MmuINT0139679 @ mm10
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65530804-65536726:-
Coord C1 exon
chr2:65536413-65536726
Coord A exon
chr2:65530923-65536412
Coord C2 exon
chr2:65530804-65530922
Length
5490 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TCTCATGTTTTCTTTTTCAGACT
3' ss Score
11.66
Exon sequences
Seq C1 exon
GCAATTCTTATGCAAGAAGCTAAACGTAATTAAATGTGCAGGATGAAAAGATGGCCCAGGCACTGCTGGTACCCCCGGGACCTGAGAGCTTCCGCCTTTTCACTCGAGAATCTCTTGCTGCTATCGAAAAGCGTGCTGCAGAAGAGAAAGCCAAGAAACCCAAGAAAGAACAAGACATTGACGATGAGAACAAGCCAAAGCCAAACAGTGACTTGGAAGCTGGGAAGAACCTTCCATTTATCTATGGAGACATTCCTCCAGAGATGGTGTCGGAGCCTCTGGAGGACCTGGACCCCTACTACGTCAGTAAGAAA
Seq A exon
GTGAGTGCTTACTTTATATGGCCAACCCATTCTCAATTAGATGTGCAAACCAGGGGCTTCTGTGCATTAGAACATTGCCATTGTCATATGTGAAATAGTTCACGGCACTCTTTACTGCTACACGTCTTGAAGAACAGAAACATTGATAAGAAATGAAATCTCTGCTACAGAAGAATAAGCATAAACCATTTCTACCATTTCATAGTATTGAGATAAGTGGGAAAACTTAAATTCGACAGCAAAGATAAGCATCTGCTATTGCTAATCCATTTGGCTGCTTGATAAACAGCCAATTTGTAATTATAAGGTGAATGCTATACTTATTTTTTAGTTCATACTTGGCTTGATATTTCTTACAGTCATATTTTCTTATCTATTCCTATAGACAGGTAATTCATGGAGAAACATGTTTATCCAGACATACATTTTTAGTCTTTTCCCTCTAACTTGGCATATGATTAGGAACTTCTATAGGCTTCATTGAGATCATGATAGGAGAACTGCTAGACTATCTACAAATAGTTAAAGCATTACCACAATGAAAGAAATATCACTGTTAGAAGAGAAAACATAGTAATGATAATAATAACAAGAATTTCCATGTAATTTAAAGGAACAACTATGACTATATTTCTCTGATGTTTAAAATAACTACACAGTTATGCCAGAATTAGTTTCACTACTTAAACCTGCTTTGTTAGACCCATAGGAAATCTAAATAAAGAATATTATTTTAATACCTACATGAATATTTTAGTACCCTTTAGTCACGATGTATAGCTTACCTTCACAATGAGAAAACAGTTTATTGTAAAGACAAATTAACATCATTCCAAGTTGATGATTTCTGGATTAACAACTAAACAGACCACCTTTACTTGTCAAAGTAGAACTTTAGAAAAGCAATGGTTGAAGACACTGCATTCTTTAAGTAGTTAGTGTATGATATGACCTTTTAAGTCCTGGGGATGGGAGACGGCTCGGTGGTTCAGAGCATTTGCTGCTCCTACAGAGGACTGGGGTTTGGTTCACAGCACCCATGTCAGGTGGCTCAGGACTGTCTGCAATGACAACGACAGCAGATCTGACCCTCTCTGTGTGAATACTCTCACACATATGTACATACATAGACAAAGGCATACAGATAGATAAAGATTTTTAAAAGGCTTTACAAACATTGTAAGTCCTTCTTACTAAGTTTAACAAAGGAAGGCACTAAATATACATTCATATGCTTCTAAAAGAAACTGTGATTTACTACAGAGATGATCAAGAATGAATTGAAATTTAGAAACTCTGATGGCTTCTAAAGGATGGTTAACAATAAGATGTTTCTCCCAGAGACTAGAAAAACAGGCCTCATTTGAGAAAAAAAAATAAATGTCTTAACATACACATTTGCAACCTTGTGTGTTGTCTCATACTTGTAAGTCCAACATTTGGGAGACAGCCAGAAGAGTCAGGAGCTCAAGGTCAACCGAAGCTACAGAAAAGAGCTTGAGCTACAAACCCCACAGTATGTTTTAAAAATTATTTTCAAGACACAGAAATTTGTTTTACTTTGATATGAAATTGTTATTACTCCTTTAAAAACAAACAAACAAACAAACAAACAAACAAACAAAATGAAGGAGCCATCAGTTTGATAGGCTTACCAGGGTAGAAAGGAAGAAAATGGAGATATTACTCAATGGGAAGAGAGCTATATTTTCTTGCATTAAAAGCATTTCCTTTCCAATGACAACACCATCTCTTTATGAAAGGGATACCCTTGGCTAATCCCACCCTTTGATTAAGTAAGCTGTTTGGACCCCATGTTCAACAAGGACTCTCCTGTCCAATTTGTTTTTCCCACAGATTTCCTGAGGGAAAGGTACCACTATAATTCTTTTTCTACATGAGAATATAACATACACATTTTAATGTCAATTGATTGTCATCTGACTTGATAGGTCAGGCTCTCAAGGTTGGTTAGTTTTCTAGTTTGCTACTAGAGAACAGAATTGTCCTCTGTGCACGGGAAAGGACAGGCATTGCTCACCCCAAACTGGAAACCATAACACTTGGATCATAATTTACTCTAGTGAATGTAAGTGACTCTAAACTCTCAAAGGAGGAGCCCTGCCTTCATTAATGAAATATCTCTAAGGATGAGAATTCAGGTGCTACTTACAGAAATGTGATTTGTGACTCTTAAAGTTAAAGGGAGAAAATAGTGTATAATTCATAGAATTTCACCATAGTACAAAGCCATGTTACTGCATGATCATTTGTGTAAAAGACCACATAGAGCTTGAGAGCTTCATGTAATGACTAGCTGTCACTGATTAGTGATGTATCTTAGTGCCGAATATAACTAGATGAGTAAGACCACAATATATTTTAATAGCATTTAAGTTGGCCAGGTTAACGGCTTAAAAATAGTGGCATGATAATAATAGCTAACATTTGTTGGGCTCACCCTATGTCAGGAGCCACTCGAATACTCCAGTTCATTTCATACCAATGAGCCAGTTCATGAAGCAGTTGCTCTCGCTAGTCTCAGTTTCCAGATGGGAACGTAAAGTCAAGGCCAATTCCTTCACTTACCAAAGTCATTCTCCATCAATGATAGATCAAGGCTTGGAGCACTTGACCGCTGGTCAAACTCTCTGCAGTAACAATAAATGTAAAAATAAGATGGTCAAAAGTTGGTTGCACCACACTTTTAAACACTTTTTATTGATTCTTTGTGAATTTCATATCTTGTACCTCAATCCAACTCGTCTCCCTGTCCCTTCGTATATAACCTCTGCCCTTGGCAACACCACCCCTACCATGAACAAAAACAAAACAAACCAAACAAACAAAAAATATCTAGCCATGGAAGTTGCAGTGTGTCCTGGTGATCACACAGTATATCTTTTGCCCAAACAGACTGACTTGCAAACGTTCATTGCAGTGAGTCATTGGTCTGGTTCGGGGCCTCTGGCCTCTGCTATGTCATCAATACAGGATCCTCACAGGGACTCCACTCAGATATGTTGTTGTTGCCCTGGGCTGTACCATCTTTTAAAATTCTGTGCCTGATATATTTCATTAAGGTATAAATCTGCTGCTTCTCTCACAAAACTAAGAACTTCAGTGAAGTTATTAGTATTTATTCAGGGAAAAAAGTAATTAGCACTCCTGATAATAACCTTTGTGAAAAACTTCAGCCACAGTGTTTATAACAATACTGGCGATAAGCACCGAATCTTTTCACAGTGCCTCACCACCTATTGTTTCTTGGAAACCCGACTTTACAGTTGGTGTAACTTCTCTGAGTTCCAGCCATCTCTTACATTCTTGTGTAGCTTTTGGTGTAGGTACATCATTCGATGACGTCAGAACCCCAGACTTCAAACATCACCCTGTAATTCTTTCACTACGTAGATCATTAGAATTTTACTCCTTGTTTCTCAACTCTCAGGGTATGCACAGTTATACCTTCAGAGTAGATGCACTATGTTCACCAGTATGGGAGCCACTAGCACCCACAGCCTAACCTTGCAGGAGAAGCAGAGGATTTCATATTTAAAGGACAATTCATTCTTGCGTAGTCTATTTTGGGAGATATTTCAAAATACACACCCCCTTTTTAATGTTGCAAGCAGAAATTGCTTTTTCAGGGAAATTGTTTAAAAGAGCATGAGTTAATGCACTTTAAATCACTGGGGACTTTTACACACAATTGCAGCCGCTGATGCCTAAATGGATCTTGATCGCTGTACTGTACTCTGAATTCATGACAGCCCACTTACGCTACTACAGTTCAAGGGCAGGCTTAGCGAGGCTCATTGTCACTTGCAGGTAATCTTGATGCTAGTAAGGGATAGTTTACTTGCCCTCTTCCTAGAATTTATAGAGCTCAGCTCATTGAAAATGGTTAGTTAAGTAACAGTTGGCTCAATGGTCTTAAACACAGAAGGGCGGTAAAAGGGTTGCTTGTTGTCCCTGCTCACAGTATAAACATTCCTGCCTGCCTCTTCAAACAGAGCCTGTTGCGGGTTGCTGTGAATGTATGTGATGTAGCCTTAGTAAAAGGGTGCAAACATATTATTAAGTAAATCAGTACATACAACAGATGTCATGAAGGTGAACAGTGCCTTAAAGGTAAACCCATATTTAATTAGAACAGCGTTTATTGGCAAAGCACGCTATTAAAAACTGTGGGGGGAAATGCAGCCATAAACTGCAGGCTCTTTGTGCTCAGTCATTTATAAAAGCACCTAACCAGGTTCTCCTACAAATGAACCCCGTGTGGAAATTGCTACCTGATGATGATTACCAGCAACGTATGAGAGAGTACAAAGTAATACACTAAGGGTTAGTGGCAGGAGAACCAGCTAAGGAATGATCAGAAGGCAGCGTGATTTATTTGGGAAAATGTAAAGGAGGGAGTGATTTGGGTACTGAGAGTGGAAAAAAGAGATTGGATAATAAGACCGCCTGCATATTAGAATTACTCAAGGAGAATGTTGAAAACACCTAAATATCTGCCATACTCCTAAACTTAAATATTGACAATTCTGAAGAACCAGGACATCCTAGCATGAGGGTCATGACAGGTAGGATAACCTTGCATAGTTAGTTAGACCTTGCTACAGGTATTGCTCTCTTCACTGAGTCTATCACCATGTGAATCACAGCTGGAGGGACAGATTGATAGGTTCTGAGTGGGACTGACAAGTGGATTAAATGGCTGGAACAGAGATGACTCTAGTGGTAAAAAATAAAGGATGATCCATCCTGGGTTTCTTGAGAGGTAGTCATGGGTCTGCATAGCTTAAATGCTAAGATGATGTTGTATGTTTCAGATTATGACCTTTAACTGTGGCTTGGTCTTTGAAGTCATATATTTAAAATTAATTTTCAACGCAGCTGTCTTTTCTCAGTACAAGCTATGAAGTGGATCATTCTTAAAACACAAAATCTGGTTCGATAACTTATTTCAATGTCTTAGATCAATTCAGCTGCTACAAAAATGATGGGAGGCTACCACAAGCTAGGGTTAGAAGGTTTGAAGTTATTAATTTCAATAAATTCTGTAATTAAATAATGATACTGATAAAAGATTATTTTAACACTTATATATACTGAATGATCTGAAAAGTTACCAAAGCTGGAGACAGATGGTAAGCCTCAAATAGAAATGAACCTTGTAAAGTTCTTTAATTTGAGTTTTGAAAATGTGTAAGACTATCAGTTTGTATGTATCAACACGTTTGGGGGCTAAGAGATAGATAAGGTAGCAGCCCAGTGGGCCTTTGTGTGTCTGTATGTGTAGGGGAGAAACGCTTAGTCTGTGTCTAGTAAACAAGATATTGGTTATGTTCCAACTGGCCTAAATGAACACATTTGTACAAAAAAAGTCAGGTAAAAGTTCTCGATGTGTGTTATAAATGCTTCAAATAAGCCTGCATGTCTAATTTGGTAATCTCTCTCTCTCTCTCATGTTTTCTTTTTCAG
Seq C2 exon
ACTTTTGTAGTGTTGAATAAAGGGAAGGCAATTTTTCGATTCAGTGCCACCTCCGCCTTGTATATTTTAACTCCACTAAACCCCGTTAGGAAAATTGCTATTAAGATTTTGGTACACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182:ENSMUST00000100069:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.330 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
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