MmuINT0139812 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66526608-66533418:-
Coord C1 exon
chr2:66533062-66533418
Coord A exon
chr2:66527085-66533061
Coord C2 exon
chr2:66526608-66527084
Length
5977 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TCCCATCCACCCTGATATAGGTC
3' ss Score
8.34
Exon sequences
Seq C1 exon
CTGCGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCACTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATCAACGAGAACTGCAAGCTCCCACGCTGGCACATGAACGACTTCTTCCACTCCTTCCTGATCGTGTTCCGTGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTTGCGGGCCAGACCATGTGCCTTATTGTTTACATGATGGTCATGGTGATTGGGAACCTTGTG
Seq A exon
GTACGTAAGAGCTATTCTTATATTTAAATTTTCTATTGCAATTATTTCCTGATGTCATTGCTGTAATTTTAAAATTAACTTTATTTCAGAAACAAAATAATATTTTTAATCTCCTTGGCCAGGAAAACCTGTATTTATATTTTTCAAAATTACTTCCTAGAGTTTGTCATATGAATTAAAACTGTGGTTTTCAAACCTCTTAAAACATGACCAGTCATCAGATATGAAACTATGGTGGTAAATAATACATGATTAAGTTAATAATCAAAAACTGATGAAGCAAGGCAAGTGAGAACACTGTTTATCAGTACTTATAGTCATGAAACTACCAAGTGGGCCAAACTCAGTTCAGTCGCTGCCTCTGTATGACTCTTTGAGTTACAAAGGGTTTCCATGGTTTACAGTGACTAAAAAGAATAAACGGAGACTATTTTGTGACATATGTACATCATGTGAAAAGGTTCAGATTTTAGTGCCCATACAAAGCTTTATAGAAAAATGGACATATTTACTCATTTACAATTTACCTATAGCTGAATTTATGCCCAGCATTCAAAGAGAGGAACTGCTTAAATGTCCCATGTCCTACAAAGTACCATTTATTTGTTACATAGCCCTTTACAGAAAAATTTACCACCCGCTAGTTTGTAGCATTTCTTTCAAGTAGCAATCTCCTTGTGTTTGCAATTAGTGTTTTTTGTCTTCTGATTGGTTTGTTTGTTTGTTTGTTTTTGTTTCGGTTTTTTTTCTCCATATACTGGTTGGTAAAAATCTCCATAGCTTACAGAAAAGAGAAAATTAGATAAAATATTCTTCTATGAGCCATTCAACTTGCTCTACAAATCCACTATCCTGGTTTGTCCTAGTAGTGGTCTGCTGGACATCAAATCATTTGAAAACCATATGGTAAATATATTCACTCCCACTGGCTTCAGAACAAAGTTACTAAATATTTTTGCCTCTGTAGCTTCCATTGAAGAATGAGGGCTAGAGAACAGATCAGAAAATCTCCATTGATCAGATCACAAAGTAAATGAGAACATGGGAAATTACATAGAGTACACTACACAATGATAATTCTATATTCTTGCTGCATTTACTAATCATCATGAATTGCCATTCTGTAATTCCTTACCACCCTCACATAGTGAGAGTGCATTTTCTTTTTTCTTTTTTTTTTTAATAATTTTTAACTTTTTTAGTTAGGTATTTTTTTCATTTACATTTCCAATGCTATCCCAAAAGTTCCCCAAACCCTCTCCCCCCACTCACTTCCCCCTCCACTACCACTTCTTGGCCCTGGCATTCCTCTGTACTGAGGCATATAAAGTTTGCAAGACCAGTGGGCCTCTCTTTCCACTGATGGCCGACTAGGTTATCTTCTGATACATATGCAGCTACAGACACGAGCTCCAGGGGGTACTGGTTAGTTCATATTGTTGTTCCACCTATAGGGTTGCAGACCCCTTTAGCTCCTTGGGTATTTTCTCTAGCTCCTCCATTGGGGGCCCTGTGATCCATCCAATAGCTGACTGTGAGCATCTACTTCTGTGTTTGCTAGGCCCCGGCATAGCCTCACATACTCACTGATAAGTGGATATTAGCCCAGAAACTTAGAATACCCAAGGCACAAGATACAATTTGCAAAACACATGAAACTCAAGAAGAACAAAGACCAAAGTGTGGACACTTTGCCCCTTCTTAGAATTGAGAGTGCATTATCTAGTGTGATAGTTTAACAAATCCTTCTAATCTGCAAAAATACATATGGTCTTCTTTTTGTCTCAAATTCATAATCCTCCTGAGAGATGGGATTACAAGAATGCAATACTGTGTTTAGCTAAAGAACTTAAGTTTTGTGTATTGCTAGCAAATTTCATTTATCTTCTCTATTTTATGTCAAAATTTTGTAAGTTAAAGCAAACAAACGAATGGATGTAGTTCTTTTCTATATGCTAGTAGTGTGTTAGTAGCAAGAAATGATTAAAAAAAAGTATCAGGTGAGCAAGAAGTGATGAATATAGTTAGGGATATTAAGGAAAATGCTCTTCTTGTAGTAAATAATGAGAAGTTCTAGACATATAGTCTTGGAAAGCTTTGAAGCAAGTCTTTGAAGAAAAAAATGTAATATTTGGGCATGAGAACAAATCTGAGAGGAATGTTCCCCTTTGAGAAGAAAAATAGGTTGATAGTAAACATGAGGGAGTGTTAAGTCTACATGGAACTAGCTATAAATAACTCACATGTCAGTCATAAAGTATTGAACCAATACAGTAAACAAGAACAGAAGTTTGGCTCTTTTTCCTGGTGCCTTCTTCCCAGACACCAGCTGTCAGAAACTCATTGAAGTGGATAATGAATGCAGACTTCATACTTTCTATATAAAGTGTATGGACACAGAAGTATCTGTAGGTACTCCAGGTGAAAAGTGGAAGGCTTATGGAATCCAAATCAATGGTGGGAAGGACAAACAAGGCTTTCCCATGAAGTCAGGTGACTTGACCTATGGCAAAGTGTACCTACCTTCGAGTAAGGAGCATTGCATTTTATAGACCACGGAGAACTGGAGAGAGAGAGAGAGAGTACAAGCCTGTTCCCAGATACATTATGAATGACAGTCTTAGTATTCTCAATTTGGATATTATTGAAGAAGGAGAAGAGGAAGAGGAAGAAGAGAAGAAAAAGAAGAAAGAAGAAGGAGGAGGAGGAAGAGGAAAAAAAAGAGAAGAAGGAGAAGAAGGAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAGAGGAGGAGGAGGAGGAGGAGAGGGGGAGGAGGAGAAGGAGAAGAAGAAGGAGAAGAAGAAAGAAGGAGGAGGAGGAAGAAGAAAGAAGAAGGAGGAGGAGGGGGAGAAGGAGGAGGAGGACAAGGGAGAGTAGACAGAAGAGGAGGAAGAGGAGGGAGAGGAGGAGGAGGGGGAGGAGGAGGGAGAGTAGAAAGAAGAGGAGGAGGAAGAGGAGGGAGGGGAAGAAGAAGAGAAGGAGGAGGAGGAGGAGGAGGGGGGATTAACATATCCCTGGACTGACAGATACTGATTCGATCCCAAAAGAGCTAGCAGAATTGAAAAACTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCCCTCAAAATTATACCCATCAACATATTGTCAAAAAAGCCCCATAACAAAGAGGGTGAGAGTCCTATAACAAGAGCACCCAAGATTCAATGCCTTGTTACTTCATGTGACCTGAATGTGACCTGAAACACAAGCACTAATATATTGATCTTCAGAAAAATATATAAGAAAAACAAGGAAGAGGCTGTGGACTATGCTAAACCCTTGGCCAAGATAATGAAGGAAGCTGAAGAAAAAAACCACAGAAACAGATTGCCAAGAGACATAAGCTGTTCTGTTCTCTTTGAGAGCTTCTACTTCTAAGTATAAATCCAGTCAAAAAGAAGTCTGTAAGATTAACAAATAAGTAATCAGTCTTTGAATAAAATTGAAGCTTAATTCACAAAGCTGATCATCAAATCTTAAGTTGCAAGGAACTACCACCAATATAAGTTTACCATGGGAGAAGTATAAAAATATATTGATGATACTGTACCTTCATATTAAAGGTTTATACTTAACTGATCTAATGTCAAATTTTCTCACTGGGCTTGAGATATGGATATGTGGATAAGAGTGTATTCAGGTTAAGAAAAGTCCCGATTTCAGATTCCAGCAGCCACTTAAAAAGCAGGGTCCTCCTGATATAGCTGTCTCTTCTGAGACTAGGCCGGGGCCTAGCAAACACATAAGTAGATGCTCACAGTCAGCTATTGGATGGAGCACAGGTCCCCCAATGGAGGAGCTAGAGAAAGTATCCAAGGAGCTAAAGAGATCTGCAACCCTGTAGGTGCAACAACATTATGAACTAAACAGTACCCCGGAGCTCTTGACTCTAGCTGCATACATATCAAAAGATGGCCTAGTCGGCCATCACTGGAAAGAGAGGCCCATTGGACACGCAAACTTTATATGCCTCAGTACAGGGGAACGCCAGGGCCAAAAAATGGGAATGGGTGGGTAGGGAAGTGGGGGGGGAGGGTATGGGCGACTTTTGGGATAGCATTCTAAATGTAATTGAGGAAAATACGTAATAATAAAAAATATTTTTAAAAAAAAAGCAGGGTCCTATGTGCCTGTAAGCCGGGCATTGTAGAGGTAGAGATGGGAAGATCACTGTGACTTGCTGGCTGTCAGTCTATCACCAGTCTAAAGTGGAGGACACAGAACACAGATAACACAGACACATGCACACTCTCGCGCACACACACGAGGAAGAAAATTCATATTTAGTCATTCTGTCAGCTTATTTCCAGTTATTGAAATCATTAAAACCACAAGTTTTAGAAGTAGATTTCGGTCCATTCTAGTCTGTGGCAGGACAGCGATGAAAATTGTTGCCTTCCAATTAGACTTTGCAAATCAATTGTTTTCGTAAGTACTTATTTTCCTTCCTAATGTAGAAGTTATATGAAATTGACTTTGTTTCCATTTTTTGACGTCCATTAAACAGTTATAAATATCACTTCTCATCACTTTCAAAGTGAAACACATCATCACAGTATGTATTCTCATGGAAGAAGTGATGCACCATAAGCGTAGTACTAGAAAGAATTTTATCACTTGGATCTAGTGAATAAACTATTGATTTAAGAGAGATCTTTGGGGTGTTTCACTGGTATTCCTATGAGAACACAAATATACATTCTTAATAAAATACTAAAAAAGACAATAATTTCAAAGTACCTAAAACTCCTTAGCAACTACCTACATTGTTCTCTATGATTCCGTGTTAGCCTGACTTTTCATCCCTGTAACAAACACCTGATATAGCATTTAAAGGAGGGAAGATTTATTTGGTTTCCCTCTTAGCAATTTCAGTCTGTCATGGCAAGGACAGCATGGTAGAGCCTAGCAGGTCACAGGATTTCAGCCAGGGAGCAGAGAGCACATCTAAGATATACCTTTCTCCTTTTCCTCCCTTAATTCCATCCAGGTCCCCAGTCTACATAGAAAAATGAAGTAAGATAAGTTGGGCATTGAAGACACCTATATTTAATTGTAGTTCAGATATGTTTGTGGTTTTCATGTAAAAAATTAAATATAAATACAATTTATATGTGTGTTTTGCTCTCGGGGAAAATCTTAGCACCTGAAATTAACCTGGATACTTAATTAAAAAGGAAATGCATAAATGGCTTTTCTTACAATAAAGACCTTGCTTCAAGGGTACAAATTTCCCTGATCTACTTGGCCACTTGTTCCAGGACTTAAGTGATACACAGTAAAGGCGGCTAATCAGTTTTATTGTCTTGCATGACTTATGTTCAATGTGCTTAAACCAACCTGGAATGGTCAAGACAATGACAATAGTCTAATGTTCTTGTACTCTTTGTTTTCTGTGAAAGTAAAGCAGTAATTACAGGTAAGTTAAGAGAACCTTTGAGAGTCCCTAAAGGGAATTTGACTGGCTCATTTTAGAGAACAGAAATAGAGTGATCAATGGCATGATGACAATGGTGTAGGATGATTCTCTGCTCTTCAGGGCAACTCATCATGAATATTGCTTGCCCTCCACTGCCCAAGTCCCCATGTCTACATGTGCAGAGTATTGAACCCTCTCTGTCCTGTTTTTATGCAGTTCATGAAACTGTGCTTTGTCTCTTTGTCATTGTGTGCTTCTTTGTGTTTCACATGTCCCTATTCTTTCCCTCCCATCCACCCTGATATAG
Seq C2 exon
GTCCTGAACCTGTTTCTGGCTTTATTACTGAGTTCCTTTAGTTCTGACAATCTTACAGCAATTGAAGAAGACACCGACGCAAACAACCTCCAGATTGCAGTGGCCAGAATTAAAAGAGGGATCAATTATGTGAAACAGACCCTGCGTGAATTCATTCTAAAGTCATTTTCCAAAAAGCCAAAGGGCTCCAAGGACACAAAACGAACAGCGGATCCCAACAACAAAAGAGAAAACTATATCTCAAACCGTACCCTTGCGGAGATAAGCAAAGATCACAATTTCCTCAAAGAAAAGGATAAGATCAGTGGTTTTAGCAGCAGTCTAGACAAAAGCTTTATGGATGAAAACGATTACCAGTCCTTTATTCATAATCCCAGCCTCACAGTGACAGTGCCCATTGCACCTGGGGAGTCTGATTTGGAGAATATGAACACAGAAGAGCTTAGCAGTGACTCAGATAGTGACTACAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.313
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=84.9)
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
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types