MmuINT0139612 @ mm9
Intron Retention
Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66161369-66163008:-
Coord C1 exon
chr2:66162661-66163008
Coord A exon
chr2:66161502-66162660
Coord C2 exon
chr2:66161369-66161501
Length
1159 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CCTTAGCATTTGCTTTGCAGGGA
3' ss Score
6.37
Exon sequences
Seq C1 exon
TCTCTGTTAAGCATTCGTGGTTCCCTGTTCTCCCCAAGACGCAATAGCAGAACAAGTCTTTTCAGCTTTAGAGGGCGAGCCAAGGATGTGGGGTCTGAGAATGACTTTGCTGATGATGAACACAGCACCTTTGAGGATAATGAGAGCCGTAGAGACTCACTGTTCGTTCCCCGAAGACACGGAGAGCGACGCAACAGTAACCTGAGCCAGACCAGCAGGTCCTCCCGAATGCTGGCGGTGTTTCCAGCCAATGGGAAGATGCACAGCACGGTGGATTGCAATGGTGTGGTTTCCTTGGTTGGTGGACCCTCAGTTCCCACATCGCCAGTTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATAATAGATAAGCCAGCTACTGATGACAATGTAAGAAAGTTTTACATAGTTCAGGCATGGCTGGCCTATGATTGCTGCACCAGCCAGTGTTTCTACAGAATGGAACTCTTGAGAATGATTCCTGGTTGGTCGAGCTGAGAATGCACCTGCATCTTGTAGCACCTTTAATAGACTAACCAGCTAAATGTTAGCGCCTCGGCACTCCTTGCACAAACCTGAATGCATTACCTACTGTATATGCTAAGGATTAATTGAACAATAATTACTTCCTTGGATGATTTGCTATGTACCCATACCGAATTTACATATGAAGACATCACCCCTAGTGCCCTATTATTGTAAGATTAAATGAATGACTTTTTAGTGTAAAGGGTGTATAGTAAATCTTCCCACTAAACTCTTACAGTTTATCTGGGCTTTAGTTCAGATTTTCAAAAACACTGTGCTTAGATAGCTTCATCATTACCTACATTTTCTAAGGATCATATTTATCTCACTAAGAAAGAAATGCTGATATAGGTATTCACAAAACAATCTACACAGAGACACCAATAAATTATTAATCCAGATAAAATAATTGGAAATATATCAGCATGACGAGGCATGACTCGGTGTAAATCAGATGACTTATTGCTTTGGTATCCTGGATGAAACTGTTGCCCCTGCATCACATGCATGGATCAGCATATACTTTATAATAAATGAGTATATGTCTTATGCTTAGAAATTGAGATGACAGCTAAGTGTGTTATGGTCTTCGGTATTTTCTTAAAATTAAACAGCTACTTTCTCGAAAGTGAAAAATGGCCTGACCATATATAAGATTTTAAGGCATTAAGATTTGACAGTATGTTCATTAATTGAAAACAAGCTATAAATGCCTATGCAAAGCTTTACTAACTATATTTTGATCGCATCCTATTTCATAAGAGTATAAAATCAAGGAGGGGTCAAAATTTTATATTTTCCTTTATGACTACATGGTTAACTGTTTGAATATTCCAGGTTAATGATCCAATAAGTCACCAGTATCTGCCATTGGCCATCAAAGATGAAGACGCATGACGCATGTCTTTCATGAAAATCACTGTCTCCATTTATTTCTGTGCTGTATTGCTCAAGCTAGTCATGTAATGCCTTAGCATTTGCTTTGCAG
Seq C2 exon
GGAACAACCACTGAAACTGAGATGAGAAAGAGGAGGTCGAGCTCTTTCCATGTTTCCATGGACTTTCTAGAAGATCCTTCCCAGAGGCAAAGGGCAATGAGCATAGCCAGCATCTTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.643 A=NA C2=0.218
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(14.5=23.3),PF119333=DUF3451=FE(51.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAAGGATGTGGGGTCTGAGA
R:
TGCCTCTGGGAAGGATCTTCT
Band lengths:
358-1517
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: