MmuINT0139778 @ mm9
Intron Retention
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100787892-100789862:+
Coord C1 exon
chr15:100787892-100788020
Coord A exon
chr15:100788021-100789770
Coord C2 exon
chr15:100789771-100789862
Length
1750 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
ACTTTGGTTTGATTCTGCAGGTA
3' ss Score
9.14
Exon sequences
Seq C1 exon
GTACACATTCACAGGGATTTACACATTTGAATCACTGGTGAAAATCATCGCCAGAGGTTTCTGCATAGACGGCTTCACCTTCTTACGAGACCCGTGGAACTGGTTAGACTTCAGTGTCATCATGATGGC
Seq A exon
GTGAGTTCCTTGTTTATTTTACTGTTTCCTCTGTGTGTGTGTGGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTGTGTCCTGAATAGGCTTGCAAGATGGTGCAAGTAAATGTGAGTTTTGGGCTCAGCAGAATAGAGACCCTTTCTTGTTTTTCTTTTTCTTTTCTTTCTTCTTCTTCTTCTTCTTTTTTTTTTTTTTTTTGGAGATAGGGTCTCTTGGAGCCCAGGTTGTCCTTGAACTCACCATATAGCCTAGGCTGTCTTGAGCTCTAATCTTTTTACCTCCATCTCCCTGAGCTGGGACTAGAAGCTTGTGCCTCGACACCTGGCTGCAGAATGGGGAATTCTTGGGTAATTGCCTGTGATGCATGGGCGTTTAACTATGGTTCTTGCTTGCAAGGCCTTCTCAGTTTTTAGACAGCAACAAACTTATGTGGGGGAAGGTAAAGAGATGATTTATAGCTGGGAGAACAGTGGGCATCAATTTCTCATGACCTTTCTCTTATATTTTATTCCCCTTTATGACACTGGCCAAGGTCCCCATTACTAGAGGGCCTCTTCGAAGGCATGAAATATTTTGGATATAAACTTTGGCTGAAAACACAGCTGAGGCCTCTGACTCAAAACTTAAGCCAAAGTATCCAGACTGGCATGTCCAGAAAATGTACTAACCAGAGTTCCCACTAGAGACTGTGTGAGTCTACACAGATGTGCCGGCTGCTTCCGGGCAGTTCATTTTTTTCCAGTTATAAAAAGTGCCTGTTTGAGAAATTTAGCTGATGGTGGCTGTAGTATTTTTATTTTTGTGTTAAGAAAGTACTTTATCATTTAAGGGGAGACCTAGAGTGGGGTACAGCTCGTGTGTATAAAGATGTGTGAACAGAAGAAAATGTTTGTGGGGGGGTGGGGTGGGGCGGGGGCAGGCGATTATCAGGAGGAAGATGTCGTTCCACTGTGAGATGGGAGAGCGTGATGTGTGCTGCATGTCTGCAAACAGAAGTGACACTTTATTCTAGGGAGACACTCTCTACTCTAGCATTTTAGAATCTACATTGATTGGTGTGCGTTTAGAAATCTGTGTCCTCAGTAGACACAAGGCTGCTGATACAGTGGGCACATGACTGGATTTTTGCTCTGATCTCATGATCTGGATTTTTTTTTTCCTGAGCCTTACTTTTATCTGCCACAGGATAAAACTTCATCTGCAGACATGACTGCAAAACATACATACAACTCCTAGGGATACTGCCACATCGGCATTTGGCTTTGTCAACCAGGGGATTCCTTTAACGTGAATTTGGGTTTTTTTTTTTGTGAGGCTCTTGCTACAAACAAACAAACAAACAAACAAACAAACACATGCCTCTGTTTCTTAGGGAATTGTTCATAAAATTGGGAACATATATCTTTGATACCTAGTGGCCTTCTCTCTTCCTAAAGAAAGGTAAATGGGCTGACAGTCAAGTTACTCTGATAAAATTAGCACACCACACACCAATTAAGAGAGTAAACCCCAGAACGCCCTGGATTATCAATTCTTTAGAATATACTCTGAATTCTTCTTGCCCATTTTTTTTAAATACCTGTTCCTTAAATGTTTATATTTTGAAATTTTTCTTTTTTCAGGGGAACACAATAAAATCATAACTTGTATATAAGACCCTTTCTTCCCCCCTGTTTTCAAACCCCCACCCAGTGATACCATTACAAGTTAACTTTGGTTTGATTCTGCAG
Seq C2 exon
GTATATAACAGAGTTTGTAAACCTAGGCAATGTTTCAGCTCTACGCACTTTCAGGGTACTGAGGGCTTTGAAAACTATTTCGGTAATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-Scn8a:NM_001077499:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACACATTCACAGGGATTTACACA
R:
TACCGAAATAGTTTTCAAAGCCCTCA
Band lengths:
214-1964
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: