MmuINT0139823 @ mm9
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66318138-66325702:-
Coord C1 exon
chr2:66325432-66325702
Coord A exon
chr2:66322662-66325431
Coord C2 exon
chr2:66318138-66322661
Length
2770 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
TATTTTTCCCTCCAATACAGGAA
3' ss Score
8.96
Exon sequences
Seq C1 exon
AACAAATTCCAAGGATGCATATTTGACTTAGTGACAAACCAAGCTTTTGATATCACCATCATGGTTCTTATCTGCCTCAATATGGTAACCATGATGGTAGAAAAAGAGGGGCAAACTGACTACATGAGTTTTGTGCTATACTGGATCAACGTGGTCTTCATCATCCTGTTCACTGGGGAGTGTGTGCTGAAGCTGATCTCTCTCAGGCATTACTACTTCACTGTGGGATGGAACATTTTTGATTTTGTGGTAGTGATCCTCTCCATTGTAG
Seq A exon
GTAAGGCCATTGACTAGTGAAATCTTAACTTTGGATAAAGTCCGTATGTGTTCTAGGAAGTGTCTGCATGTTTGAGATCCCTTTTACTATAGAATAAATTACTAGCATGGTAGAAGGAAGTAGATTTAGAAGAAAAGCAACGTTTTGTGCAATAACTCCCAAGTTCAAACCCTAGTCCTGAAAGCCAAAAAATGTGGGTCTGTCAGAAAGAATTCCTATTGAGATTAGTTTCTTAATCTGCCTCAAGAAGCCTGATAATTGACATCTATTCACAGATGTGTCTTGGAAGCCAATGAAGAATTTGAAATTATTTTTAGTTTTATCAGGGACAAGGCTAATTGATATGGATACCAGTTTGTTTTTGAAATTTATCCTGAACTTAAAATATCAAAAAAATGATGTTTTATCTTTAAAATTAATACTGGATCAGTCAATAGATTTAGTTATTTCTCACTTAGCAGCTGTGTCTGTGTATCACAGGCATGATTTATATGTCTTTTCTTTCACTGTCATGTCTTACCTGTTCTCTTCATACCCAACATGCCTAATATCTTAAGGTTACATTTAATTTCTAGCATTGAAATTTCTTGATGGAAGAATTTGCAGGATAAAATGCACAGCTAATCAAACAGGGCCATAAAAATCTAAAGGTTATATAATCCAAAACCACAATGAAAAAATGTCAAAATGGCTTAAAAACAGTTTTCAAGTAATATTATCACCAGATGTGATATAACCAAGCAAATTAAAATTCAGGTAATGATGGCATAGTGACAAGATAAAGTATAATGATGGGAACATTATAATATACTTTTATCAGGACAATAAAAGAACATAGTCTTAGCAATACTAGCCAGAGGTTTCAATAAGAGAACAAGGAGGTATATGCATTAAAACCCAGGAGTCACTCATCTTTATCTTTATTACATCATGGCACTCTTCTAAAGGGAAAGAGTTGACTTTGGCCACACTTAACTGCCATTCCAGCATTCAAGATGCTGTGGTCCTGAACAGCTATCTGTAATCCCAGCATTAAGGAGGCTTTACCAGGAGGATATGGAGTCCCAGACCATCCTAGGTTATGTAGTCAGACAATCTCAAACTTTAAAATAAATAATAATAATAATAATAATAATAATAATAATAATAATAATTAATCAATTGAATTTCAGAAAAGTCAAATTATAAATTGCATATCAACATTGAAAATTTTGTTGACCAAAAAAATAGAAAAACTATTTGAAGAAAAGTTAAATTCAAACTTGTAATAAATATAAAATTACAAATCTAGTAATAAATGTACCATATAATGTATCAGATGTCTATGAAAAAAATGAAGGACAAAAAAAAGCTGAAATAATTGAAGGCTTATCTTATGCTTGCTTCCAAAGGCTTTCAATGAAATTATGACTTTTTGAAGATTTGTTAGTTTTTATTCATATGTATGTGTCTATCTGTGTGAATGTATATCATGTGTGTGGCCTCCCACAGAAGCCAGAAAAAAGATGCTAGGCCGCCCCACCCCCTACCCCCGGAGCTAAAGTAACGGGCTGTTGTGAGTCACCAGATACAGGGCCTGGAAATAATAATAATTCATCATCATCATCATCATCATCATCATCATCATCATCATCATCTTAACCTTTGAGAGACCTCTCCAGCCTCAGTGACCACCTTTCACAGGAAAGATTTTATAATTTCAATAAAACTATCAGGGAAACTTTTTATGTGGCAGTGGTGTATAGACTGAAAATACAGCAATGAGGACTTCTGCAACAGTGTGTGAAAATAAAGGTTCAAAGGATTCTGAGAAGCTAAACACTAGACTTTCACACACAATAGGAATTTATGCAGTTTGATGGCCATAAAAATCAAAGGATGGTATTTAAAACATGGGCAGCTGGAGTGCCGCACATCATTAGTCCCAGCACAGGGGATGCACAGGCAAGCAGATCTCTGTGAGTTCCCAGCCAACCTTATTTACACAGCAAATTCCATTCTCCTTCTGAGGGCAAAGGCTACATAGTCATACTCTATCTCAAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGGGAAGGAGGGAAGGAGGGAGGGACAGAGGGACAGAGGGAGGGACGGAGGGAGGGGAAAATGTTTTAAGCTAAAAATTTTCATAAATAATTTTACTTACACACACACACACACACACACACACACACACACACACATTTGTGTGTTACTAGTAGGATTTAGTTTACACATAGCTCTAGCACTGAGCTACATTCTGAGCCCTGGAAATAATTTTTTGAGCCCTGAGCATGCATAATCTTTTCTATTCACGACACAAACTTTAGTCTCAAGAGAATGAAAAAAAAAAATCTTACCAGCCAAAATAGAAAGGAGTATGCCCATGAATTTAGTTAAGATGAAAACTGTCACAAGCAGTTAATAAGATAACGAATCAAAATAGAACAGCAGCTGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCAGGAGGCAGAGACAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCCACAAGGTAAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGGCTCAAAAAAAAAAAAAAAAAAAAAGATAGAATAGCAATTCTGAATTTATCAAATGTCGAATGAAGCTATTTAGATGCATGATACTGTGCCGCGTGGATCTTTAAACATTTCTGTTTATTTTTCCCTCCAATACAG
Seq C2 exon
GAATGTTTCTCGCTGAGATGATAGAGAAGTATTTCGTGTCTCCTACCCTGTTCCGAGTCATTCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGCGCCAAGGGGATCCGCACGCTGCTCTTTGCTCTGATGATGTCCCTTCCTGCGCTGTTCAACATCGGCCTCCTGCTTTTCCTCGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTACGTTAAAAAGGAAGCTGGAATTAATGACATGTTCAACTTTGAGACCTTCGGCAACAGCATGATCTGCCTGTTCCAAATCACCACCTCTGCGGGCTGGGATGGACTGCTGGCCCCCATCCTCAACAGTGCACCTCCTGACTGTGACCCAAAAAAGGTTCACCCAGGAAGTTCAGTGGAAGGGGACTGTGGAAATCCATCTGTGGGAATTTTCTACTTTGTCAGCTACATCATCATATCCTTCCTGGTTGTGGTGAACATGTACATTGCTGTCATCCTGGAGAACTTCAGCGTTGCCACAGAAGAAAGTACTGAGCCCCTGAGTGAGGACGACTTTGAGATGTTCTACGAAGTCTGGGAGAAGTTCGACCCTGACGCCACCCAGTTCATAGAGTTCTGCAAGCTCTCTGACTTTGCAGCAGCCCTGGATCCTCCCCTCCTCATCGCAAAGCCAAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTGAGTGGAGACCGCATCCACTGCCTGGACATCTTATTTGCTTTTACAAAGCGGGTCCTGGGCGAGAGCGGAGAGATGGATTCCCTTCGTTCACAGATGGAAGAAAGGTTTATGTCAGCCAATCCTTCTAAAGTGTCCTATGAGCCCATCACAACCACACTGAAGCGAAAACAAGAGGATGTATCTGCGACTATCATTCAGCGTGCTTACAGACGGTACCGCCTTAGGCAAAACGTCAAGAATATATCAAGTATATATATAAAAGATGGAGACAGAGATGACGATTTGCCCAATAAAGAAGATATAGTTTTTGATAATGTTAACGAGAACTCAAGTCCAGAAAAGACAGATGCAACAGCCTCTACCATCTCTCCACCTTCCTATGACAGTGTCACAAAGCCAGATCAAGAGAAATATGAAACAGACAAAACGGAGAAGGAAGACAAAGAGAAAGACGAAAGCAGGAAATAGAGCTTCGGTTTTGATACACTGTTTACAGCCTGCGAAGGTGACTCACTCGTGTTAATAAGACTCTTTTACGGAGGTCTATGCCAAACTCTTTTTATCAAATATTCTCAAAGGCAGCACAGCCACTAGCTCTGATCCAGTGAAACAAGAGAGAAGCATTTACACATGGCTACTTTTTGCGTTGGTCAATGATTCTTTAAGAATTGTGCATGTAACTCTACAGGGAATAATCATTATTGCAATCAAGGGTGACTTAATGATTTTAAATATCAGAAAACCACATAGAACATTTTCTCTTTTGCCTCCATTTCTTTCCCTAGATTCTAAGTAGATGTGTACCCATGTGAATATAGAAATTCAGGCGCACATGCTCACAGTCACAAACACAAACAGGATTAGCTGTGATTTGGAATTCGATGTAAATATTTCACCTGTGATTTGCAATGAAATTCCTTGTAAAAGAAATGCGAATTAGTGATGAAGGTTTTGTGAAAACATCTTATCATTAGGGAGTCAGAATTTCTGTCCATAAAGAATTCAGTTTATATTTTGAGGTGCTGAAACTTATCCTACATTGCATCAAAATCAATTTATAGGTATCTGTAAAATGTCATGGGACTGAAAAACATATATAGGCTACTTGTTTAAGAAATGGCTTTCATTCATATAGATAGGCATTCACCTTGATTTATGGACATCTTTGGCATTTTGTGATCACATGATTCTTCCACAAAATTGCTTAGCTGGAACTTCAGGCACACATCACAGAGAACAGCTACCCAGTCTTATGCCCCTCTCTGTTTGTACAATAATCACAGAGCTTGAAACATTATTTGAACTATAAATATCAGGTTTCTCCACATAGACATATGAATATTGTTAACAGAAAAAAATTTTATTTACAGCGTTTTATTTACTAATATTTATCCAATCTAGTTTGCCCAATGAGACAGCTCATGACTCACATCTGAAAGCCAGTTGCCACATTTATCTTCTTATGTAACTTTGGTTTGTCATACTTTATGTCTAAGCAAATTGAATGTCTCCTTTCTAATGAGATGTACCCTGAAATGCAGTTAGGTACTTGATACTTTAGCGCTTGTTTGAGCAGATGACTGGAGCACAGTGTGGACTGCATCTCTTAAATACAATCCTTAATGTGTTTGGCAGCTTCTCAGGTTACAAGGAACACCCGGCTTTTAGTGTCTATCTGTTCACCAGGTGTTTAGTATGAATGAAACGGCATTCAAAGAGTGAGTCTCACTGGCTTGCTTTATTACTGATGCCTTCCCTATGGAGAATTAATCCTCTGAAGCCCCATTATGTCCCCCTGTAAATAATGTAGATGTCACTTCCTTCTTAATATTCTAATCCATACTGTGAAATCGATTTTGCATTTATCGGTCAAATAGAGCATTTTGAGATAGTTGGAGTTACCCTGCCAAGGATTAGAAATCTACTTCATGTTTTTAAAGTACTTGTTAAAAATGAACGACCCTGGCACATTCTCTCATAATTTTATTCCAGCCATGTGAAATCTTTCTTCTAAACACTTTATCCTTGCGGAGGAAAAAAAAAATGAGCTGATGAGCCATTTAAGCACAAAGGGGCTTTATTTAGAAGATTCCAAGGGGGAACTTTGAAGTAAATATATAAAACATACTTCATCAATTTGCCTATAAAACTAAAAGAGGAACACAGGAATATTGATAAAATAAGTCATTAAAACACATTCTTTATTTCTTGCCCAGTTTAAAAGAAAGAACTAAACATCCCTAGAGAGAGGAAGAGACATAGAGAGAGAGTGACTAATAGAAAGAGGGAGAGAAGAAACAAGGCACCAAGGACAAAAAGAGATAATTAGACAGAACTTGTCCAGGTTTTCACACTATGTGCTCTGTCCAGTACCGTACACAAGAACCTCTTTCCAAATATTTGTCCTAAGGCTCTAAGAAGTTAAGTACGAGGCTGAAGGTTGAATACAACTGTCTTTAATCATTAACAGTTTGGGGAGCTACTTTTAAACGTCTATGGAAGATGCCAAGCAGTGGTAAGCCAGACAATACAGAGCACTGCATATCTGTCAAGCAGCTGAAATATGTTTGGGCAACTTAATGGTGAGCCACACAAAACATCCATTTGTAACAATTTTAATACATTCAATTAAGAAACCAGGATTTTTATTATTTTGCACCCATAAAAATATAACTATATTGTTCATTTTTATTGATAGAGTATGTGTGAATCTTATTGATTATCTGTAATTTACTATTAATGTTTTTACAGTGACTGTTTTTTTTGTGTGTGTAAACTTAATATATGTCAGCAACTGGTTCCTCAACACAATTTTTTTTAGCATTACAAAAAAATGAACAGGTATAAAGGTTCTCTTTTTTCTACATCATGTTGAACATATTTTGTTCTGAATTACATAGTTTTAAATGTAATATTAAGTTTTATATTCATATATGTTTAACATCAAAATCACTACTTATGACATTGTTATCAATTTAAAAAATAGTATTTGACACTAGGATAGCATTTAATTAAAGCTAAAAAGCTTACACCCCATTTCATGTTGATTAGTGTTTGGACTAACTCTAAAATGTCATCAATGGAAGCTAGTCACTGAAATTATTTTATCTATTGTCATAGAATGGTGACTACCCAAAAAATATAAGTTAGCATTAAATAGAAGAAAGCGTACGTGACCACAAATCCATGCACAGGGTTGTGTGAAGACAGGAGAACCTCATTTTTCTGTTTTGTCTCTTTCCACTGTGTAAAAAGTCTACATCTGTGGGCTATTTCTAAATTCAAATTGTCACAATTTGCAATCATAAATGTTTAGCATACTTTGTAGAATTTTGATAGTTTTGTAAAAGAGTGAAAAACAAATGCATATGTAAATAAAGCAGCCCATACTAGCAGATTCCTCAAATGTTAATATGTAAATAAAGCAGCCCTTACTAGCAGATTCATCAAATGTTAATATGTAAATAAAGCAGTCCTTATTAGCAGATTTGTCATATGTTAAGGGGAGTAATGATAAGGAGGCAACTAAATCAGGATGGTCAGTAACTGATCTGGGTTTAGAACTGTGTTTGGAGCCATCAATTTTTAAATATATGTTCTCACTATGTTATTAGTTGTCTGAAGAAGCAATCAAGAATTGCTCCCAGAAAATGAGTAAGTAGCCATGAATATATGAATGCTGTTTACAGAACCCATAGACCTATGAATGCTCAAAATGTTTGGGTTTGTCAAAAAATTACATTGTAGTTATACTTGATACTTAAAAACTGTTAATAGAGTCTAAAATAAAAGTCGCTAAAATTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316-Scn9a:NM_018852:27
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.215
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=42.2),PF0061222=IQ=WD(100=5.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
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]
SPECIAL DATASETS
- Pre-implantation embryo development
Other AS DBs: