MmuINT0139654 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65581122-65586488:+
Coord C1 exon
chr2:65581122-65581175
Coord A exon
chr2:65581176-65586350
Coord C2 exon
chr2:65586351-65586488
Length
5175 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TACCTTTCTTCATATTTTAGGTA
3' ss Score
11.1
Exon sequences
Seq C1 exon
GCCACATTTAAAGGATGGATGGATATCATGTATGCAGCTGTTGACTCAAGAAAT
Seq A exon
GTAAGTTTACTTTGGGAAAATGGCTTATGTATATCAATGAGTATATCCATATTATTGTAAACTGTTGATGGCCAAAAATCCACACATAGCTACAGATAAATGTATAGAACACAACTATTTTACTAAAGTAAAATATTTTTGTTACATTATTTCTTTCGAAGAATTTTTGTTGGGGATTCGTTTCTTTAGTTAAAGATTTCTTATCATGTGAAAAGGTCTAATAGGAACCTTCTTCAAAATAACTAGTAGTCAAAAATGAAGCTGGCCAATTTTTTTATTTTTTAAATTAATTTATTTTTTACATTCCATATTTTATTACCCCCATCCACCCTCCAACTTTCCCACATCCCATACCTCTTCCCCACCCCCTTGTCTCCACATGAATGTCCCCATCCCCCCCATGCGACCAGACCTCTAAACTCCCTGTGGCCTCCAGTCTCTTAAGGGTTAGGTGCATCATCTCTGAATGAACATAGACCTGGAAGTCCTCTACTGTATGTGTGTTGGGGGCCTCATATCAGCTGGTGTATGCTGTCTGTTTGGCAGTCCAGTGTTTGAGAGATCTCAGGGGCCTACATTAATTGAGACTGCTGGTCCTCCTACAGGATCACCCTTCTCCTCAGCTTCTTTCAGCCTTCCCTAATGCAACAACAGGGGTCAGTTGCTACTGTCTATTGGTTGGGTGCAAATATCTGCATCTGACTCTTTCAGCTGCTTGTTGGGTCTTTCAGAGGGCAGTCATGCTAGGTCCCTTTTTGTGCGTACTCCATAGCCTCAGTAATTGTGTCAGACTTTGAGACCTCCCCTTGAGCTGGATCCCACTTTGGGCGTGTCACTGGACCTTCTTTTCTGGCTTCTCTACATTTCCATCCCTGTAATTCTTTAAGACAGGAGCAATAATGGGTCAGAGTTTTAATTGAGGGATAGCAACCCCATCCCTCACTTGATGCCCTGTCTTTCTGCTAGAGGTGGACTCTATAAGGTCCCTCGCCCTACTGTTGGACATTTCATCTAAGGTCCCTAACTTTGAGTCCTGAGGGTCTCTCACCTCCCAGGTCTCTGGTGCATTCTGGAGGGTCCCCCCCAACCTCCAATTTCCCAAAGTTGCTTGTTTCCATTCTTTCTGCTGGCCCTCAGGGCTTCAGTCCTTTTCTCTCACCCAATACCAGATCAGATTCCTCTCTCACCCCAACTCCCCCCCCCCGCCCTCTTTCCCTCCTATGTCCCTCTCTCCCTCCCCACTTGTTATTGCTTTCTTCTCTCTCCCAAGTGAGACTGAGGTGTCCTCACTTGGGCACTTCAGCTTGTTGAGCTTTTTGAGTTCTGTGGACTGTATCTTGGGTATTCGGTACATTTTTTTCTTTTTTTTTTGCTAGTATCCACTTATTAGTGAGTACATACCATGCATGTCCTTTTGGGTCTGAGTTACCTCACTCAGGATGCTATTTTCTAGTTCCATCCATTTGCCTGCAAAACTCAGGATGTCCTTGTGCTTAATAGCTGAGTAGCTATATCTATTGTGTAAATGAACCACATTTTCTGTATCCATTCTTCCGTCATGGGACATCTGGGTTGTTTCTAGCTTTTGGCTATCACAAATGAGGCCACTATGAACATAGTGAAACATGTGCCCCTGTGGCATGGTGGGGCATCTTTTGGGTATATCCCCAAAAGTGGTATAGCTAGGTCTTCAAGTATATCTATTTCCAATTTTCTGAGGAACCTCCATATTGATTTCCAGAGTGATTGTACCAATTTGCAATCCTACCAGCATGGAGGAGTGTTCTTCTTTCTCCACATCCTTTCCAACATGTGTTGTCACTTGAGGTTTTCATCTTAGCCATTCTGATTGGTGTAAGGTGGAATCTCAGGGTCGTTTTGATTTGCATTTCTCTGATGAGTAAGGACTTTTTAATTAGAAAGTTTTTCTTGACTCACTATACATTTTTTGAAGACATATTTCATAGATGTGAGTGGTTTTGCCGTGTTTGTATGTCTGTGTGTCTTATGTGTTCCTGGTGCTCAAAAGGCCAGAAGAGGGCTTCAGACTCCCTGGAACTGGAGTTACAGACTGTTATGAGCCACCATGTGAATGCATTCCAGAAGAGGGCATCATATCTCATTATAAATTGTTGTGAGCAACCACATTTATGATAATTTAATGGGATTAAATGTGGTTGCTGGGATTGGAACTCAGGATGTCTAGAGTGAAGCCAGTGCCCTTAACCACTAAATCATCTCTCTGGCCCTGCAACCAATGCTTGACTACTGGGCTTCTCTCCAACTCTTGATTGTGATTTTTTTTCCCCTTTCTTTTTGGTCTTTTCTCATAAGCTTGGGCCCTGGTGCTTAAATTTTTTATGAAGTATACTTTCAAAATGAGATGTTTAGTTCTTGTGAAGAGGAATCCTCAGGGCAATTTTCTTTATCTGCCATGAGTTTCCTCCAGTATTTGATCTTCGGTGAGGACGGATATGACTAATGATGACTAACGTGGGGAACATAGGAAACAAAACAAAGGAGCCATAACTTAATAGTGTCTCCTACCAGGAGGCAAAGTGGGTAAGGAACGGCGGGGACTTGCAAAATCTACCTTAGAGCACAGAGGAGTTTTTTTCTTTGATTTTTATTAGTTTCATACAATTGACCCAAAGAAAGTGGCATTTTGGAAGTATTTCTGGTTTTCTAGAGCCCCCGGATTACTCTCAAAATGACATTTTTCTGTACTGGCAATTAGCTCTCCATATTAAAAATCCCGGTATTGTCTTTTTAGCCCCATAAAAAGAGAGAATAGAATAGACGACCAGCAGAGGCAGAAGATGCTAAAAAGCCCTTCATGGCATCAGCAATTTAAGCTGTAGTTATTTTCAGACAGTATACCAAGGGTTACCTCATATTATTTCATTTAATTTACATAGTAGCCTCATATGCTTGCTAGTAACTCAATTCATTATTGAAGCAAAGACGTCCAACATGTTCAATGGCAGAACATTTTTGAACAACGATTTGAAACTGTGTTACAATGGTTTCTGCAGGAGCTCTCTCTATCTGTCTCTTGGATTAATTTACTCAAAGCTAATTCTACCTTTAGCAACAGCCTACATGGCACACAGCTTACTTTGCTTCTCTTCCTTAGAAACCTAGCAAAAATTGTCTACAACAGAAGCCCTCACACCCAAGCATACTGTACAAGAGGAAAACCAATAGGCCACTAAAATTATGAGGAAGAGTTTCTGGCTCTTTTTTTTTAATGTTCATTGTTGTTTAATGTAGTTTACTTATCTGAGACAAAGCCTCACTGTGGAGCCTTGACTGACCAGGAACTCTTATGTAGATCAAGCTGGTCTGGACTTAGATATCCACCTGCCTCTGCCTCCTGAGTGATGGGTTTAAAGGCTTTGCCACCACACCAGGTTCTGGCTTTTACTTTCATTAGTCAACATGAACATGAAAATTGAAATCAAAATGTGACATTACCTATACACCTACCAAACTGACACTACTAAAGTGTGATAATGTCAAGTGGTCCCAAGAACAAAAAACAAAAAGGACCCTGTTTCATGCTGGTGGTGGAGAACGATATGAGTATATATTATTTATAATGTAGTTGAGAGGGCAGAGAAATGGCTCAGTGAGTGAAGGTGCTTGCTGGTTTGAGTTCAGTTCCCACTACCCACATATTTCAATGGGAAAACTGACCCCTAAAAGTTGTCCTCTGTTATCCACATGTACACACACACACACACACACACACACACACACACACTACCACCATTACTACCTCCACCACTACCACTGATAAATAAAATAGTGGGTATTATCACATTATTTAATAAAGTTCAATTTATCATTTGCTCTTAGCTTTTATACTCATGAACAACTGTATAGGACAATTTAAGTACAAAAGATTTTGGAACAACATGAACTTGAATTAACTGAAAAAATAAATGCGAACACATTAAGGCAAAGAAACTGCGCACACACACACACATACACACACGCACACGCACCACAATTTTGTTTGTCAGTTCAAAATTGATACAAAATAATCTTACTGTTGAAGAATCAACCAACTCTAGGCACCAACTCTAAAACATAGAGAATTAATAATTACAATAAGGCAAGGCTAATGTCACTGCCAGTGGTGGTGTCTAGACTGCAGAAGAAAAAACACATAATTCCTGAAGTACTTGAGTTGTGTGTTTCTCTTACAAGATTTTATGTTAGACAACAGTTTTACTCTAGTGTGTTATATTTGATCTTATAAGGTTCGAAAATGTTATTTTACATTGTTATGCATATACACACAAGAGAGAAGTCAAATGATTGTCAAATAAATAATGCTCAGCATTACAATCATTTTGTTGCTGTTTATTTTATCGTATTTCATTTAAAAATAGGTTGGTTATGGTGCTCAGCATTGATGTCATGATATCAATGTAAGTTAAAATAAGCTGCAGTTTGTGTTCTCACTCACCCATGATTGATTAACGGAGTTATTAGAAGCATCCTGTGAGCCTTGAACTTTTGATTACAGCCGAAACTTTCATCATCACTGATTTTCCTCCAAGCTCTGGTCAAGACAGAGAATCACTATAACACAAACACAGCAGCTACTAGAGAGAGTGGGTCAGCATGTCCACTATCAGGAAGGACAGACCCTAGTCACGTGTACACACACAATGTGGTTCCTAGACTTCGTAGGAAATGTGTAAGATTAAACCTTACGCACTCGTACTCATATTTGCGTATTTGACTTTCACAAGTTACTCTAAAAGCTATGGGTTTGAGAGTTGCCACATCACGAGAGCGAGGACTAAGGAGAGAAAGTAAATATCAACTATTCAAAAAGATGGTAATGAGACTCTGACTTCGCCACTGTAGGAAGAAGTAATCCTGTTTGTGTGGTGTGTTGAGATCTTTGCTTCCTAAGGAAAAGCACATTCACAATGTAGGGGTTTATTTAGTGAGACGATTATAATCACTTAAACTGTTGCTCGAACATATTTTATTTTCTCAAGAATGTGAAGAGTCTTGCAGGATTCAACAGACATGTTAGACCTGGGCGTTCCTAAAATCTGTTTAACATTGTCTATTTGTTTCATGTTTAGAGATTCCGTGATGTACCTCTAATGAAACTATTGACTTTACTGGTTACCTTTCTTCATATTTTAG
Seq C2 exon
GTAGAACTGCAACCCAAATATGAAGACAATCTATACATGTACCTTTACTTTGTCATCTTTATTATTTTCGGCTCATTCTTCACACTGAACCTGTTCATCGGCGTCATCATAGATAACTTCAACCAACAGAAGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:22
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:
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: