MmuINT0139678 @ mm10
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65482151-65483197:-
Coord C1 exon
chr2:65483043-65483197
Coord A exon
chr2:65482325-65483042
Coord C2 exon
chr2:65482151-65482324
Length
718 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
AAAGTTTTCTTGATTCACAGGCC
3' ss Score
6.75
Exon sequences
Seq C1 exon
GATGCATTAAAAAATTTCCCTTCTGCCAAGTAAGTACGGAAGAAGGTAAAGGAAAAATCTGGTGGAATCTTAGGAAGACCTGCTATAGCATTGTGGAACACAACTGGTTTGAGACGTTCATTGTGTTCATGATTCTCCTCAGTAGTGGTGCTTTG
Seq A exon
GTAAGTGATTGTGCATTGGCACGAACCAAGCTCTGCTGAGGTAGCCAACTCCCTGGTGATACTACAAGTGCCCACTCAGTTTAGAAATCAAAACAATAGGTGTATCTGTGTCATGCAGAGCTGAGAACTCTGTAAAATTGTGTTCAAAACAAGTCAGAACCATGAAACTGACAGAAGGGATTTCACATCTGCTGTTTGCCCACCAGATGTTTTGCTCGCTGATCTACCATTTGCAGACACATTGCCCTGGCTCTGGTAGCATCCCAGCCAAATGTCGGCCAATCTGCCTTAATAACTGTATTTATGGATTATCTGTGAATCTTGCTTTCTTTACGTACAATGAAATTATCCTTTAATAATAAGTGATGGAATCACAGAAGATATTGTTGGAAGAAGCAAGTTCTATCTCTTATGAACTAGATGTCTTTAGTTCATCTTCCATGAATGGAAGCATGCTTTTGGCAGTGATTGAGGTAGCTGCTTTTGGGTGAGAAGTAAAGATAACAACATATATAAAATCAATATAGATGCCAACATTCCTGTGCCAATATTCCCTAGCTAGCTTTGGTCTTTAGCTTCTGCCTGATGGAAAAATATTTGAGTGATTTAAGCCAATACTCCTTTAAGTGTTTCTTGGTTCTCATATGACACTAGAAATATTTGTAAATGTTTTGGGAAGGCAGATCATTAAAGTAAATAAAGTTTTCTTGATTCACAG
Seq C2 exon
GCCTTTGAAGATATATACATTGAGCAACGGAAGACCATCAAAACCATGCTGGAGTATGCTGACAAAGTCTTCACTTACATCTTCATCCTGGAAATGCTCCTCAAATGGGTGGCCTATGGATTTCAAACCTATTTCACCAATGCCTGGTGCTGGTTGGACTTCTTGATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182:ENSMUST00000100069:19
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:
PF065128=Na_trans_assoc=PD(20.0=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.3=67.2)
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:
AAAAATTTCCCTTCTGCCAAGTAAGT
R:
CAACAATCAAGAAGTCCAACCAGC
Band lengths:
318-1036
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