MmuINT0027920 @ mm10
Intron Retention
Gene
ENSMUSG00000003352 | Cacnb3
Description
calcium channel, voltage-dependent, beta 3 subunit [Source:MGI Symbol;Acc:MGI:103307]
Coordinates
chr15:98642502-98644530:+
Coord C1 exon
chr15:98642502-98642651
Coord A exon
chr15:98642652-98643256
Coord C2 exon
chr15:98643257-98644530
Length
605 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACT
5' ss Score
8.63
3' ss Seq
AGATCTTGTGTGGCCCCCAGAAC
3' ss Score
6.97
Exon sequences
Seq C1 exon
GAGTCATTCGACGTGATTCTGGATGAGAACCAGCTAGAAGATGCCTGTGAGCACCTGGCTGAATACTTAGAGGTTTACTGGCGAGCGACCCACCACCCAGCACCGGGCCCCGGACTGCTGGGTCCGCCTAGTGCCATCCCTGGACTTCAG
Seq A exon
GTAACTGTTTCTAGTGGGCACAGCTGTGCAGGCTTCCCCAGTCGAGGCAAAGCTCCCGTCCTGACCAAGGATTGTTCTTGGTCTGTGTGTGAAGCCAAGGGATTGCTGAGACTGTCAGCTCTGCCTGCTCCACAGACCTTATGGCACACAGGTCAAGGGACTTCCTGATTGGACAGCACAGTGACTGAGATCAGATGGTCCTCCTAGGGACAAAGGAAACACTCTCCACACCTATCTCCGGGGGCACTTTTTTTTTTCTTCGAGACAGGGTTTCTCTGTATAGCCCAGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTACCTCCTGCGTGCTGGGATTAAAGATGTGCGCCACCACGCCTGGCTTTCCCGGGTACTTTTTAAGGGAGAGCCTGAATTTGTAAGGAGCTAAAACTACTTTCTGCACTTAACTTGGAAAATACCCCAACTTAATTCTTCCTTGCACTGCATACTTTTAAAAACCTAGGCATTGAGAGTAGGGGGAGTGTTAGAACCTCATCTCCCTACGAAGGCCAGGCTTCTCTTCCCTTACCTAGATCTTGTGTGGCCCCCAG
Seq C2 exon
AACCAGCAGCTGCTGGGGGAGCGAGTGGAGGAGCACTCACCCCTGGAGAGGGACAGCCTGATGCCCTCAGATGAGGCCAGCGAGAGCTCCCGCCAGGCCTGGACCGGATCTTCACAGCGCAGCTCTCGCCATCTGGAGGAGGACTATGCAGATGCCTACCAGGACCTGTACCAGCCTCACCGCCAACACACCTCGGGGCTGCCCAGTGCTAACGGGCACGACCCCCAAGACCGGCTCCTAGCCCAGGACTCGGAGCATGACCACAATGACCGGAACTGGCAGCGTAACCGGCCTTGGCCCAAGGACAGCTACTGACCACCTCCTGCCCCACCCTGGCAGGCGCAGGCACAGCGGCTGGGGTGTCCACCTCAGGCAGGTTGGAGTTAGATTGGCATTAGGCTGCCGTTAGGTTCAGCTCACACAACCCTCTGCCCAGCCCCAGGTCCAGGGCTGACTGTGGTCCCAAGGTTCTGGGAGAAGCAAGGGGCCCCTCACCTCCTGGGCACAGTGACCCCGTAGGTTCTCATCCGGGTACTAGCCGTGTTCTGCATCCTTGGCACCTCCCCCTGCATAAGCTGCCGCCCCCGTGGGCAACAATCTCAGGCCAGGATCACTTAGCAGGGGCCTTCCAGCCAGAATGGATGCCCCTCTAAAGAGCAAGAGGGTGTGAGTGTGGGCAACATAGCCTGAGGAAGAAGAAACTCGGTTCCTAAGCAGGCGTAGATCCTAAGCAAAGGGACTCCATTCACGCCACTGCCACACATCAGAAATGAAGCAATCAGAGCTCAACATGGCGGCACTTCTGTCCCATCAGCTGGGGTGGGCACTTACACCTAAGACAGGAGCAGTGCGGGTGAGGCAGGACAGACAGACTCACAGCTGTAGCTCTGCTAGAAAACGGCCCACTCACCAAACCGGGACGCTTAGCATCTGGTGAGACTAGGGAACTGGGGCATATTCAAGCCAAGAGCCAGCCTGGACTGCGGGGGAGGGTGGGACAGCTTCCGGCCCCCCTTGCTCTTCTCATTCTTTGCCCTTGCATCTGTCATTTCTGTCCTTTCCCTCCATGGCTCCTGCAAGATAGGGGCTTCCTGACTCATAGCAGCCACTTCAGTTAGGGTTAGATGAGAGGAACAGGACACAGTGAACAGTCCCCGAGGCTGTCCACCTGGCTACCCTTGCCTTATGGCTCTAGCGTGTGACCTACAGAGCATGCTCCATTAAGAACCCGCCCCACCTCATTGTCATCTCCAATAAAACACCACGCACAGTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000003352:ENSMUST00000003442:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.360 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0062516=Guanylate_kin=PD(13.8=50.0)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGAGGTTTACTGGCGAGCGA
R:
TTCCGGTCATTGTGGTCATGC
Band lengths:
358-963
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