GgaINT1008187 @ galGal4
Intron Retention
Gene
ENSGALG00000025788 | CACNB1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:HGNC Symbol;Acc:HGNC:1401]
Coordinates
chr27:4114215-4114573:-
Coord C1 exon
chr27:4114451-4114573
Coord A exon
chr27:4114338-4114450
Coord C2 exon
chr27:4114215-4114337
Length
113 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGA
5' ss Score
6.03
3' ss Seq
CAGCCTCTTCCCACCTGCAGACG
3' ss Score
9.53
Exon sequences
Seq C1 exon
CAGGGCTCAGCTGAGTCCTACACCAGCCGCCCCTCGGACTCGGATGTGTCACTGGAGGAGGACCGCGAGGCGCTGCGCAAAGAGGCTGAGCGCCAGGCACTGGCACAGCTGGAGAAAGCCAAG
Seq A exon
GTGGGACTGGGGGAATTGGGACCCTCATCGCTGGGAGCCTTCTGTGGGGCACCGGCTCTCGCTGTGGGGTTTGAGGGGGATGCTGCCCCCACTCAGCCTCTTCCCACCTGCAG
Seq C2 exon
ACGAAGCCAGTTGCATTTGCTGTCCGGACAAATGTCGGCTACAACCCGTCTGCCAATGATGATGTGCCTGTGCAGGGCATGGCCATCTGCTTTGAGCCCAAAGACTTCTTGCACATCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000025788:ENSGALT00000043800:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.878 A=NA C2=0.293
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PU(92.9=95.1)
A:
NA
C2:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(44.2=46.3)
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:
GCTCAGCTGAGTCCTACACCA
R:
TGTGCAAGAAGTCTTTGGGCT
Band lengths:
234-347
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]