GgaINT1008190 @ galGal4
Intron Retention
Gene
ENSGALG00000025788 | CACNB1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1401]
Coordinates
chr27:4113910-4114337:-
Coord C1 exon
chr27:4114215-4114337
Coord A exon
chr27:4114047-4114214
Coord C2 exon
chr27:4113910-4114046
Length
168 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
GTGTCCATTCCCTGGTGCAGAAG
3' ss Score
6.17
Exon sequences
Seq C1 exon
ACGAAGCCAGTTGCATTTGCTGTCCGGACAAATGTCGGCTACAACCCGTCTGCCAATGATGATGTGCCTGTGCAGGGCATGGCCATCTGCTTTGAGCCCAAAGACTTCTTGCACATCAAGGAG
Seq A exon
GTGAGGGTCTGGAGTGGTGGGGGGGAGCAGAGCAGGAGGCTGGGGGTGGCGGGGACTTGGGGATGGGGGTTGGCAGGGCACGGGGCTGAGGGTGGCAGGGTGTGGGGCTGCTGTGCGCCGTCCGTTTGCAGGCTTTGAGGTGTTTTCTGTGTCCATTCCCTGGTGCAG
Seq C2 exon
AAGTACAACAACGACTGGTGGATCGGGCGGCTGGTGAAGGAGGGCTGCGAGGTCGGCTTCATCCCCAGCCCTGTCAAACTGGAGAACATGCGGCTGCTGCAGGAGCAGAAGATGAGGCAGAACCGACTGAGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000025788:ENSGALT00000043800:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.293 A=NA C2=0.348
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)
A:
NA
C2:
PF0001823=SH3_1=PD(51.2=47.8)
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:
CGAAGCCAGTTGCATTTGCTG
R:
TCAGTCGGTTCTGCCTCATCT
Band lengths:
252-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]