MmuINT0139808 @ mm9
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66375327-66378692:-
Coord C1 exon
chr2:66378354-66378692
Coord A exon
chr2:66375457-66378353
Coord C2 exon
chr2:66375327-66375456
Length
2897 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
TGATTGCCTTTTTTCCTTAGGGC
3' ss Score
10.2
Exon sequences
Seq C1 exon
TCACCACTCAGCATTCGTGGGTCCTTGTTTTCTGCCAGGCGCAGCAGCAGAACAAGTCTCTTCAGTTTTAAGGGGCGAGGAAGAGATCTGGGATCTGAAACGGAATTTGCTGATGATGAGCATAGCATTTTTGGAGACAACGAGAGCAGAAGGGGTTCACTATTTGTACCCCATAGACCCCGGGAGCGGCGCAGCAGTAACATCAGCCAGGCCAGTAGGTCCCCACCAGTGCTGCCGGTGAACGGGAAGATGCACAGTGCAGTGGACTGCAATGGCGTGGTGTCGCTTGTTGATGGACCCTCAGCCCTCATGCTCCCCAATGGACAGCTTCTTCCAGAG
Seq A exon
GTGATAATAGATAAGGCAACTTCCGACGACAGCGTAAGGATGTTTTCCATAGCTCAGGCATGGCTGAGCTCTTTCTTGTGCATCAGTCATTGTCTCTGCTGGGGGGCCTGCTCTCTGGTCTGTGAATGGCTCTGCATTTCGTGATGCCTCCTCTGTGAAAACACGGGTTTAATTCATAGCTCAGCCCTCAAGTTAGGTGTCATAATCACTTAATTAAAATCTATTTTATGGGGCTAGAGAGATGGTTCCGTGAATAAGAACCATAGGCACAGCACCCAATTCAGTTAGCTCACAAAATCACCCACTGTAATTCTGGCTCTAAGAGATCTGGCTCCCTCTTCTGGCTTCAATGGGTACCTCACATACATGTGCATAACAACACACATACAGACACACAGACACACACATACAATTAAAAATTTTATATCTCATGCTGGAAAATACATTTATTTTATGATTACAGATTTTCTAAAAGCATCGCTTTAGAAAACAGTTGCCTATAATATATATATGCCTATATAAAAGATGCCTATCGTTTATTGAATAGGCTGACCTTCTTAGAAGACAGGTTCCGCTCTGTAAAGACACCTGGATCCCCTGGCACCTACTTGTTTATTTCAGGTTATTTATTTAATACATGCTTATTGCAAGGGACTTTTCCTTGGGTTGTTGATAACAGTGGTAAAAACAGCAAACACGTTCTTTGCTCCATCTGAATGAGCTGAGTCATTACTATCACTGCAAACAGGGGAGATAAGCCAGAATGTTCACATGTCACCATTGTTCATGAGCAGCTCTGACATCTCCACAAAGACCCTGTGCCCTGAGGGTGTGCCCTGAGCCTCCATCTCCACTGTGTCTCCTAAGAGCATTAGGCTTCCAAACCTGTATATAGTTCAGAATCTCTGCACTTATTCCTGTAAACGAATGAAATGCACCACTTTCATTTAAAAATATATCTTGTCTGAGGTCTATCAGTACAAAGTATCCAAAATATATACATTGAAACAAATAAACATAAATTTAAAAATATAGTGATGCTGACATAACAAATTCCAGTCCTTCGGAATCGCTGAAAACTTAGACAATATCACGTTAGGCCTGACTTGAAAACCAGTCTGGAGTTTTCAGGATACATATCTCACCCACTCACTATGGTATTCTGCATTACCAAATATCAGCATGGGCTGCATTAACCCAGCAAGTCTCCACCATCCCTTACACGCCTATGTGTTTGTAGTGGCAAACTGTGTAGTCTTTCAAGTGAGAATTACAGTTCCATCAATGTTATGGCTACACATACATTTCAGTTTGAAAAACAGAAAACTGCATGTGCTCTGGGGGTAACTTGCAACCTGTCTGCTTGCATGGCACAAATTAGGCTGCTCTGTTAAGCTGCTTTTCTGTGGAAGTAGCATGTGACCTTTCTATGAAATGGCACTCAGGCTTTGTCTTCCAATGGTGTTTGTAATCTAAAATGTTATTATGCAATGTATGTCATATTTGAAGCTGAGTTGACATTTTGTTAACTAGTGTTTTATTTAAGAGTTTGGTTTTTTGTTGTGTTTTGGGTTTTTTTGTTGTTGTTGTCGTTGGTTTTTTAGTAGAGAGGGAGAAAAAAACTCAAAAACCACAAAAGTAAAAAAGCTAAAATTATAAAAGCCGAAGAATTACAAATGTGATTATTATAGAGGGTAGGCATAGTGCACAGTTTACAGGTATACGTCTGTCCTTGCATGACAATAAAATCTGTACACTGCACACATGCCCATGTGGGAAAGGATTTGTATAGTCGAATTCTTTTTGATTTCGAAGAATAAAAGTCAATTAGAGCATAAAGCAGAGAAAATGCATCACATGCCTGTACACATATATGCAAATGTGTTGTATGTACACATGTCTATATTCTGATATGTATACATACATACATGACTATATACAACTTTGCAAACTTAAAATTATTTATTCATAGTCATATGGTGAAGTACCTACTGTCTATCCCGTAGCACATACATGCTGGTACATGACAGCTGTAGAGTTGTATAATTGTTTATGTATATTATGTGTATGGGGGTGTTGCCTATACTGTATATGCCTATACTGTATATGCCTATACTGTATATGCCTATATAAAAGATGCCTATAGCTTATTGAATAAACTGACCTTTTTAGAAGACAGGCTCTTCTAAGAAGTATAGTCTTCTAAAAAAAATTAAGTTTGCTGGTGTGCTTGGAAATGAAGCATTTTCACTTAAAGATGAATATGCCTGGTGTGCCTCTGTTCATATTCCTGCATGCCCTCACTTTTAGAGTTGCACCATGGTCACTTCTTTGAGATGGAGACAGTCTCTCCATGCTGCAACTGTTGCCATTGGTCAGAAACACCTTTTTCAAACTGAGTCACTCAGCACTATCTACTCATCATGTCAGCTATAAGAAAAAATTTTTTCTAAAGTGGTTTTCATTAACGTTGACATCATGATAAATAATCTTGGGAGTAATAATTAAAAAAATCAGAGTGTGGTACTCTATCCTTTCTACACACACCTCTACAACTCTCGTCCGGTTGCTTTCATTTGTGGCTTTCCCTTGGTAAATGTTGGATTACATTGTGTAGGCAGAGAGAACACAATAGGGCCATAATGAGAAGAACAGCTGCTTTGTTTCTTACTGGAAACAAGTGTATGAGGCAAGATGTTTTCTTATATGCATCTTACTCATGATGAACATGTGCCCTTTTGAACACAACTAGAAAGTAGCAACATCACCATTTAAATCTAGCAACCAAACCTCTACATTCAATTATTTATTACAACTACCAAGCATGACTTTATTCTTACATATGTTATATTAGAGTTTTGTTCTTAAGATTGGAATTGATTGCCTTTTTTCCTTAG
Seq C2 exon
GGCACAACTAATCAGATGCGTAAAAAAAGGCTCTCTAGTTCTTACTTTTTGTCTGAGGACATGCTGAATGACCCACATCTCAGGCAAAGGGCCATGAGCAGAGCAAGCATTCTAACCAACACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316-Scn9a:NM_018852:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.616 A=NA C2=0.097
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.7=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.3=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
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]
Other AS DBs: