MmuINT0027897 @ mm10
Intron Retention
Gene
ENSMUSG00000020882 | Cacnb1
Description
calcium channel, voltage-dependent, beta 1 subunit [Source:MGI Symbol;Acc:MGI:102522]
Coordinates
chr11:98012185-98012934:-
Coord C1 exon
chr11:98012812-98012934
Coord A exon
chr11:98012322-98012811
Coord C2 exon
chr11:98012185-98012321
Length
490 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGT
5' ss Score
7.07
3' ss Seq
TCTTGGGCGCTTGTTCACAGAAG
3' ss Score
4.71
Exon sequences
Seq C1 exon
ACCAAACCAGTGGCTTTTGCTGTTCGGACAAATGTTGGCTACAATCCGTCTCCAGGGGATGAGGTGCCTGTACAGGGAGTGGCCATCACCTTTGAGCCCAAGGACTTCCTACACATCAAGGAG
Seq A exon
GTGGGTGCAACACTTGGCACCAGGAGTGGGGCGAGGGTGGGACATTAGAGGTGTATGGGAGGGATGCCAGGAGAGGGGGCTAGTGGGAAAAAGCTGCCCAGCTGAACGCAGCTGGCCCGAGTCTGCTATGCACCCTTAGGCAAATCTCTTCACCTCTCTGAGCTCAGTGAATTTTCATTGGTTGGTAATGCCTAAGTCGCAGTGACGCTGAGAGGGCTTGTGAGCCTTGGGCGCCGGTGCATGTGTCTGCTTTCCTACCCACAGCATAACTCTCAGGGAGGCAGGAGCCTTCTTCCTACCTTCTCTCTAAACGAGGGTGGGTGGTCGATGGTCACAGAGGGAATTGGGAGGATCTTATCAGAGGCTGAAGCCGGGGGCGGGGCTTCTTTGAGGGAGCTGTTTACTGGCAGGGTTGGCAGCCTGGGGGTCTCCCTAGAAGGTAGCTATGGCTCCCATCTCCAGTCTCTCCCTCTTGGGCGCTTGTTCACAG
Seq C2 exon
AAGTACAATAATGACTGGTGGATTGGGCGGCTGGTGAAGGAAGGCTGCGAGGTTGGCTTCATCCCCAGCCCGGTCAAACTGGACAGCCTTCGTCTGCTGCAGGAACAGACCCTGCGCCAGAACCGCCTCAGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020882:ENSMUST00000017552:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.484 A=NA C2=0.203
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:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAACCAGTGGCTTTTGCTG
R:
CTGGAGCTGAGGCGGTTCT
Band lengths:
259-749
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types