MmuINT0139604 @ mm9
Intron Retention
Gene
ENSMUSG00000034115 | Scn11a
Description
sodium channel, voltage-gated, type XI, alpha [Source:MGI Symbol;Acc:MGI:1345149]
Coordinates
chr9:119720234-119722304:-
Coord C1 exon
chr9:119722176-119722304
Coord A exon
chr9:119720332-119722175
Coord C2 exon
chr9:119720234-119720331
Length
1844 bp
Sequences
Splice sites
5' ss Seq
AGCGTAAGA
5' ss Score
6.21
3' ss Seq
CCCTGTGTTTTGTCTTCCAGGAT
3' ss Score
12.97
Exon sequences
Seq C1 exon
ATACGTCTTCATTGGGATTTATGTTTTAGAAGCTGTGATTAAAATATTGGCAAGAGGCTTCATTGTGGATGAGTTTTCCTACCTCCGAGATCCTTGGAACTGGCTGGACTTCATTGTCATCGGAACAGC
Seq A exon
GTAAGACTGTTAAAAGATTTTTGTGAGAGGCACTTGGCGGGGGTGGGGGAGACTCGCTTTGCGTCTTTTGGGGCTCCGTGTGGATCTACAAGAACAACAGTGTGGCCTGAAGTTGTGTGGATCTCTGAGAGTAGAAATGGTTGATCCAGAGGAAGCCACTGGCGGAACCTCCAGGCCCCCACCCTCCCTTGCGTTGCGTTCTCACCCATTCCGCGACCAGCTGTGGCTCTGACATGCCAGGCTCTGTAAGCACGAGGTTGTAAAAACAAAACGCAGAGCAACAGAAAAGCCTCATGAGGCTCACAATTCAGGGGTAAAGAGAGGATTAATGCTAGTCACAGTATGGTTGGTGGGTCACCAGGATAGGTATGTGTCAGAGCACGTGGGGAGAGCCAAGAACTCTGGCCAGTATCTCTGGCTACAATGAGATCACAAAAAGTTTCGTTTCAGGTTTTTGTGTTTTGTTTCTAAAGTTTAGGCTTCTAAGTTTAATGTTGAGTGAATTGTGGTGGTGATTTCCCACTTGAGGCCTTTGTGTTAAAGCCCAATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGGTTGGGGGGTGGTGGCAGAGTCTGTATTGGTAAGGTGGGAGCAATCCCAGAACGTCCACCTGCTCTTCCATTTTATTAATCAGGCAGGCCTCTCAATCAAACCCAGAGCTCACTGATATGGCTACTCTGAGTGACCAGCTTGCTCTGGGGATCCTTTGCCTCTGCTTTCTGAGGCTGGAATTACAGGTGGGAGGCCATAAGGAACTCCCACCCAACACTTATGTGAGTTCTGGGGATCCAAACTTTGTACCGTGTGCTTTCAGGCAAAGTACTTTAACCAAGAGCCACCTCCCCAGACCTCCCACCCCACCCAACTTTTCTTCCTATGAATGTGCGCGGAGGTCGGAGGACAGCTTCCGGGAGTCTGTTCTCGCCTTCTGTCTTGTTGAGATGGGGCATCTTTTGCTTCTATTGTACCACATATTCCAGGCTAGCTGGTCTGTGAGCTTCCGGGTGATCCTCCTGTCTCTGCTTCCTGTAGGACCATAGGACTGCCGGGATTACAGATGTGTGCCACTGCGTCTGGCTTTTTATGTGGGTTCTGGGCATCGGACTCAGGTTGTCAGGCTCGGATGGCGTGCACCGTTACTCGCTGAGCCACATCCCCAGCCTCCGAGATCCATTTTGAATTAGTTATAGATGACTCAGGCTGAGTATTGAGACTATTCCGTACGGAAACAAACAGTTTCCACACCTGAGTGATGGAATAAATAAAATAAATCAAGCCAGTGCGACCGTGGTACATCTGTTGAAGGTATTTGTGCCAGACATTGTGGTTAGTGCTTGGCTTGGGTTTTACTCATTTCGGTCACAGATGGCGCTAGAGGCGCTATTCATCTCAGAGTTTTACATTTGAAGATCACTGCTTGCATGCTCCTGGCTATTGAAGATGCCCTGATTTAGAGATTAAGGGCATAGGCTCCAGGCTCGGTTGGTAAAGTCCTTGCTGTGCACATATAAGGTTCCTGGGACTGAGCCCACCACCCACATAAAAGCAGCTGTTTGTGGTGCCTTGTGCTTATAATGCCAGCTCTAGTGAGGCAGAGACAGAAAGATCCCCTGCTTGCCCACAAGCTAGCTCAGCCCAACCGGAAAGCTCTGAGTTCAGTGAGAGACCCTGTCTCAAAAAAAAGTAAGGTGTGTAGCAACTCAAGAAGCCACCTGCTGCCAGTCTCTGTCCTCCGTGGAGATGTGTGATGTAACCACACTGAGCCGCCCTGGGCTCTCCCTGTGTTTTGTCTTCCAG
Seq C2 exon
GATAGCGCCTTGTTTTCTCGGTAACAAAGTCAATAATCTTTCCACTCTACGTACCTTCCGAGTGTTGAGAGCTCTGAAAGCCATTTCTGTAATCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034115-Scn11a:NM_011887:5
Average complexity
IR-S
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=FE(18.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(13.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGTCTTCATTGGGATTTATGTTT
R:
TGAGATTACAGAAATGGCTTTCAGA
Band lengths:
224-2068
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: