MmuINT0139735 @ mm10
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119512981-119516064:-
Coord C1 exon
chr9:119515903-119516064
Coord A exon
chr9:119513102-119515902
Coord C2 exon
chr9:119512981-119513101
Length
2801 bp
Sequences
Splice sites
5' ss Seq
GAGGTAACA
5' ss Score
8.1
3' ss Seq
TCCCCTCCCCTCCCCCACAGACT
3' ss Score
12.56
Exon sequences
Seq C1 exon
CAGGAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCCCCCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACATCCTCTGAAGCCGAGGCCAGTACGTCTCAGGCAGACTGGCAGCAAGAGCGGGAAGCGGAGCCCCGGGCCCCGGGGTGCGGTGAG
Seq A exon
GTAACAGTGGGGTCTGCTGCTGGGGCCAGGGTCAGGCTGTGAGGGGCCGCAGCACTGGCTACGTTTACCAAGGGAAACCAGAGCAAGTGTGTCACGGGCAGCATGGAGATGGTTGCAGAGAAGAGGGTGGGAAGCCAATGTCCTGACAGGGAGAGATGGTGTCCATCCCAGCTCAGGACTCTGAGGCCCGACTAAGCCAGTCCATCCACGTGTTCACCCTTCTCACGCTTTGCCCTTGTGTTCTTGTGCTGATCGGCAAGCGTTTGTCCTGTGACTTTCCGTGTCCAAAGAGGGCTTGGATGATCTTCAGAACAGACCTCCCCACATCTGTCAACTGATGCCTCCTCCCTGTGTTCCCTGCAAAGATTACAAAGAGGGGATGGGGCATCTCAGCCTGTTATCAGGAATTACCGTGGCCACAAAAAGACTTTACTTTGAATTAACTGCCACACACTTGGGAGCTTTTGTGTTTAAAAAAAAAAAATCCACACTTTTTGTTTCTCTTGAAAACTTGAGAGTGGTACTACCCTACTGTAGACAGGAGGTAGCCATTCCCCAGCCTGCCCGATTGCATGTGTGACCTGCCTGGCTTCCTCCGCAGAGCCTCCAAGCCAAGGGCTAACCAACTGCGCTGTTCAGCCTCACTTGCTTCAAGCATGTGGAAAGGAAGTCATGTGCTCAGAGAGTGCCGGGTGACCTCCGTCCTCAGCCCAGTGCTTGGGACTTTGGTCCTAGTGTAAGACAGGCCCCAGGATGCTCCACCGTCGTGACTGATCTTGGAGCATGAGGCCCTGGTGACTGTCCTCACCATGGGGGTTGGCCTTCTCCCTAGATGGCCTAACACTTGACTTGGGTTAGGAGGACCCGGGATCCTAAGCCTCAGGAGAGAGTGTGAGCTTTGTGGCTTCTTCCCTTCAGGTGTTTGTGGTCTGGGGAGAGGAGGCGAGAAAAATGCCGTGGTGTTCCCGAGGAAAGGACTTCTTCCAGGCTGGGCCTGTAGCTGGGTTGGTAGAGGGCTTGCATAGTGCACCCCTAGCACTGCATAAACTGGGAGTATCGGCCTACAGTTGTAATCCCAGTGCTTGGGAAGTAGAGGCCGGAAGATCAGAAGTTCAAGGTCAACAGCAGCTGCAGTGAATTCCTGTTTCTGACAGAAAGGAACAGGGAGGGAGAGGAAAGGAGCTTCCTCCCTCCTGCAGTAGGATCCTGAGAACTCCATGACCACCCTCTGGGCCATGCTCAGCTCTGAGCCTGCAAAACCCCAGCTGGATAGCCAGCGCATGGGCCAGGAGACGGAGCCCTACCCCTCTGGCCACTCCAAGCAGGCTGTCCCCTCCCCTGAGACTTAGTCGCTGAGACCACAAACCTCAGAAGTGACAAGTAACAGGAGGTACAGATGTGGGCATGGGGATTCATCCCAGGAAGGGGAAAGAAGGCAGCAGGGACCAGAGCCAGGCTCCAGCATTCAATCAAGAGCCTAGGCTGGCCGCGGGCAGCCAGCTGAGAGGAGAGTGAGACAGGGTAGAAGCAAGTCGGTGGGGGATGAGGGGTCCTTTCTTTATGGAGGCTCTCCTGACTCTTCTGTCATTAAGTTCTGTTCCCCAGAAACAGAGGTAGGGACGGGGACTTCTGTGTAAATGACTTGTAGAGGCAGTGCACCCTAGAGAGGCCAGGAAGGACACAAGAGAAGCATATTTGGAGAAGAAAGGAGCTAGACCAAGGCCAAGAGCAGGTTTGACTTCAGCGTGTGCTAGTGGGGAGCTACAGAGCATCAAACTGGACCCCCTGCGCTGTCCCACATTAAGGCTGAGGTGACTACCCAAGGGCCAGTCCACTGGCTAAGCTGGAGGAGGGGCCGGCTAAGCCTCAGGTTTCACGGTGGCGGGACAGGGTGTTCTACCTACTCACAGGCATGTGACATTGCCCTCAGCCACAAGGCACAGACACTCACAGGCCGTCATATGTCCTTCCTACAGCAGAGGTCCTCACCCTTCCTGAGGCTTCGACCCTTTGATACAGTTTCTCATGTGGTGGTGACCCCCACACACACACCAGAAAATCATTTCGTTGTTACTCTGTAACTATAATTTTGCCACCCTTTGATTCAGTTTCTCATGTAGTGGTGACCCCCCCACACACCAGAAAAATCATTTCGTTGTTACTCTGTAACTATAATTTTGCTACTGTTATCGATCCTAATGTGAATTTTGTGGGCAATAGAGATTTGCCGAGGGGGTTGCAACCCAAAAGGTTGGAAACCACTGACCTGGGACCTCCCTGGGAACCAAGCAAGTTCTCAAGGTCTAGGGCCAGGGAGGGAAGGTTCCAGCACTTTCTCTGCCCCAGTTGTAGCGTGTGTGAGGTGAGCGGGATGCATGTTCTGCTGCTGGCATGTTCTCTGTATGTCTGACCTGCTGCTGTGTGCCCGCGTCTTGGTTTTGATTCTGTTCTGGATAATGTGTCTGGGTACTAATGGGTGATTCCCTAGTCCCCGCCATTTTGTCTGTCTTGTCCAAGCTAGATGTGTTCCTTCCTCTGAGTTCTCAAAAATCCCTCACTCCGGCACACCCCAGCCCTAAACCCCACACGCCAGAACCACAGACCCAGGAGTCCTGAATCCCAGACTCCACTCCACCCTCCCTGAGTGGCTCTGTGGCAGACATTGAGACACCTCCACCTCAGAGTCACGGGTGTGCAAAGAGGGAGCCATCTGCACTCAACCTAGGCTTACCCCAGATGCTAGGCTGGAGCTGGAGGCTGGTCCTCAGCCCACACCATCCCTCCCCTCCCCTCCCCCACAG
Seq C2 exon
ACTCCCGAGGACAGTTACTCCGAGGGTAGCACCGCTGACATGACCAACACCGCAGACCTCCTGGAGCAAATCCCAGACCTCGGGGAGGACGTCAAGGACCCAGAGGACTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511:ENSMUST00000117911:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.683
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(20.1=100)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(15.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
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