MmuINT0139685 @ mm9
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65302772-65305083:-
Coord C1 exon
chr2:65304979-65305083
Coord A exon
chr2:65303043-65304978
Coord C2 exon
chr2:65302772-65303042
Length
1936 bp
Sequences
Splice sites
5' ss Seq
GCAGTAAGA
5' ss Score
4.95
3' ss Seq
CCTACCTCTTCTCTTCCTAGAAC
3' ss Score
10.35
Exon sequences
Seq C1 exon
TTTGGAGGTCAAGACATCTTTATGACAGAAGAGCAGAAAAAGTACTACAATGCAATGAAGAAACTTGGCTCCAAAAAACCTCAGAAGCCCATCCCTCGACCTGCA
Seq A exon
GTAAGAAGGCTCTCTTGTACTCATTAAAATTCTAAGACAGCGTTTCTGCTCTAGTATCTGGACCGCAGCATATTGGGTGATGCCACCAATCTTTCACAGCAATGTAATCACAAATCCCATACTGTACAGCAGACTCTACAGCTGCTGCGATGCTTGGTGGCAGGTATCATGTTCTTAAAACACTGGGACATTCTTGATAGTTGGTGAGTTGAGACTTCCAACTCAAGAGTTCCCAAGAACTGGCACAAAAGCAAGAGTCACCCTCCTGCTGCCGACATGTTGACTGCCCCTCTGACTATATTGATGTGTCTGTCCTTTTTAAGTGGATGCAGGCTCCCAGATGGCCCTTTCCATCTCTACATCTTTCCTCCACATTCTGGATTCTTCCTTTCCTTTCTTCCCCTCCCTGTTATAAATCTCATTTCAGCTTTTCCTTCTTTTATTACCCTTTATGGTACCATACAAAGTAAACAATATTTAATAGAATTTTCATATATATGTATCATTAGATTGTGTTATAACTTGTGTCTCCTTCTGCCCTCTCCTATGTATGCTCTCTGTACCCTTCAGTCCAGGTGCCTCCCTTTCTATAAATAGTAACCTCCTGTTTTCACCTCACACCTGCTCTATAGCTCTCTCTACAATCCCTTACATCCTTTTTCTTTCCCATGTTCCCTTATCTATCTAGATTCATGACATTCTTTCTCTTCATATTATCTGTAATTTAATATATATTAAATTTAGGTTCTATACATGAGAAAACCGTTTGTCTTTCTGGGTTTTCTCATTCTTGAGGCTAGAAAATATTCCCAATTTTCTTAGAAAGGAAAACTGGCTCAAGAATTTTGTTTCGATGAAAGAGAATAGAGACCATTCAAATGCATATAGTCTATAACGCTTGCTTCCTCGTGTGGAACAGCACAATGACGGTGGGTCACGTTCACAGAACCTACTGTATCCTAACTCACCTACCTTCTCAGATAGGGAAAATCCTAAGGCACTGAGGCCCATAACATAACTGTACACCTGTTCACTAAACCTGTGATCAGCAAATTCATAACAGAAAGGGTCATGAACCCTATCAGTGATTTCACCTGACTATATATTTAAAAGTAATTGAAACTGGGAGGTGTTAGGTAGGGAGAAAAGATAGGAAGGTGCCTCACACAAAGGAATGAATAAACCTGCTTTAACAAAGGTCACTGATATCAGGAAACATGGTTGGTTTATGGCCTTGGATTTTTCCATAAGCCATAGGATTTTGTGTTTTTATTATAAATGATTTTAATTATCTAATAAGACCACATTTAACATTTGTATTTACACAGGACTCTAAAAGCATATGTTTTCTGAAATGGGTATTAATTTTACAAGCATTTCTTAGGCATTTTTAAAAAGATTCTTGGGGAGGCAGGTAATTTGCTCATGCCTGTATCCATGGATGGGAGAAGATGGAGTCCAGAACCCTGGAACTAAAATTATCAAGAGTTGTGAGCCATCGTATGGGTGCTGGGAATTGAACCTTGGTCCTCTAAAAATCAGCCTGTGCTCTTAGCTACTGAGCCATCTTTATCTTTCTTTCACACATCTTTATTGAAGAATGAATAGGGAAAGATGGAAAGGAAAACACTAAATTAACAATTAAACTCACAAGCATACAGAACTAGAAATGGTAGAACTAAGTAAATTTAACTAGTTCTGTATGCTTGTGAGTTTATTTATTTATGAGACCCAAATTAAAAAAAAAAAATGTTTGTTACTGGCGTGTGGTATGGTGCCTCTCATTTAAAAAGAAAAGGAAGTGAAATGGAGCTTATGTAGGGTACTGTAAGGAGGGCGCATACCCCAAGGCCACCTGTGGAAAGATCTTAATTGCAATGTAACCAGACCCCTGATGATGCCATGTGCACACTAACCCTACCTCTTCTCTTCCTAG
Seq C2 exon
AACAAATTTCAAGGAATGGTCTTTGACTTTGTAACCAGACAAGTGTTTGACATCAGCATCATGATCCTCATCTGCCTCAACATGGTGACCATGATGGTGGAAACGGACGACCAGAGCAAATACATGACCCTGGTTTTGTCCCGAATCAACCTGGTATTCATCGTCCTCTTCACTGGGGAGTTTCTGCTGAAGCTCATCTCTCTCAGATACTACTACTTCACGATTGGCTGGAACATCTTTGACTTTGTGGTGGTGATTCTCTCAATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182-Scn3a:NM_018732:25
Average complexity
IR-S
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:
PF0052026=Ion_trans=PU(20.4=47.3)
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:
TGGAGGTCAAGACATCTTTATGACA
R:
AAGATGTTCCAGCCAATCGTGA
Band lengths:
342-2278
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: