MmuINT0139704 @ mm9
Intron Retention
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106189334-106191787:-
Coord C1 exon
chr11:106191311-106191787
Coord A exon
chr11:106189470-106191310
Coord C2 exon
chr11:106189334-106189469
Length
1841 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
ATGCCCTGTGGTCCCCACAGAAG
3' ss Score
8.53
Exon sequences
Seq C1 exon
GTCCTGAATCTGTTCCTGGCTCTCCTGTTGAGTTCCTTCAGCGCTGACAGTCTGGCAGCGTCAGATGAAGATGGTGAGATGAACAACCTACAGATCGCCATCGGGCGTATCAAGTGGGGCATCGCCTTTGCCAAAACCTTCCTCTTGGGGCTGTTGCATGGCAAGATCCTGAGCCTCAAAGACATAATGCTCAGTCTCGGGGAGCCTGGGGGTGCTGGGGAAAACGGGGAGAGCCCTCCCGAGGATGAGAAGAAGGAACCACCTCCGGAAGATGGGAACAAGGAGCTGAAAGACAATCATATCCTGAACCACGTGGGCCTGACTGATGGACCCCGCTCCAGCATCGAGATGGACCACCTTAACTTCATCAACAACCCCTACCTCACTATCCATGTGCCCATTGCCTCCGAGGAGTCCGACTTGGAAATGCCCACAGAGGAGGAGACTGACACCTTCTCGGAGCCTGAGGACATCAAG
Seq A exon
GTGAGGCCATTGCGTGTCTGCCTGCAGAGGATAAGAGCCAATAAGACCTAGCTTTAAATTTCTTTAAAGAATGCCACCTGGTGGCCCTTTCTAGGACCACATGGCATTCTTCGACAAATGTTCCTATCTGTGGCACATCAGCACCACCCCTAGGAACCCAAGAGGCCTCTCTTAAATATTTCTCTGGGCTTGAAGGCCCTGCTAAGTCTTTGCTCCAAATATGTTCAGATCTGATCCGAAACCCTGAGGCCCCCGTGCTGGCTGATAATGGCATGTTCACATTTCTATGTAGAATTCCTCTGGGACTGTTCCAATCTTCCTTGTGTAGGGCTGGGTACCAGGGCCAGGGCAAGGATACAAGGATAGAAAACCCAACAGGAGTTGGGAGACACAGGTGGTGGTCACCTTTAGAGTCTGGGACCCTGTCAGGGCTGCCCGGGGTGAGCTGGCTTTGAGTCCCCTCACTTTTCTTGCAGCCCTAATAGGAAAAGGATTAATATGTGATGGAAGCAAGGGACATTTACCCATGACACCCTTCTGCCCCGGGCCCGTTAGGGCACTAGAATCTAATGAACTTTGCCCTGAAAACTCTTGACTCCTTATCCCAGCCCCCAACACACACCAGTATGTGATTCGTTGACTTAGCAGAGGTTTGAGTGCCTACTGTGCTATAAATACCCTAGGAAACGTGGCACCAACCTCGACCTCGGTATGAGGAACTCAGTGGAGGAGGGGCTAGCTAGAGAGTAGTAGGTCCTTGACTCTGGGGAGGCAAGATATCTGAGGGGCTGCAAGCAGAGCTTAAAGGGCAATCATGGGAGTTAATTTGCAAAGGTGAAGCCAGCAGTCCAGTGTATGTCCTGATTGATCAAATGCTCTGTGCCTCAGTTTCCCTTCTGTCAATTGGCAGCAAGACCCGCCCACTCTTGGCTTTCAGACTACTGCCCTAGTTACATGTGCATGAGAACACACACACACATGCACACATATGTGCACATACACATACATGCACACACTCACACAGGCACACATGCACACAGGTGGGAGGGACTGCCCAATTCATCTTTCTCTTCAGAGATTTCACCGTGAAGGATCTCCCTGAAGCATGGAGGCCAGCCTGAGAATCTGGCCTGGGACAGTGCTAGGAGGTGGGAGGAAACTTAGCTAAGCCAGAGTACCAGCCCCCACACCCTGCCCCCACACCCTGCCCCCACACCCTGCCACCACACCCTGCCCCCACCGTGATCAGATTCCCTTGGCGCCACACCGGAGCCTTGGCTGGGGAAAACTTTCCATCCTTTCTGGGTCTCTCAGCCAAATAGACCCTGGGGGTGGCAAGGCTTGGACTCTGGGGGCACCATGTGCCTGCTCTCTGCAGCTGTGGCAGCCCAGATCTGTCTTGGCTCCGCTTCTTAACCTTGCTCCTGCAAAAGCACCTTCAGGCCTCTTTTCTTCTACTGACTCCTTCATATATCCCTACACCTCCTAGGACCCCACAGGGCTGAGCCAACCAGCCCCCCCCCCAGCCATCCTTCAGCCCATCTCCCGTCCTCCCCACTCTCCTCCCCAGGCTTCCTCACGTCACCCCTGTGCTTTCCTAGATGCCACGTACCACGAGGGCAGAACTGAGGACATTTTTGTCACTAGGGTGCCTTTGCCAGGGCACAGTGGTAGTTTTATAAGGGCTGAGTGAATGAATGAATGAATGAATGAATGAACTAATGGATGAGTGGCTCCTGCTCTATTCTCTTCTTTCTCTCTGGTCTCCCTTACTCCCACCTATTGGGAGAATGAAGGGATCTCTTGGGACCTAGGAGTCACATGCCCTGTGGTCCCCACAG
Seq C2 exon
AAGCCACTACAGCCTCTGTACGACGGGAACTCCTCCGTCTGCAGCACAGCTGACTACAAGCCCCCCGAAGAGGACCCTGAGGAGCAGGCTGAGGAGAACCCTGAGGGGGAGCTACCTGAGGAGTGTTTCACAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-Scn4a:NM_133199:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.447 A=NA C2=0.630
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(59.7=84.9)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(19.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGGCAAGATCCTGAGCCTC
R:
AGGAGTTCCCGTCGTACAGAG
Band lengths:
355-2196
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: