MmuINT1030758 @ mm10
Intron Retention
Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66335440-66337996:-
Coord C1 exon
chr2:66337878-66337996
Coord A exon
chr2:66335530-66337877
Coord C2 exon
chr2:66335440-66335529
Length
2348 bp
Sequences
Splice sites
5' ss Seq
CTCATATCC
5' ss Score
-13.36
3' ss Seq
GTTCCTTAACACTAACCTACATT
3' ss Score
-4.86
Exon sequences
Seq C1 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCCATCTTCCGGTTCAGTGCCACCTCCGCCCTGTACATTTTAACACCCTTCAATCCTCTTAGGAAAATAGCTATTAAGATTTTGGTACACTC
Seq A exon
ATATCCTTTTGCAAGTGGTTGGTGTTAACTGTTTGTATTCATTGTGTCTTCTATGTATTATTAAGTTAAAAAAATGTGCATATACTCTATAGCTTTCATCTAATATCTTTTGTTGGTCAAGGAAATCTCTTTTTGTTTTTGTAGTGCTGAGAATTGAACCCGGGGCCTCAGAAATGTCAGGGAAACACCCTACCATTAAGGCACCCCTTCAGCCCTGAACCCTAGTCTACATTCCAGGATCCCAGCCAGGGAACGGTGCCAGCCACAGTAGATGGGTCTTTCCGTCTGAATTAACAAAGCAGTCACAATAATTCCCCAGAGACATGCAATGAGGCCCGTCTGTTAGAGTATTCTAGATTCTGTCAGATTGACAACTAACACTAGCTTTCATATATGTATTGAATCCCCTAAGTTTTGTGCAAGATCGCCATGTTTCTTGTCAACATCTTTGTACAGAGTTGCATAAAATTTTCAGTAAAATTAATCACACACAAAAAAACTATTTTCAAAGTAAAATACAGATTAGACACAGATATGATGTATGCCATTTTAAAGACCTTTGGGGGGATCATGTAAGCTTATAAGAATCTCAAGACACTTCAGGCTTAGCTAGTTAGTCAACTTTTCTGATCAGTTTTATGAAGTTGGCTGAATATCAGATTTAAGCCACAGAATATATGGGTCTGTTGTATAGCATTGTCTCTTTAGTGCAGATTCAGGAAAGAAGCTAAAACTGTTCTAAAAGGTTGAAGGGAGTTTGCCTCTGTGGTCGCCTTTGGGTTTAAAGGTTTCTGCAACTCAGTTCCGGCGTGGATATTGATCAGTGAAAAACCTTCATTTATGACTGAGTCTCTTTTGGTGGCCTTGGTCACAATTAGTATAAAAATACTATTGTAAGTATCATAAGGTCATACTAGCAAGATTTTTTTTAAAATCACAAATTCTAAAATCTAAAGAGTTGTCCAAACACAAGGCTCTGGGTTTGATTTGTTCCCTGGCACTACAAAAAACAATGACTAAAGAAGAAACGTTCATTTAAAAAAAATAAAACAAACAAACAAAAAAACAGCACTACACCAACAAAAGGAGATACAAAACAAAACAAGAAAGTAAAATAATAACTAACAAAAACAATAAAAGCAACAACAAAAAATAAAGGCCCTTCTTTTTGAGTCCAGTTGATCACAAGTAAATCGTTAGTCCTATTAATAGTCTATCATCGAACACTAAAGATGTACCTTATAAAAAGTGCCTATGCTCACTCAAAAGCTTTTCCATCTTAGTTTGCATTTCTAGTGCCATCATGTGGTCATTTGATGAAATCTTTCCCTACACCTAATGGAAATGTTTTGTGTGGTTAGTCGAGTGTAGTAGAAAGAATACCTGCTACTAAGACAGAAAACACATATTTTAAGATCCTGCGGATCATCTGTTTTCTCCAGGACGTAGCGGTTATTTCTGGCATTTCTAAAACACTTTTTACAGCCACTTTCAATGGCCCTATTACCTGTTCTTCTCTGACCTACCACTCAGTGCGTACACATTTCTCCAGCGGCATTGCTTCCGAGCATTTCATACTCACTGATTACTTTAATCTACGCGACCAATAACAAAGTCTGTCCAGCTTAACATCCGGGTGTTGAATGTAGGTGGAGCCAGAGGGTGGTTGAAGGCACAGAAAGGATAAGTGACCGATTGGCCCAAGAACAGGTGTCACTGTGGAATTTCAATTACATCCCAGTGGCGATGAGCCCTGACCTTCACACATCTCCCCTTCCATCTTCTCATGCTGTTGTGCTTACATAAACTCACTCAAAACACGGCTACTTAGCACTCTGCACCACGCTCTGCTTTGACCGTGACGTCAAAATTCTATCCATTAACGACGAGATCTCGGTATTGCAGAAATGCACCTTCCTCGAAAATTTACTATTCTAATTGTGCAATTAATTCACATCCATGCTTTCTGCTCAACAATGTTGCAAATAAAATTTAAATACATTTTAAAAGAGAGAAATGCATCCACCACCCCCCCAACCACCTCCACTTCCCGCTTAGAAAAAGCACCTTGGAAGGTAATCATGCTGGTATAAAAACAACCGCAATAGCAACTTGTATTCTTATGTCCTTCCATACTCTCATTTACTCTGAAATTGTGGAGGTCACACTATGATGCATATTTAGCATCATATGAAATTTGAGTGAAATGTAAGGAGATTAGGTAGTATTTGTGCACATGTTTACCCATGAGTCCTGTTGAACTGAGGTCTGGGTTTTTCAGTGTTACTTTGGTTTTTTTTAATACAATGCATGAACTTTCTTTTGTATGTTCCTTAACACTAACCTAC
Seq C2 exon
ATTATTCAGCATGTTAATCATGTGCACTATTTTGACAAACTGTGTATTTATGACAATGAGTAACCCTCCCGACTGGACAAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329:ENSMUST00000112366:3
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:
PF0052026=Ion_trans=PU(0.7=6.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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
- 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