MmuINT1005955 @ mm10
Intron Retention
Gene
ENSMUSG00000041460 | Cacna2d4
Description
calcium channel, voltage-dependent, alpha 2/delta subunit 4 [Source:MGI Symbol;Acc:MGI:2442632]
Coordinates
chr6:119300328-119302119:+
Coord C1 exon
chr6:119300328-119300425
Coord A exon
chr6:119300426-119302025
Coord C2 exon
chr6:119302026-119302119
Length
1600 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGT
5' ss Score
6.96
3' ss Seq
TCCTGTGACTTTACCCTCAGGTG
3' ss Score
9.76
Exon sequences
Seq C1 exon
GATCTACTGTATCACAGATATCGACCCGGACCACCGGAAACTCAGCCAACTGGAAGCTGTGGTTCGTTTCCTGACAGGGGTGGATCCAGACCTGGAGT
Seq A exon
GTGAGTTCCCTCACCCGTACCTCTGAACTTGTCCTGTGGGTCCCAGGGTCCCAGGGCTTCCCAAGAGCGAAGAATGCCATCAACTCCTCCTGGGACCACAAGGGTGGTTTGAGGAGAACAAGAAGAGCCCCACAGAAACAGGAAGAACTGTCTGGGGAGGTGGGCCATGTGGAATGTGGGCACCCAGAATCCTTATCTCAGAAGCCAGGATCCTCCTTAGCCCCTTCAGACCCTCCTACATGTGCAGTCTGTCCCCACCACTACTTCACAGTAGGCAAGGAGCAGACCCTGCCTTGAAGTCCTCAGTTCTGCCGAGCATCGCATTTTTCCAGGCAGTCTCTTCAATCCTAAAGTCTGGGAGGATCTTCCAAGTCTGTGCACTCGGGCCCGTGGCCAACTCATTTGACCTTGGCTCTCAGGAAGCCCCTTTCTCCTCTTCATTTGCCCTGCTACATATATGTTCTCCCCATGAAAAGACCATCTCCCAAACCAACCTACCAAGGCACCCATCTATCTATCCATCAGTCAACAAGGCTGATGTGAATGTGTACTTGCACCAGACCTGGGCAAAGGCTGAGATCCAGACAAGCCAGCCAAGGCCTATGCTTGAGGAACTGCAGTTTGGGAGAGAAGCCAGGCAGTGAGCAAGTCTGCACACACATACACACACACACACACACACACACACACACACATACACACACACACACACATACACACACACACATACACACACACACACACACAGAGTGTTACAGTAATGACAGGTGCTATGGACAGAGTGCTGATAGGGATGTGGGGTGCATACAGGCTAAAGTGGGGTGCAGATGAAGAAGAGCCCCAAGTGTCTGGGATCGTCTTTGAAGAGGATGAAGATATCTTGGAAGTAGAAGGGAGTGAGTTATACAGTGGTGCGCATGTAGCAATTGAGTTGAATACTGTAAGTTAGTCTTGTGCTATGTAAATTTCCCTCCAATAAAAAATTAAAACAACTCTAAGAGGAGAAGAGAGTGCTGCCTGTGGAGAGTGTAAGATGAGCAGCCAGGCCAGGGAAACAGCAGGTACTAGGGCACTGAGCCAGGTCAGGTCTGGGAGCACACACAGCCACCAGCATGACCTGCATTAGGGAACAGAGAAGGTGGGAAGTGACACAGGCTAAACAGGCTCTGGCTGGCTCAAGAGAATATGTAGACTCCACAGTGCTGAACTGGAAGGGCCTTCAACGTCAACCTAATATCTATTTTGTAGATGAGAATTTCGAAGCAAAACAGGAAGGGTTGTTATCTTTATGCCCATACAGATGGCTTTAACACCCAGGACACCTGTACACAGCTCAGCCTTCTCCTGATCTGCTATAGGGTAGAGGGCTGTGTTGTGGGCATTGTTAATATTATTATTATTAGACAGGCTAGTCTCAAACTTGCTATGTAGCCAAAGATGACCTTGAACTTCTGAGCCTGTACTTGCAAGAGCCAGGATTCCAGGCTTGTGCCATCATGACAACTGAGCTAAGTCCCCAGCTTCTAGGAGGTGTGCTCTTCTTAATGGGATGATGGGGTAATGGATGACATGCAACTGGTTCCTGTGACTTTACCCTCAG
Seq C2 exon
GTGACGAGGAACTGGTGCGGGAGGTGCTGTTTGATGCGGTGGTAACCGCCCCCATGGAAGCCTATTGGACAGCACTGGCACTCAACATCTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041460:ENSMUST00000037434:22
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
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTATCACAGATATCGACCCGGA
R:
GAGATGTTGAGTGCCAGTGCT
Band lengths:
182-1782
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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