MmuINT0139737 @ mm9
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119469380-119471796:-
Coord C1 exon
chr9:119471470-119471796
Coord A exon
chr9:119469499-119471469
Coord C2 exon
chr9:119469380-119469498
Length
1971 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
ACAGTTCCCTCTGTCCACAGACC
3' ss Score
11.57
Exon sequences
Seq C1 exon
CTTCCTTCCAGGCAGCCTGAGGAGAGCCTGTGCCCCCAGAAGCAGGATGAGAAGATGGCAAACTTCCTGTTACCTCGGGGCACCAGCAGCTTCCGTAGGTTCACCCGGGAGTCACTGGCGGCCATCGAGAAGCGCATGGCTGAAAAACAAGCCCGTGGTTCGGCCACCTCACAGGAGAGCCGTGAGGGCCTGCCAGAGGAGGAGGCTCCCCGGCCCCAGCTGGACCTACAGGCCTCCAAAAAGCTGCCAGATCTCTATGGCAACCCACCCCGAGAGCTCATTGGGGAGCCCCTGGAAGACCTGGACCCTTTCTATAGTACCCAGAAG
Seq A exon
GTGACTGCCGCCCCCTCAGCACCCTCCTCACCCTTTGGGTAGCTCCTGGGAAGGCAGCAGACAGATGGAGCTTTGCTCCTGTGGAGTTCTGTGTGGGGCCGGCTCCCCTGGGCTTTGGGGGAGTGATTCACCATTAATCTGTATTCCAATCACCTTAATTTTGGAGTTCTGGGATACAGACATAAATCACGCCGTTTGAGCCCCTAACATAGGGGTGGGAGGACCACTGAAATGTTACCTTCTTTTGTCTTTCTCCGGCATATACCTCTAGGGGATTCCTTCCTGTCCCCAGACGCGTGGGCGCTTGGAATGAAGCCCTGAGCGGTCCCCCTCCTAACTCCTGCATGCGTTCCTCCTGTCCCTCTGGCAGCTCAGAGAATTAGCCAGGCATCCTCCTCTGAGCCAGCTGGCTCAGGCTGAGCCACAGTAGAAGTCTCCTGGGCCTCGTGGCCTTCCCTGAACCACAGAGGTCATGGGAAGGCTGAGGGGTGAAGAGGGCGTGGCTGCTAAGGCATGGAGTGTGGGGAAGCCTTGTGCTGCCCTTGTTGCCTGGAGAGAGGGAAGGGAGTGTTGTGCTGTTTCTCCAAGAGGCCCTTCCCTGCACTAATGATGTGACAGGCACACAGGTCCCCTACAGAGGGACAGGCTGCTCACACAACTGTCCACTTCTGGACCTGACTGTGGGGGTCATGGCAGGAGAACAGGCTGGGATCTAGAGGAAGGCCTTTCCAGGAAGGCTAGGCAACAGAGACCAGGGTGGCCACGGGAGTCCCTGTGGCCAGCTTCAAGCTGAGCGCAGAGCAACACCAGCGGGACTGGAAAGATAAGTACAGTCAGTGTGGGGGTCTGGGTAGCATGTGTCTGTCGGTCTGTCTGTCATGGTGGTTGAAGACAATGTTTAAGAGACTAAGAGCCTGAGTGTGCACGTCTGTGTGTATGTGCATATGCATAGGTGCATGTGTGATCAGCTGTGGGTGCGAAGGGACACACACACACACACACACACACACACACACACACACTCACTCCATCTATACAGACAGTTAGCAGGAGAGACGACCTGGGCCCTGCTTCTAGGCTGAGGCTCCAGGACCTCTCCCTGGCTCAGGTGACTGGAGCAGGGTCCGAGTGGGATGTGAGCCTGAGCTGTGAGTGAGTGAGTGGGTAGGCTCGGGTCGTGCTTGCTCCGAGCTGACAGAATTGGGATTAGGGTTAGGGACACAGCTGAGGGTGAGTCTAGGTCATGGAGGGGAACAGAAAGGACTAGGCAGGACTCAGACGAGACCAGTAGTGAGCACGGCAGGTGAACCTAAGATGGAGTCCAGGCTGGCTGGGCTTAGGAGACCCCCCCCCCAACAGGTCACCAAGGACGCCATCTCTTTTCTTAGTCTCTATATATCTGGGGATGCTTGATGTTTTCCGGGTACCCTGGGTTCCATCCTGTTTCTCTTGCCGTCCCTGGCTACACCGCCTGAGGTCTCGCAGGCTGGCACCCCGTGGAACTCCTAGTTCTGACCTCTCTGCTCACCGTGTCCCAGCAGCCAAGGTTAAATAGGACTTTGTCCCATCCCCTCAGCCCGTGAAGATGGGTGACCTCATAGCCTGTGGCTGCCATGCTCTGGTGTGCTGGCTCCCTTTGCCTCCGGCTTCTGCTCTGCAGCCTTGAGATCTCACAGCTCCCCTGCCCCATGATGCCAGACAGGCATATCTTCTAGAAACGAAGGGAGGTCCTCAAAGCCCAGACCGTGTGTGCTATTCGGAGGCTGACCTTTGACCTCAGGCAGGGAAGGTCCCAGGGAAAGCCGTGGATAGCTCTTTAGCATTCCTTCCTCACCCATAAGTCTCTGCTGCCCCAGCTGTGAGCAGGGCTCTCTGTTGCAGCTCTATGCAGGGTGGGAGAGGGGGAGGAAACTGCTTGAGGGCTCCTAGATGACAGCCGTCTCCAGACCTAACAGTTCCCTCTGTCCACAG
Seq C2 exon
ACCTTCATCGTGCTGAATAAGGGCAAAACCATCTTCCGGTTCAGTGCCACCAATGCCTTGTACGTCCTCAGCCCCTTCCACCCGGTGCGCAGAGCGGCTGTGAAGATTTTGGTACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511-Scn5a:NM_021544:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.363 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
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCCAGAAGCAGGATGAGAA
R:
GCACTGAACCGGAAGATGGTT
Band lengths:
342-2313
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: