MmuINT0139821 @ mm10
Intron Retention
Gene
ENSMUSG00000075316 | Scn9a
Description
sodium channel, voltage-gated, type IX, alpha [Source:MGI Symbol;Acc:MGI:107636]
Coordinates
chr2:66487982-66493216:-
Coord C1 exon
chr2:66493079-66493216
Coord A exon
chr2:66488087-66493078
Coord C2 exon
chr2:66487982-66488086
Length
4992 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTCTTTTTTATTCCTTTACCTT
3' ss Score
1.26
Exon sequences
Seq C1 exon
GTAAATGCACAACCAATATATGAATACAACCTCTACATGTACATTTATTTTGTCATCTTCATCATCTTTGGCTCATTCTTCACTTTGAACTTGTTCATTGGTGTCATCATCGATAATTTCAACCAACAGAAGAAGAAG
Seq A exon
ATAAGTATTTTAAGTGTTTCCTACATTGCACTGAAAAAGAATGAACTTCATATAAATGGATTATTTTGCATTTATTTTTCAAAATAATTGGTCAACTATGTAATTGTATATATGTATAATCTTATTGTTTTGTTCTGTAATTTTAAATGTTATATCAATAGTTTTAATTAAATTATTACATTATATTATATATAGTTACATATTATTATCTATTATATTTATTATCATTTATTTATAGTATTATTTATTCATATACTACTATATATTAAAATTTATTAAAATATACTTATAATTAAACACAATAGTCTTAAACATTATATTAATTCTCTGATTTCTCTGATGTTGCCTATAGAGGACTGAATAATAAATATACCACTAGCTCAAAGCAGTAAGGTACTTTTTTCAAAGTAGTTTTATTTATTTATTTTCAGAGGTATTCTTTTTTTCCTGCTAACCATCATTCTGGGGTATGTGTTATGATGGAAGTTAAGTGACAGTTACTTATAATATGGCTGCTGAACTCATGTCACTTATGTTATAGCATAAGAAATAATACTACTGAAAGTAAGACCTGCTGAGTGTGTGTGTCAATCACTCTCCTTAGCTTTTGAGCTCAATAACTTTTATATCAGCTTTAGAGTCTTTTGATTGTCATAATAAACCACAACAAAGAATGTGACTTAAAACAACAGTAATTTATTCCCCACACATCTAGAAGTTAGAAGTCCAATACCAGAGTTAGAGGAGTCATGAGTTTTTCCTGACCTCTATAAGAGGAGCCATCCTTTTACCCCCTAGTCCCTGTCAGCCCAGGCTGCGATTTTGGATGGGGACAGGGAAAATCTACGATCGCATTCTTTTTCCCCTTCTATATTGGCTCCTCCTTTAGTGAGTACCTTATTATGAATCTGCTCTACTCCACTTGGACCTCCTTTTGATTAAGAGACACTAGGCAGTAACAGTATCTTTAATCAATGTCACATTCTGGGGTGCTGGAATTAGGATTTACATAGATTTTTGAAGGAAATAGAATTCAACACATACACTCAAACATTATAGTCCTAATTGTTGCTACAATGCCCTAGGAAAGAGCATATGGAGTTGGCGATCTAACATATGTAAAGCACTTACGTAGGAAGCACAAGGTCCTGTATTTGTCCAAGCATGAAAATAAGTAACCAAATAAAATTGGGAAAAATAGAAAAGAGGAAAGGCACATAGAACAAGAAATTACTCCAAATCAGATATCAGACTAAGTAGAATTGGTAATATATCTCCTATCTGTTGGATATTTAATCAAATCTTTTTATTTATTTTTAAACTTGCCAACAAGTTCAAAGTATTTTATTTTAAGAAATTTTTCAGTGTTATGTCCTAAGGAACAGAGCAAATATTTGAACTTTTGTACAAAATTACAATATATTAAGTGCCTTGGTTTCTTGAGTTTCATCTCAAATTTCAAATACTAATTATCACTATTTTTATTATTTATTTATTATTAGATATTTTCTTTATATACATTTCAAATGCTATCCCGAAAGTTCCCTATACCTTCCCTCCACCCTGCTCCCCTACCCACCCACTCCTGCTTCTTGGCCCTGGCATTCCCCTGTACTGGGGCATATAAAGTTTGCAATACCAAAGGGCCTCTCTTCCCAGTGATGGCCGACTAGGCCATCTTCTGCTACTATTCCATACACTGCACATATAAAATAGTAAAAAGCACAATGAGAAAAATTTACAAAGATGCACATGAGCAGTCAGGAAGCTGATGCAGTTGTATGTGGTATCTGATTTGCCTTTTGAAGGTAAGAAAGAGAAGATGCAGCAACTGAGAGATCAGTGGGTAGACTATCTTCATGAAGGAGAACAGAAGTGTGGGCCTATAATGACTTGCCCTAATTAGCAAGGCCACTATTCAAGATGATCAGAAACTCACTCCGTTAATATGGAGTTTAGATTTGAACATAGAAATTTTTAAAAATATGTGATGTTTGTAGTTTTGAGAAAGCAGATTTGAAAATCCTTATTAAATATTACTCAGTAGGAGCTGCTATGTCATTGGGTATTTTAAGAAAGGAATAGCATTCAAGCATTGACATTTTTGGAATTCTGTTATGTCTGATACTACATAAGATGCCTCATGTGTGTAATTTAGAGAAATGAACTCTAATTAACTTTCTAGAAAGGTTATGTGACATTTAGAGTCTGACCCTAGAGAGTAGCTTCATCAAAAACCAAGCTCCAAAATTCTTTCAATCACAGATTGTGAATCTGGGCTTTAGTACACGTAGTAAATGTGTCTGTGACTAGGAAAACACAGGTTAGTCCAGATTTAATCTGTCATCTGAGATGCTCTTAGAATATCCAAAATAGCCCACCATGACATTAAAACAAGACATTCTATCAAGGAGTTTAGACATTTAAAGATAGCAGAATCTATGTCTTAGGTTTCTTGATGATTAGACAACTTACATTGATTTGGGTACCATCTCCGGGAAAAGAGATGTTTATAGAATTAGGAGTAGGATCACTAGAGAAAATTATTCCAGGTTTCAGATTAGCATCTATAAGTATATATTGCATGCATTGGCATGTATGCAGTGCACAGAATTTACTACCACAAGTGCAGGAAGTTGTCTATTTGGTTCACAGTCCATATGTAATCTGGGATTCAAGGTAGATGCTTAACTATCTTTAATATAAATATTTTAATTACAGCTTATGGCTCTACTGATCCCTTTGGAAGAAACAGTCACATTTTACCAGTTTTCTGTACAATACATAATCTCTGTTAGTACTGTCTTCATCGTTAATATATTCATGTGACATTGAAAATTTCTATTATTAATCATAAGCATTCAACTGAAGATGAGTAAGTAAGTTATGAATAGGTTCGTTATTGGAAAATTAGAAAGATAACAGATTTGACTATGAATGTGGGCACCTATGTGCAAATTGTAAGTAACAACAACCCTTTTAATAACTACATGGTTATGAGGAAGATGAATATAACTACACTAAACCACCTCTCATTCTAAACTTTGGAGCCCCAATGTTTCAGATGTCGTACTTTCTTGTAATTTTAAATATTAATATATATAATAAGATACTGAGATATGAAGCCCAAGCCTAAACAAAAAGACAATCATTTATGATTCATAGATATGAGATGAAGGTAATTTGACAAACAATTAGAAGTGTTCCTGAATTTTCACTAAGACCCAAGCCATTGTGTTAGGGATGGAATTCTCCACTTTAGGTGTCATGCCAGTCCTTAAAACATTCAGAATTTGAAACATTTCAACTTAGTGTAGAACATTTATAAGGTGTTTTTCTTCCCTAGTTTTACACTAAATATTTGACAAGTAAGATTTCAGTTGATCCTTTCAGCAAATAAATGGTGTATTTACTGTATAACAGTACAATAATAATGCATTGAGGAAATCAAGAAACTTACATATGGACTGAGAGATGAGATTTGAACAAAGATAAGAACCTAGTCTTAACTGATATGCAATAGAGCTTTGACATCCAATGAACATTCAGATAGGACAAACTGATCTCTAAAATGTCTGTCTGGCTTCTCTAGGAGGATATTTTGCACAAGGCCTATATAGTCTATAGTAAAACACAACAGTTCGAGGCTCTGGGTTGCACAGTCTCCTCTAGAATTCACCATACCCATCATGATATTTTGCAATCAGAATATCGTCCCTGGAAAAACAAAGTGTGCAAGATTAGTTTACTAAAAAGCACTAAGGACAAAGGCTGCTCTTAACATTAGCATGAACTCTCTGTCATCAGATGAGTACCAAAATGAATGACATAAAGACTGTGGGCCAACTAGAAAGAGTGAATAAAGTCTAAGAAAAAAAAAGTGTGGCTACTATCAGGTATAAGAAATAAACCCAAAACGGAGCTGAATATAATTTAAACCAAGAAAACAAAATAGAAGGCACGCCAGGTTGTCCTTAACTTCAAGACAATATAAGTTAAGTAAAGGAGTTGGAGCTTCAAGTTCTCCGAAATGAGTCTATAACACACACACATTATTCTACATTGTGCTATGAGTTTAAAATGGCAATAGTAAAGACCAAAGCAGAGTCCATACAAGTCTGTGAAGATTACAGATAACCTTCAGAAGTCAGCAAAGCATCAAGAAGTAACCAAAGTTTCTAACCTTCGTTTCCGATGTTTTGTCTTGTCTGATGAAGAAAGGGTTAAAATGTGAATTTTTTTTTTACCTCAGTTTTTGCTGTTTAATCTTGGTGACTACATTTCTTTTTGTTTAATCATTTGATAGTCTTTCAGATAACTCAAGACTAAGAAGCACTGGTAGCTTCCTTTGTACCTGAACTTTACAAGTGTAATGTTGATATCCAATAAAATGTTTATATTGAAACCAGAGAGGGATTATTAAAAATTCAGATTCCTTATATGATAACAGACACAGACATGGATGTTGACATAGAAAATGAGCTGCACATTCATTTCTAAAAGTGTCTGTAATTTTTCTCCATTAGTGAAATGGTGTCATTGGGAAATAAATATAAATTAATAGAAAATTAGTACTGTCATAGTTGTTATTTTAGAGCCCTACTTGCAATGAGAGTCCTAAACATGTGCCAAACCATGAAAGACATTTCAAAATCTTCCTAATTTATCTTTTACTTAGCACTAATATTTTCCAGTAAAAGAAATATCAGAGGAAACAAAACCCTAACAAATAGGCTAAAGTAGAACATATTAGTATATCAAAAGGTAATGGAGCCAGTCATGATTATATGTTGTGTATATTCTACATACTTGAATTATAGTATGTCCATGTTTACACAGAGATAATCCCTTTTAGGCATCTTATGTATAGCTCCTAGGTATTATGAAAGTGAATATCATCTCTATATTTGTATATTTAACCTTTTTATGAAGTACAAGAAAGAACTGCACTTTGGTTCTGGTTTTAATTGGATTTCTTTTTTATTCCTTTAC
Seq C2 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAGCTGGGGTCCAAGAAACCACAAAAACCAATTCCGAGGCCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075316:ENSMUST00000100064:24
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.3=76.1)
A:
NA
C2:
NO
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