MmuINT0139663 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65526375-65526871:+
Coord C1 exon
chr2:65526375-65526516
Coord A exon
chr2:65526517-65526664
Coord C2 exon
chr2:65526665-65526871
Length
148 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCCATTCTTTTTTTTTACAGACC
3' ss Score
10.57
Exon sequences
Seq C1 exon
CCAGTGTCCGGAAGGATACATCTGTGTGAAGGCTGGGAGAAACCCCAACTATGGCTACACGAGTTTTGACACCTTCAGCTGGGCCTTCTTGTCCTTATTTCGTCTTATGACTCAAGACTTCTGGGAAAACCTTTATCAGCTG
Seq A exon
GTAAGAACTGACATAATGATTCTTCTAGGAAGCATGAGACTCTTGACCAAGGGAACTGCTGAGGGATATATTATTACTTTAGAGAAGGAGCTTGAAACAGCAGATGTGAAATTTATAAACATCTTTCTTCCATTCTTTTTTTTTACAG
Seq C2 exon
ACCTTGCGTGCTGCTGGGAAAACATATATGATATTTTTCGTGCTTGTGATTTTCTTGGGCTCATTCTACCTAATAAATTTGATCCTGGCTGTGGTGGCCATGGCCTATGAAGAACAGAACCAGGCCACGCTGGAGGAAGCTGAACAGAAGGAGGCAGAGTTTCAGCAGATGCTGGAGCAACTTAAGAAGCAGCAAGAAGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:8
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=0.043
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.5=100),PF0253517=Zip=PU(12.6=43.8)
A:
NA
C2:
PF0052026=Ion_trans=PD(11.6=44.9),PF0253517=Zip=FE(40.7=100),PF0043013=ATP-synt_B=PU(79.5=89.9),PF0293211=Neur_chan_memb=PU(29.4=89.9)
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:
ACCCCAACTATGGCTACACGA
R:
GCCTCCTTCTGTTCAGCTTCC
Band lengths:
256-404
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: