MmuINT0139624 @ mm9
Intron Retention
Gene
ENSMUSG00000064329 | Scn1a
Description
sodium channel, voltage-gated, type I, alpha [Source:MGI Symbol;Acc:MGI:98246]
Coordinates
chr2:66123968-66125833:-
Coord C1 exon
chr2:66125780-66125833
Coord A exon
chr2:66124106-66125779
Coord C2 exon
chr2:66123968-66124105
Length
1674 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
CAAATTCCCTCCGTTGGCAGGTT
3' ss Score
7.76
Exon sequences
Seq C1 exon
GCCACATTTAAGGGCTGGATGGATATCATGTATGCTGCAGTTGATTCCAGAAAT
Seq A exon
GTAAGTATTTTTTATATCCAATGTCTTCTGGAAATATTGATTTGGTGCTTAAATTAGCTTATGAATTAGCCAAACAAACTAACTCCATTTTAGTTAATTAAAAAATAGGAAGACAGTATATTGAGTTTGTACTTAACACAGCAGTGTCTATCAGAGATATTGTACTGAGTTCAGAAAAAAAAATGGAAGTCAAAAAATGAAAGAAAAAATTCAACTCTTTCATTTAATAAGCAACAGATATTCTCCAAAGTGTTTCTATTTGTTGTATAAAGGACATAGAAGAATATATGACTGTCTTCAGTAGCTGAACTGTGTAGGCAGGCTCCATGCTTTGAAGCCTGAAAGGCTAAAGATGCAGGCTAAACATCTTAGAAATGTGTCATAGTCTTTTCTAAATCCATCCTTTATAAGAACAGCACCCATGCATTCACTGGAGTGTGTACCAACACTGTTATCACTTCTACTTTTTAATTCCATACTTTTCTTAGCTTTCAGATGTACCAACACTGTTATCACTTCTACTTTATTGATTCCATACTTTTCCTAGCTTTCCTATGTACCAACACTGTTATCATTTCTACTTTATTGATTCCATACTTTTCCTAGCTTTCAGATGTACTCAAAAATCACAGGCTTCCTCTAAGATTGATCTCCAAAACTGTAAAATCTCTGTTTTCTTCTTTCCTGTTACTTGGTTGTTTTTTGTTTTTTGTTTTTGTTTTTTTATTCTTGTTCTTGTTTTGGTTTTCTTCGGTAACCCAGACCTCTAGCTTACTATGGAGACAATGATAAATTTGAAATCGTCCTGTTCCCCTACAAACTTCTTGATCACCTCTGGAATTGCATCATCTCACCTTGTTGCATAGAGTTTGTCTTAGATGTTCAGTTAATTTTAGCTGTTGTCTTTAAAAATAGAAGACTGCAGTAGTTACCTATTTATACTAAATATTGACTCCATTGTTATGCATTGAGTGACAGCCCTGTGTCTATTTTTATAACTGCAAGTCTGAGAGTCAGTCGTCAATGGAGGATTTTATAAAATAAATCATTGAACGTGTCTATTCAATCCAAAAATTTTAATGACTTTGTTACTGGTAGGGCAAGATGCCAGCATCCAAATGAATACTTCAGTTCCTTCATTTGCTATATAAGTTCATACACAAGTGAATCTTGACTATAAAAGTGTCCTCTCTATATTTATAAGAGCTAATTTTTCACTAACTTTTTCTTTGGTTGTTTTAAAGACAGGATGTTGCATTGTGGCCCAGGCTAGAATAGTACTCAACAAGTCTCCAGCCTCAGCTTCCCAAATTCTGGAGTTGCACAGACATAAGACACCACACTAGTATTTTCAAATTACTGAAAATCAATTAACTTAAAACTTACCAAATCTAAAGTCTATTATCCAAATAACAGAATGTCAGTTATACTATGTAAAATTATGCAATTAGTGTTAGAGTGACGAATTGCATCACTTTTTACACAAAAACTTTTTGCTTCCTAGTTTCAAGGATGGTTTTTGGTTTTTTGTTTCTTTGAGGCTGTTGATATGGGAATAAAATACACTAAATTATTTCTAAGAATATATATAGCCTTCTACTCTTGTGTAGAAGCACCGACTTGCTCCCAGTATTCAAACTGCTTTATCAGTTAACAAATTCCCTCCGTTGGCAG
Seq C2 exon
GTTGAACTACAGCCTAAGTATGAGGAAAGCCTGTACATGTATTTGTACTTCGTCATCTTCATCATCTTCGGGTCCTTCTTTACCCTGAACCTGTTTATTGGTGTCATTATCGACAATTTCAACCAGCAAAAGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064329-Scn1a:NM_018733:23
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:
PF0052026=Ion_trans=FE(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
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:
GCCACATTTAAGGGCTGGATG
R:
TCTTCTTTTGCTGGTTGAAATTGTCG
Band lengths:
190-1864
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: