MmuINT0027894 @ mm9
Intron Retention
Gene
ENSMUSG00000020882 | Cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:MGI Symbol;Acc:MGI:102522]
Coordinates
chr11:97866443-97867097:-
Coord C1 exon
chr11:97867002-97867097
Coord A exon
chr11:97866629-97867001
Coord C2 exon
chr11:97866443-97866628
Length
373 bp
Sequences
Splice sites
5' ss Seq
CCCGTGAGT
5' ss Score
8.4
3' ss Seq
CCCTAACCCCACCTCCACAGGAA
3' ss Score
7.23
Exon sequences
Seq C1 exon
GTACTGCAGAGGCTCATCAAATCCCGAGGGAAGTCTCAATCCAAACACCTCAATGTCCAAATAGCAGCCTCGGAGAAGCTGGCACAGTGTCCCCCC
Seq A exon
GTGAGTGCTCAGACCCAGGGGAGGGAAGGGAAGGTGTCTTTTTGGGTTCTCCTGTTTCCTTCAAGCCTGCATGGAAGACAGCACTTGGGCCAGGTCCTTGGGTAAAGAGGGATGCCTGATTGGCCAAATGGCTCAAATACTCCCTACTGCGTGCCCAGCCATGGCCTGATTTCCCTATCCCTAGAATGAGAGGGAGTTGGGCTGAGTTCGGTCTTTTGTAGGTCTGAAGTGTCCTTTCCTTGGGCCACATCCAGAGGCCTTTTAACCTTGTCCTTCAACCCCCTTGACTCCACCCACTGCACCCAGGCCACACCTTCAACCCTTGGTCACGCCCCCGCTCATCCCAGCCCCGCCCCTAACCCCACCTCCACAG
Seq C2 exon
GAAATGTTTGACATAATCCTGGACGAGAACCAATTGGAAGATGCCTGCGAGCACCTGGCTGAGTACTTGGAAGCCTACTGGAAGGCCACACATCCGCCTAGCAGCACGCCACCCAATCCGCTGCTGAACCGCACCATGGCTACCGCAGCTCTGGCTGCCAGCCCTGCCCCCGTCTCCAACCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020882-Cacnb1:NM_145121:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.379
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=FE(17.1=100)
A:
NA
C2:
PF0062516=Guanylate_kin=PD(13.8=40.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAGAGGCTCATCAAATCCC
R:
CTGGAGGTTGGAGACGGGG
Band lengths:
278-651
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: