MmuINT0027867 @ mm10
Intron Retention
Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119307246-119308804:+
Coord C1 exon
chr6:119307246-119307341
Coord A exon
chr6:119307342-119308676
Coord C2 exon
chr6:119308677-119308804
Length
1335 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CATCAATCCTACTCTCACAGGAA
3' ss Score
6.65
Exon sequences
Seq C1 exon
AGAGTCAGAGCCTGGCGTGGATGTGGCCTTCCTGGGAACCCGGGCTGGCCTTCTAAGAAGAAGCTTGTTCGTAGGCTCCGAGAAAGTCTCTGACAG
Seq A exon
GTGAGCCCTGGGATGGGGGACCTCTGGGAGGAAGGAACATGACACAAGACTTGGGTCCCTTTGGGGCATGCAGGGCAGAGACGGTTTCAGTATGCTGTGCCCTGTGAATCCACTGACATAGACACGGGGGAACGGTTGGCTGATGGGTGCCGTCAGATGCCCATCTTTCCTCCCACCCGCACCAGATCCCTCTCACTAAGTCCCAATGCCTTCAGCTACGGAGCTCCTCGGTGCCTCCATCAGGACTCAGTGACAAGTCCACACACCATGAGCAAGGTTGGAGGCTTTCTAGGAAAACAGTTTTGGCGGGCTTTCCCTCTCCTTTCTTCTTTCCCTCCCCTAATTCCCAGAGAGGCAGGGGTGGGGGTGGGGGTAGCACCATCCTTAAAGGGCTTCTAAGGATGGGAAGATGTGGCAACACAACCAGGCCGTCCCCAGGTGATCAAGGGCTTTGGGAAGCTGGGAAGGCAACTGCCTGGAGGGCCACAGGTGCCCTGTGTACGCCCCGGTGGAGAACTCCCTTTACCTGGACCGCGATGCAATAGGCAATCTGGGGACTGTGTAACAGCAAATCTGCTTCCAGAGCAGGCAAGCCACTCACTCAAACTTCAGTCCTCTACCTGGGAATTACCCACAGGTGCCACTTAGTTTTGCGCCCCACCCAGCTTCACCCACTTCCTAGTCAGCTTCTGGACCAGCCTCCCTCTGTAGGCTTGCGTGTGCTCAGGGAAAGCAAACCCATAATTAGCAAGGAAAGGCTTCTCCAAAAGCAGACTAATGTTGCACACCGAAGGCTTTCACAGTAACCATGTAGGGTAATCCGGGCCTCTCTACGGCAGTGATAGAATTGACTGTGGGATTCCCTCACTCAGATCTGCCAGGGAGCCAGACAAAAGAAATCACCTAGACCCAAAGGAAATGTACTTTGTTGCCAATACATCTGCATGCTCGGCTGGGTACCAGCTCCGCCTCTGCTGCCCTCCCCTTCTACCAGATGCGCCAGCATTTTGCTTCTGGAAAAGGCAGGAATGGCCTGGAGCAACTTAAGAGCTGATACCTCTTCTCATTCTTTTTTTTTTTTTTTTTTTTTTTGAGGGCACTTGAGACAGGTCTCACCATGTAGCCAACATAACAGAATCGTGAACATCCTCTCTAGCCCTGGGAGGGCCAGGCTAACAGTGTACCACCTCTACTAGGTGCAGGGGCTGTTTCCTATCCACAACCCAGCCAGCACAAGATGCTGGTCTTAGCCCAGCCAGGATGATCATGTATGGCACAGGGAAAAGGGACAAACATCTTCCCGGATTTGAGGAGACATCAATCCTACTCTCACAG
Seq C2 exon
GAAGTTCCTGACCCCTGAAGATGAAGCCAGTATTTTTACCATGGACCACTTCCCGCTGTGGTATCGCCAGGCCTCTGAGCAGCCCCCCGGCAGCTTTGTCTTCAATCTCCGCTGGGCAGAGGGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460:ENSMUST00000037434:24
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=0.030
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
AGAGTCAGAGCCTGGCGTG
R:
CTGGTCCCTCTGCCCAGC
Band lengths:
224-1559
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