MmuINT0027910 @ mm10
Intron Retention
Gene
ENSMUSG00000057914 | Cacnb2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:MGI Symbol;Acc:MGI:894644]
Coordinates
chr2:14958766-14960857:+
Coord C1 exon
chr2:14958766-14958888
Coord A exon
chr2:14958889-14960654
Coord C2 exon
chr2:14960655-14960857
Length
1766 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGG
5' ss Score
6.38
3' ss Seq
ACTTTGGATTTTGTGTGTAGAAA
3' ss Score
5.36
Exon sequences
Seq C1 exon
ACAAAACCTGTTGCATTTGCAGTTCGGACCAATGTCAGATACAGCGCAGCCCAGGAGGATGACGTTCCGGTGCCTGGCATGGCCATCTCCTTCGAGGCCAAAGATTTTCTGCATGTTAAAGAA
Seq A exon
GTAAGGAGAATTTGTTTCCTTCCATGTGATTTTTCACCTTCAGCTCTCACTTACTTCTTAGTGTTGTGAAATAGACTTAGTTCTAGCTGCTGTTGTATAACCCACAGCTAAATCGGTGTCTCAGAACCTTTTCTGATATAAATAAACTTCAATGTAGAAAGGAGTCAGAGGCTCCTAGCAGGATTGCCAGGGCCCCTTTGGGCTTTGTGCCCCAGAAATTAGGAACTATTTTGCTGAGTGATCCAATTTTATGTGTGCCCTGCCTTTTATCTCTTAATGATTTACCTTGATTGACTACTGGTAATGTTTTTCCTGATGACTGAAGTCAGAGCCATATAAGGAAGAGGCTTTTTAGGTTTTTGGGGTTTTGTTTTTTGTTTTTTGTTTTTTGTTTTCTTCTTCTTCTTTTTAATGAGACAAGATTTCACTCTGTGGCCCAGGCTGACCTAGAATCTTTTATGTGGCCCTGGCTCTAAAACTCACTATATAGCCCAGCCTGGCCTCAAATGTGCTACAACTCCCTACTACCCACCATCCCTCCCTCCACTTCATTCACCTGGGTGCTGGGAGTCCAGTTGTAAACGTCCATGCCTGCCTCCCTGGAAGGGTTCGGTTGCTTCTTTCTACCAGAGAAGCATCATTTCTGCAGCAGAATGGAATGGTGGGAAATAGAGCAAATGAGACATGAAGGAAGCTGATGCCAAGAAAATGTTTGTTACCCTAAACAGACAAGGACAGCCTTTAAATTAGAAAAATTCACGTTTAATTACATTTTTTTTTGGTGTCCACATATCACATGTGTGCTCTGTGGGACATGATAATTTTTCCTAGAGTTCACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGGACCTGAGGGAATTTAGAGTTGGAGGCATTCACACAGGGAGAGTATGAAAATTAACTGGGCCATGCACTAACTGATGCAAGTGAAGGAGGCTAGAGAGCTCACAACTGCAACAAGTCATAGACAAAGATGTAAAAAAAAAAAAAAAAAGGATGCAAAAAAAAAAAAAAGGAAATCCAAGTGTTCAGAATTGATGGTGAGCATCCACAGGAACGGGTGAACATACAACAGGAAGTTAAACTAATATAGAGACTTTTCTTGATGCTAATACCTTGAGCAGAATCATTTTGTACTACAGAAAGAAAAATCATGAGCTTTTTAGAAAATACTTGATAATAGATTTAATTGAGGAAAATAAAATTAGATCCTGAAGATTCAAGATAAATATTTACCTGCAAGATAAGCTACCAGCATAAACATGAGAAAAACCACGTGTGAATGCTGTACTGTATGCCTATAAAACTGCAGAGGTACATTTTGCTGATACAGAATATTTCAAGTATATTTCAGTATTCCTCTTCAATATTAATACTTTGAATTAAACCAATTTCATAAGCAAAAGAACTCTGCAAGACTTCCTAGATTGTCTCTTGCTAGGGATATTAATCTTTGAATGTTGACCAATTATTACATATCTCAGCTTAGACCTAAATGCAGCACTGGAAAGGGAAAAACAAGGAGATGCAGTCTCTATTGGACTGCTGGCTGGCCACACCGAGCTGGGCACACACTTTTCTGAGCTGAACACACAAACCCAAAGGCTTCTTGAATTTTGGTATTAGATGTATGCTTCTAACTGCCATGTTTTTCTCCCGTGAAAACAGTTGATGTAGAAGAAGTCAATTCAGACGTTTAAACCTCTTGAACTGATTCTAATACTTTGGATTTTGTGTGTAG
Seq C2 exon
AAATTTAATAATGACTGGTGGATAGGACGGCTGGTTAAAGAAGGCTGTGAAATCGGATTTATTCCAAGCCCAGTCAAACTAGAGAACATGAGGCTACAGCACGAACAGAGAGCCAAGCAAGGGAAATTCTATTCCAGGTATGAACAACAACAACAACAACAAATCACTGTTTATATAAAAATGCAGACGTTGTCCTCGCTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057914:ENSMUST00000156027:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.435
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0001823=SH3_1=PU(51.0=61.0)
A:
NA
C2:
PF0001823=SH3_1=PD(44.9=47.8)
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:
GCATTTGCAGTTCGGACCAAT
R:
GCGAGGACAACGTCTGCATTT
Band lengths:
310-2076
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