCCCCCGCTCCATTGCAGTCAGCAGCTCCGCCCTCGTGGCAGATGCTCCTCCCACCATCCTGACCTGTAGGCTCTGCCCTGTGCCCATAAGCCCCACCCCACCTCAGTCTCCCCCTCCAG
Seq C2 exon
GAGATGTTTGACATCGTGCTGGACGAGAACCAGCTGGAGGAGGCCTGCGAGCACCTGGCCGAGTACCTGGAGGCCTACTGGAAGGCAACGCACCCCCCCAGCAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000025788:ENSGALT00000043800:10
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=0.086
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(17.1=100)
A:
NA
C2:
PF0062516=Guanylate_kin=PD(13.8=71.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTGCAGCGGTTGGTG
R:
GGTGCGTTGCCTTCCAGTAG
Band lengths:
190-735
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]