MmuINT0027871 @ mm10
Intron Retention
Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119337882-119338177:+
Coord C1 exon
chr6:119337882-119337926
Coord A exon
chr6:119337927-119338114
Coord C2 exon
chr6:119338115-119338177
Length
188 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
GGCCTCTCCCCCCACCCCAGGAT
3' ss Score
7.35
Exon sequences
Seq C1 exon
TGCAACGCTGTAGAGGGGCCGTGCCTGAAGAGCTGCGAGGACACT
Seq A exon
GTAAGTTCTTCCCAGAGCACAGGTTCAGTGTCCTGTGTTGCTCTGTGGACTACTTCTTCCTCAAAGGCCCCCTTCCTGACCCTGACTGCAGGGTTCAGCCCTCCTCGGCTGCTAGAGTGAGCAGGAGGGTTGGAGCCAGCGATAACCCTGGCTATGACCTCCTGTCCTGGCCTCTCCCCCCACCCCAG
Seq C2 exon
GATCTCGACTGCTTCGTCATAGACAACAATGGCTTCGTCCTGATCTCAGAGAGACCCCAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460:ENSMUST00000037434:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAACGCTGTAGAGGGGC
R:
TCTTGGGGTCTCTCTGAGATCA
Band lengths:
106-294
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