MmuINT0027882 @ mm10
Intron Retention
Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119241153-119242940:+
Coord C1 exon
chr6:119241153-119241212
Coord A exon
chr6:119241213-119242777
Coord C2 exon
chr6:119242778-119242940
Length
1565 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
CTGTTCCCCTTTCGCCCCAGTTT
3' ss Score
8.88
Exon sequences
Seq C1 exon
AGCCTGGTGGAGGCCGCTGAGGAGGCTGACCTGAATCATGAGTTCAATGCATCTCTGGTG
Seq A exon
GTAAGTCCTCTGGGGAGCGGGTGCTAGGCCGGCTGATTGGCTCTGCCCCACCCCCATGGCAGCTGGAGGACCAGCTGTGAGCAGATCTGAGCAGCAGACACTCATTCTATGTCCTTGTGCCAGGCTGTGCCCTGGCTTTGCCAGTGAGGCTTTCTTTCCACCTCCTAAGGCTCTCGGAGAAGGAATAGAATAAACATGTGGTGTGGGGGTGGGTCGGTGACCCCGGGAAGCAGAGGGAAGAGGGACCGACTGACCCCGCGCGGCAGGGATAGCCTCGAGGAGGGGACTTGGGAAGCTAAAGCACTAAGGGGCATCTCTGTGCCGAGAAACAGAAGACACAGGAAGAAGAAAGCTCAGGTTGTGTGAGGAGGTGACAAATACAAGCCCTCTGTGTCCAGGGGTCAGTAAGTCAGGATATCACCCGAGAGGGGCCAGGGTTAAGATCTGGTCTGGGATGCTGGGTGTCCTGGTTGCTTTCCGTTACTGTGGTAAACACCACGGTCTAAAGCAGCTTGGGGGAGGATTCGGCTTACACATCACAGTCACAGACCATCAGTGGCTGCGGAAGCCAAGGTAGGAATTCAAGGCAAGAATCTGGAGGCAGAGACTGAAGCAGACCCCTGGAGGAAAACCCGCTTTGTGGGGTTTTTCCCTTGGTTCACTCAGTTTGCTTTCTTATGTAACCATTCACCATCTGCCCACGGGTGGCACTCTTCACAGTGGACTGGGCCCTCCCACCTTCCACAGACTTGCCTCCAGGCCAATCGGATGGAGGCATTTTTTTCAACTTAGACTGCCCTCTGCCAAGATGGCCCAAACTTGTGTCAAGCTGACGGAAAACTAGGAGGCTCTCAGGGAGTATGAGGGCTGGAGTCAGGGAGGAACGTGGCTGGGCCTGAGCTCACAGAGCTAACACTGACTAGAGGCCAGCAAGGTGGAGCAGGGAGGGGTGTTATGGCCACAGTTCTAGAGGGACTTAAGGTATGAGGCTCGGAGTTGGGGGCAGCCAGGGGAAATGGATCTGATCGTGGTCCCTTGGGTCACAGCCTTCCCGCCCTATGGGAGGAAACGGAACATGGCACAGGTCCACTTGCAGGGCAGAGCCCCAGAGGCTCCTCAAGCCCTCTGGCTCTCCAGCACCCTCACCACCTAGAAGAATCAAACAGTGCCAGCAAGGTCCTTTGCATCCTTGTGGCTCCCTGAGTCTCCATCTGTCTGTCAGTCAGTCTGTCTCAGACTAATTTTGCTACATACACTAAACCAAGTGGAGAATCAAAGCAATGATTGGGCCAATCTGACCCCAACCAGCCAATGAACCTTCAGCTCCAGTTATCTTGTCGTGCGCGTTGTGACCACATATCTCTATCCACCACTGGCAACATAACTGAAGTGCAAGGCCATTCCCCACCCCACCCTTCACCTCACTTCCAGTTGCCCTTGAAGCTTCCACTCCTTTCCCTGGGTCCCTCCTCCCTTCTCTTTTTACTCTCGGCCTGACTCCCTTCCTCCCCTCCCCTCTTTGTCTCTGGGCTGTCTCTTCTGGGCCTGTTCCCCTTTCGCCCCAG
Seq C2 exon
TTTAACTACTACAACTCGGTACTAATCAATGAGAAGGATGACAAGGGCAACTACGTGGAGCTGGGAGCTGAGTTTCTTCTCGAGTCCGACGCGCACTTCAGCAACCTGAGGGTGAATGTCTCCATGAGCAGCGTTCAACTGCCCACCAACGTGTACAACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460:ENSMUST00000037434:4
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=PU(12.0=70.0)
A:
NA
C2:
PF083996=VWA_N=FE(46.2=100)
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:
GTGGAGGCCGCTGAGGAG
R:
CACGTTGGTGGGCAGTTGAA
Band lengths:
207-1772
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