MmuINT0139642 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65539774-65545417:+
Coord C1 exon
chr2:65539774-65540121
Coord A exon
chr2:65540122-65545284
Coord C2 exon
chr2:65545285-65545417
Length
5163 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
CTGGAATTTTGGTATTTCAGGGC
3' ss Score
4.94
Exon sequences
Seq C1 exon
TCTCTCTTGAGCATCCGAGGCTCCCTTTTTTCTCCGAGACGCAACAGTAGAGCAAGCCTTTTCAGCTTCAAAGGTCGGGTGAAGGATATTGGTTCTGAAAATGACTTTGCGGACGATGAACACAGCACGTTTGAGGACAACGACAGCAGGAGAGACTCTCTATTTGTACCACACAGACATGGAGAAAGGCGTCCCAGCAACGTTAGCCAGGCCAGCCGTGCCTCCCGGGGGATACCCACTCTACCCATGAATGGGAAGATGCACAGTGCAGTGGACTGCAACGGTGTGGTCTCCCTAGTTGGAGGCCCTTCTGCTCTCACATCTCCTGTGGGGCAGCTACTACCAGAG
Seq A exon
GTGAGGACCATTAAAGCTGCATCTGAGAGCACAGAAAAAGAAAGGACATGGGTACAATCAGGGATGTGGGTTTTGATTTACACAGATGATAATTTTCCTGCATCTTTTATTCCCAGGCCAAGAGGTGGCTGGTTTTATCAAGCTATGAACTTATCTCCTTAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAACCTTCAACACAACTCTACAAATTAATATCATACAATGAGTTTCATAGGCATATTTGTTCATTATTATTCCTACAGTTTGGACTTTAATGTAAAAGTCAAATCACATCTTTGTCATGCAAGCATGTAACTATCATCATCATCGTTGTTGTTGTTATTATTATTATATTTTTTCGAAACAAGGTTTCTCTATGTAGCTCTGGCTATACTAAAACTTCCTTTGAAGACCAGGCTATCCTTAAACTCAGAGATTAACCTGCCTCTGCTTTCCAAGATATGGAATTAAAGGCCTGTGCCACCACACCTAGCAATATGATTAAATATTAAGAAATTAAAGAATATAAACATGAGCATGATTACATATACACATATAAAAGGACAGACAGACAGACAGACACACAGACACACATACACACATACACACACACACACACACACACACACACACACACACACACACACGTATATATGCATTTCAAAGGTTTTTCTATCCTGTCCCTTTAAAACAACTTCACACCTCCACTTGCTGTCATGCTCACACTATCCCATCTAAATCCCTTACTTCACAGTTCTCCAGATTTTTCATAGTGTGCCTTGCCCCCAGTACCAACTCTAATGACCCAGCCACCCTTCATCAGCAAAGAGACTGCTTGAATAGCACAGGCTACAGTCCCATGTTTTCTTTTGGATTTCTATTTCTAATGGATTTAGCCTTCCATATTACTGCCATGAATTCTTCCTATATGCAAAGTCACCCCAAATTGAGCATATGGAAAAGATTTTCAACTTAATAATGTTTATCAGGATGTATCACTGATGGTCCCTTTATAAAGAGGGGCATTCCTCAAGTTGGCATTAAATGAAACATCACTTAACCTTTATAAAACACTTCAGCCATGTTGTCTGATCACATCACAGTTTCCCCAGCTGGGATAAAATCTCCTTTATATTATTACTCTTATATCATTTCTTTTTTTTTTTTTTTAAAGCAGACACATCCCTTACGGCCGTGTTATAATGGTCCAAATAGTTTTCAATTACTTCTTTTTTTTTTTAATTTTTTTAATTAGGTATTTTCCTCATTTACAATTCCAATGCTATCCCAAAGTCCCCCATACCCTCCCCCCACTCTCCTACCCACTCACTCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTTCAGTGATGGCCGGCTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCTGGGGTACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGGTATTTTCTCTAGCTCCTCCATTGGGGGCCCTGTGATCCATCCAATAGCTGACTGTGAGCATCCACTTATGTGTTTGCTAGGCCCCGGCATAGTCTCACTAGAGACAGCTATATCATACAAGAAGCCTACAGAACTTCAATTACTTCTTAGAGGAATGTCTTGCCCTGGAATATGACAACAGCGGCTGCTCACCACTGATTTCTTATGGCCTTTTCTCAGCTTTTCCTTCCAAGGAAATTTCCATGTATCCTGGAAAAATAGCAAGCCATGGAAGAGTAGAACTTTGTTGTGAAGCAGACAAGAAGAATGATAAGGAAATGTCACATGTTCTTAGAGAAATAATTTTAGCCAGTTATGTTCAACACATTTCCCAGAACACTGTGGGTTTATTTCATTGAACCCTCACAATTACCCATTATAATAGTTACTAGTTTATGCCCATTTTACAGAGGGACAATTGAGGCCTATACATGCTTAAACTAAGATCTGATCCCAGATGTGCTGTTTACAAGCCCTACTATACTCTATTCACAGTGAAATACAACATTCTGTTGGATTTTCTTAAATGGTAAAATCATTACCATTATAAGGTTAGGTCTTCTCACCGAGATCTGCCTGACCCAGCCTCCAGAGAACTTGGATCAAAGGTGTGCACCATCACTGCCTGGCTAAACCTTTTTCTTTCTGTTTGTCTTTCTATCTTTCTTTTGTTCTTTCTGTCTGGCTTTCTTTCTTTTTTCTTTCCTTAATCCGCAAAATCTAAACACAGTTTAATTAAAATACCAGAGACATATTAAAAAAAACAAATAAATCAATGCCTTAAAATGGCCCCAACCTAGTGTCTTAGTTAGGGTTTTACTGCTGTGAACAGACACCATGACCAAAGCTACTCTCATAAGGACAACATTTAATTGGGGCTGGCTTACATATTCAGAGGTTCAATCCATCATCATCGAGGAGGTAGCATGGCAGCATCCAGGCAGACAAGGTACAAGAGGCAATGAGAATTCTACATCTTCATCTGAAGTCTGCTAGCACAATACTGGCTTCCAGGCAGCTAGAATGAGAGTCTTGTAACCCACACCCACAGTGACACACCTACTCCAACAGAGCCACACCTTCTAATCTTACCACTCTCTGGGCCAAGGATATAAACCATCCCACTTAGGATATGAATGAGTTCACTGATAAAATGGAAACACTGACGAGGGAAGTTGAGGAAGACACCAGAAGCAGAGAGTTCCCATGCATGCAATGGCACGTGCTGTTCCACTGAGCTACTTCAATCCAGGTTCTGATAGATTGATGTAATACTGAAATATTGATGTATAGATAAAGAAAAAAAAAGTTTTTCTTAAGTCATGCTTCAAACTCTCTCAGGAGATTCTCAGAAATGGAATTTCCAAATTTTCTGGCTGTACCAGAGCTACTCGGAGTGAAACTTTGCAGCAGGATCCTGGAAATCTTTTTCTTATGAAACAGTTCACACGGTTCTTGAATACAGAAGTAGGTCCATCACTGCTATTGTTACCCTTGGGATAACATTCCCAATTTCATTGCATAAATATAACTGCAAATCCATATATCAGAACTGTCAAGGACTCACCATTCATTTGCCCTATCAGAAAAGGCAGAATAAATCTCAAAGGTTGATTGGACTTAGTTTGACACCAAGCCTAGTGTAACCTGGTAAGCTGTGGATTCCCACACCTGCATCCCTGCAGCCATGAAGTCAATGCTTTGGGGCAGGACTCTGTTCGGTGGAAGAAGCTGAAGGGACACACAAGTGGCAATGGGGACATGTGAACAGGAAACAGACAGTGGCAAGCAAATGGCAGGTCCTAAGCAAGGCACACAATTTCCTGTTCTTTACATATAAATTCCATTGAGACAATTAAACTTCAGAAGAATTTGCTGAATAGTATCATTAGAGATTTTGGAATCTACGATTAAAACTTCCATAGGTCTGGAGTTTTGGATGTGGTTTTGCCTAAAACGAAGAGATTGAATGATATTTATGTGGCCTCTGCTCTTTTTTTTTCCTAAAAGGTTCATCTTTCAGGAGGTAAATATTTCCTTTCCATGAGCCCATCTTTGCATCTTTACTTTAATAGTTTTATTTTCAATACTTCATTCTCTCTTTTCTCCTTGCTTCAATTACTCCTGCATCTTGTAGTTAAGCTGAGCTGATAGCATGGATCTTTATCCCCATTGGTGATAACATCAGTTGAGTAGAAATCCGTTTGAAATACCCAGTCATGCAAATGATTAACATAGCAGTAATGGCCATTGCTCATATCCCAGTGATGTCTGGATTCATAAGCAACTCTTAGGTTGCCATTTAGGCAACAGCAGTAACACAGAACTAAGAGTCTCACTCAGACTTGCCTTTGAAGTGCTTGAGATTCTTTTCTTTGTCCTGTGTCTGTTAACACCATGCTGGGTAGAAACATGTTCCTACCTAGCTCCAAACCTGGAGAGTGTCTTAGGGTAGGGAATAACTGAGTCATTGTGTGATTGTTAACATCCAAACACTCCAACTGGCACGTTCCAAGAGTTGCGATATTTTAAGTAGCTCATCTGTGAATAGATCAGTTTCATAAGTATAAGATAAAAAGATAGGTGAGCTAAGATTATTTTAAAATATGAATATTGGGAAACGATATCTGTCTCCAAAAACAGAAATATTTTACATACAGAGTTTATTTTTTTAAGGGAACTATTATGGAAGTATAAGATGAAATGATAGGTTAGCTAAGATTTGTTTTTTTTCTTAAATATGGTTATGGAAAATGATTTCTGTCTCCAAAAAAAAAATAAGAAAATATTTTACATTCAGAGCTCACATTTTAAGGGAACTATTATGGATACATATTGGATAACGATGCCTTTTCACACCTATTTATAACGATCTAAAAACGGACCTGGGAGTACATCAGAAACAATGCGTTTCAGTTTGAAGATGGAGGTTGAAATGGGTGAGATGCTCTGAGTTTATACAGTTGATCTTAGTTTTGGTCCTTCCAAGCCAAATTTCTGGCATGGAGAAAGCTGGAATCACAGAAGACTGAAGGGCTGATAGACTTTCAAAAACAGTCCGAATATAGTAATTCTAGGAATATCACAGGGAACTATTGTGGTCTAGCTATGAAATGTCTACCATGGGCTCATATGCCCCAATCATGGCTGTCTAGCTGATGGTGCTATCTGGGAACGTTGTAGAACCTTAATGAGTAGAGAACAGAAGAAGGTGTTAGGTTGCCAAGGATGGGATTAGAGGCTTTATAGCCTGGTCCCACTTTCTGTTCACTGCCAGATTCCTGAGTGTAGACAGCAGATGAGTGTGACAAGCCAGTCCCCTTTTCCTGTCACTATGCCTACCCTTTCTGCTGCCATGTGGCCTCTTCCAAGTAGGCTGTACCCACTTGAAACTTCTATGAGTCAAAAAAGAGTTTCTCTTATGCTGCTTTTGTTTGCTGTTTTATCGCTGCAATGAGAAAGTAAGACACTCCTTACATCTGAGGAAGCATGTAGAACTCTTGGTTAAGTAACATCTACAACTGGAGTGCTCTGAGGTTTGTTACCGCCAAGAATAGTGATTATTTTGTTGTCTGGAATTTTGGTATTTCAG
Seq C2 exon
GGCACAACTACTGAAACAGAAATAAGGAAGAGGAGGTCCAGTTCTTACCATGTTTCTATGGACTTGTTGGAAGACCCTACATCAAGGCAAAGAGCAATGAGTATGGCCAGCATTTTGACCAACACTATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.606 A=NA C2=0.526
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(24.2=44.0),PF119333=DUF3451=FE(51.3=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.5=82.2)
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: