MmuINT0027910 @ mm9
Intron Retention
Gene
ENSMUSG00000057914 | Cacnb2
Description
calcium channel, voltage-dependent, beta 2 subunit [Source:MGI Symbol;Acc:MGI:894644]
Coordinates
chr2:14880393-14882418:+
Coord C1 exon
chr2:14880393-14880515
Coord A exon
chr2:14880516-14882281
Coord C2 exon
chr2:14882282-14882418
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
AAATTTAATAATGACTGGTGGATAGGACGGCTGGTTAAAGAAGGCTGTGAAATCGGATTTATTCCAAGCCCAGTCAAACTAGAGAACATGAGGCTACAGCACGAACAGAGAGCCAAGCAAGGGAAATTCTATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057914-Cacnb2:NM_023116:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.109 A=NA C2=0.351
Domain overlap (PFAM):
C1:
PF120523=VGCC_beta4Aa_N=PD(2.4=2.4),PF0073614=EF1_GNE=PD(39.0=56.1),PF0001823=SH3_1=PU(52.9=65.9)
A:
NA
C2:
PF0001823=SH3_1=PD(44.9=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:
GCATTTGCAGTTCGGACCAAT
R:
GGAATAGAATTTCCCTTGCTTGGC
Band lengths:
246-2012
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: