MmuINT0139628 @ mm9
Intron Retention
Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66173497-66176053:-
Coord C1 exon
chr2:66175933-66176053
Coord A exon
chr2:66173585-66175932
Coord C2 exon
chr2:66173497-66173584
Length
2348 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
TCCTTAACACTAACCTACATTAT
3' ss Score
-4.48
Exon sequences
Seq C1 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCCATCTTCCGGTTCAGTGCCACCTCCGCCCTGTACATTTTAACACCCTTCAATCCTCTTAGGAAAATAGCTATTAAGATTTTGGTACACTCAT
Seq A exon
ATCCTTTTGCAAGTGGTTGGTGTTAACTGTTTGTATTCATTGTGTCTTCTATGTATTATTAAGTTAAAAAAATGTGCATATACTCTATAGCTTTCATCTAATATCTTTTGTTGGTCAAGGAAATCTCTTTTTGTTTTTGTAGTGCTGAGAATTGAACCCGGGGCCTCAGAAATGTCAGGGAAACACCCTACCATTAAGGCACCCCTTCAGCCCTGAACCCTAGTCTACATTCCAGGATCCCAGCCAGGGAACGGTGCCAGCCACAGTAGATGGGTCTTTCCGTCTGAATTAACAAAGCAGTCACAATAATTCCCCAGAGACATGCAATGAGGCCCGTCTGTTAGAGTATTCTAGATTCTGTCAGATTGACAACTAACACTAGCTTTCATATATGTATTGAATCCCCTAAGTTTTGTGCAAGATCGCCATGTTTCTTGTCAACATCTTTGTACAGAGTTGCATAAAATTTTCAGTAAAATTAATCACACACAAAAAAACTATTTTCAAAGTAAAATACAGATTAGACACAGATATGATGTATGCCATTTTAAAGACCTTTGGGGGGATCATGTAAGCTTATAAGAATCTCAAGACACTTCAGGCTTAGCTAGTTAGTCAACTTTTCTGATCAGTTTTATGAAGTTGGCTGAATATCAGATTTAAGCCACAGAATATATGGGTCTGTTGTATAGCATTGTCTCTTTAGTGCAGATTCAGGAAAGAAGCTAAAACTGTTCTAAAAGGTTGAAGGGAGTTTGCCTCTGTGGTCGCCTTTGGGTTTAAAGGTTTCTGCAACTCAGTTCCGGCGTGGATATTGATCAGTGAAAAACCTTCATTTATGACTGAGTCTCTTTTGGTGGCCTTGGTCACAATTAGTATAAAAATACTATTGTAAGTATCATAAGGTCATACTAGCAAGATTTTTTTTAAAATCACAAATTCTAAAATCTAAAGAGTTGTCCAAACACAAGGCTCTGGGTTTGATTTGTTCCCTGGCACTACAAAAAACAATGACTAAAGAAGAAACGTTCATTTAAAAAAAATAAAACAAACAAACAAAAAAACAGCACTACACCAACAAAAGGAGATACAAAACAAAACAAGAAAGTAAAATAATAACTAACAAAAACAATAAAAGCAACAACAAAAAATAAAGGCCCTTCTTTTTGAGTCCAGTTGATCACAAGTAAATCGTTAGTCCTATTAATAGTCTATCATCGAACACTAAAGATGTACCTTATAAAAAGTGCCTATGCTCACTCAAAAGCTTTTCCATCTTAGTTTGCATTTCTAGTGCCATCATGTGGTCATTTGATGAAATCTTTCCCTACACCTAATGGAAATGTTTTGTGTGGTTAGTCGAGTGTAGTAGAAAGAATACCTGCTACTAAGACAGAAAACACATATTTTAAGATCCTGCGGATCATCTGTTTTCTCCAGGACGTAGCGGTTATTTCTGGCATTTCTAAAACACTTTTTACAGCCACTTTCAATGGCCCTATTACCTGTTCTTCTCTGACCTACCACTCAGTGCGTACACATTTCTCCAGCGGCATTGCTTCCGAGCATTTCATACTCACTGATTACTTTAATCTACGCGACCAATAACAAAGTCTGTCCAGCTTAACATCCGGGTGTTGAATGTAGGTGGAGCCAGAGGGTGGTTGAAGGCACAGAAAGGATAAGTGACCGATTGGCCCAAGAACAGGTGTCACTGTGGAATTTCAATTACATCCCAGTGGCGATGAGCCCTGACCTTCACACATCTCCCCTTCCATCTTCTCATGCTGTTGTGCTTACATAAACTCACTCAAAACACGGCTACTTAGCACTCTGCACCACGCTCTGCTTTGACCGTGACGTCAAAATTCTATCCATTAACGACGAGATCTCGGTATTGCAGAAATGCACCTTCCTCGAAAATTTACTATTCTAATTGTGCAATTAATTCACATCCATGCTTTCTGCTCAACAATGTTGCAAATAAAATTTAAATACATTTTAAAAGAGAGAAATGCATCCACCACCCCCCCAACCACCTCCACTTCCCGCTTAGAAAAAGCACCTTGGAAGGTAATCATGCTGGTATAAAAACAACCGCAATAGCAACTTGTATTCTTATGTCCTTCCATACTCTCATTTACTCTGAAATTGTGGAGGTCACACTATGATGCATATTTAGCATCATATGAAATTTGAGTGAAATGTAAGGAGATTAGGTAGTATTTGTGCACATGTTTACCCATGAGTCCTGTTGAACTGAGGTCTGGGTTTTTCAGTGTTACTTTGGTTTTTTTTAATACAATGCATGAACTTTCTTTTGTATGTTCCTTAACACTAACCTACAT
Seq C2 exon
TATTCAGCATGTTAATCATGTGCACTATTTTGACAAACTGTGTATTTATGACAATGAGTAACCCTCCCGACTGGACAAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:3
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(0.7=6.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: