MmuINT0027885 @ mm10
Intron Retention
Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119267807-119268346:+
Coord C1 exon
chr6:119267807-119267867
Coord A exon
chr6:119267868-119268195
Coord C2 exon
chr6:119268196-119268346
Length
328 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGC
5' ss Score
8.69
3' ss Seq
TTGCCTTTCTTTCTGATAAGGTA
3' ss Score
8.34
Exon sequences
Seq C1 exon
GAATAAAGTGGATGCCTGATGAAAACGGAGTCATCGCCTTCGACTGCAGAAACCGTGGCTG
Seq A exon
GTAAGCACTCCCAGAGGAGAGGTACTGTGCCCCAGCACCTCTCTTTCATCCTTTGGGCTTGCCTTGGCTTTCTTGCACCCTCCCCAACTCAGAGGCTTGGGAAGGGACCTCAGTGGTTTAATCCAACCAAGGAATAAGAAGGCTTACTTCCAATCTCAGCACCCCAGCAGCCTCCATGTCCAGGGGTCACAACACACAGTGAAGGACAAGGGGGCACTGGCCTAAACTTGGGGAAACCCATGGGCCAGACCAAATAAATGAACTGGAGTTTCCCAGCCAGGTGCAGTACAGCCTTGGCCTCCCTCCCATTGCCTTTCTTTCTGATAAG
Seq C2 exon
GTACATACAAGCTGCCACATCTCCCAAAGACATCGTAATTCTGGTGGACATTAGCGGCAGCATGAAGGGGCTGAGGATGGCTATCGCCAAGCACACCATTACCACCATATTGGACACCCTGGGAGAGAACGACTTCGTGAACATCATCGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460:ENSMUST00000037434:7
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:
PF083996=VWA_N=PD(2.6=14.3)
A:
NA
C2:
PF137681=VWA_3=PU(24.7=80.4)
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:
AGTGGATGCCTGATGAAAACGG
R:
CGCGATGATGTTCACGAAGTC
Band lengths:
206-534
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