MmuINT0139600 @ mm9
Intron Retention
Gene
ENSMUSG00000034115 | Scn11a
Description
sodium channel, voltage-gated, type XI, alpha [Source:MGI Symbol;Acc:MGI:1345149]
Coordinates
chr9:119667525-119669062:-
Coord C1 exon
chr9:119668958-119669062
Coord A exon
chr9:119667796-119668957
Coord C2 exon
chr9:119667525-119667795
Length
1162 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
CCTTTCTTTTTCCTCCTCAGAAC
3' ss Score
12
Exon sequences
Seq C1 exon
TTAGGTGGCCAAGACATTTTTATGACAGAAGAACAGAAGAAATATTACAATGCAATGAAAAAGTTAGGAACCAAGAAGCCTCAAAAGCCCATCCCAAGGCCCCTG
Seq A exon
GTGAGAACAACTGACTCTAAGCACACATGCAGGATGCATGATCTGAGGGTGCAGGGTTCTAAAAAGCCTCCTGTTAATGCTTAAAGGAAGTATTTTTTTTATTGTTTAAAAAGTACTTGTGTATGTGTATCTTTGTGTATGTGTATGTTTAGGTGAGTGCAGTGCTTTCAGTGGCCAGAAGAGGGCATCAGATCCCTCAGAGCAGTCATTCGTGAGCCATCTGACCCAGATGCTTAGGAAATGAACTGAGGTCCTCTGCAAGAGCAGTATGCAGTCTTAATCATTAAGCCATCTCTCCAGACCCCAGGATGTTTAATATCATAATAAATACATATATGTTTTCTTAGAACTTAAAAAAACAAGATGCACCCAAGTTCTTAGGAAAATTAGACATGTATGTTCATTATTGAGAGTCTGACTGATACATTTAATTTTCTCCTAACACAGAGTCTCATTAGGTGACTCTGGTAGCCTGGAGCTCACTGTGTAGACCAGGCTACCTTGAACTTATATAGATACCTACATGTTTGGATTAAAGACATGCGTCATTACACCCAACAAAAATAAATATTAAAATATTTAAAACTTAAAAAAAAAGAGCCAATGCTCAACTTCATGCCCAGTGATACTATGAAACAGCCAGTTCTCCATCTTTAATAATTGCTGGACTGAGATGTTGTTTTTCTAGCCTATTCCAACTAGAATTAAACACTGACATTAAAGAATTGTGTGAATACAGAGTTTTGCTCACATTCCGAGTATTCTGAACTGGTGAATAGAGCCTTGGAGGTGTCTGTTCCATTTTGCCCAGGATAAGTGGACGCTCTCTGCATCCATCTCTTGGGTAAATGCAGATACAGACATCAAGGGCCATCTTTATATTGTTGAGACATACATGAGCCATTTTATCTCAGCCTCACTGACTGTTCATCACATCAAAATTCTGTTGCTACTGGGGCTATTTTTGATTTATGTTTTAAAGTAGAATGAAAACTCAAGCCCAAGCACATAAAACAGTTACCCAGCCACAATGGGAAGCGATGAGAATTTCTTGTCCTTTGAAGGGGTCTTGCATATATTTCAACGAATTGCCTTCATTGTAAGAGAAAACAAATTTTGTCATCTTAACGACATAATTTTCTCCTTTCTTTTTCCTCCTCAG
Seq C2 exon
AACAAATGTCAAGCCTTCGTGTTCGATTTGGTCACAAGCCAGGTCTTTGACGTCATCATTCTGGGTCTTATTGTCACAAACATGATTATCATGATGGCTGAATCTGAAGGCCAGCCCAACGAAGTGAAGAAAATCTTTGATATTCTCAACATAGTCTTCGTGGTCATCTTTACCGTAGAGTGTCTCATCAAAGTCTTTGCTTTGAGGCAACACTACTTCACCAATGGCTGGAACTTATTTGATTGTGTGGTCGTGGTTCTTTCCATCATTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034115-Scn11a:NM_011887:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(21.2=47.3)
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:
TGGCCAAGACATTTTTATGACAGA
R:
AACCACGACCACACAATCAAA
Band lengths:
358-1520
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: