MmuINT0139597 @ mm10
Intron Retention
Gene
ENSMUSG00000034115 | Scn11a
Description
sodium channel, voltage-gated, type XI, alpha [Source:MGI Symbol;Acc:MGI:1345149]
Coordinates
chr9:119768349-119770030:-
Coord C1 exon
chr9:119769761-119770030
Coord A exon
chr9:119768403-119769760
Coord C2 exon
chr9:119768349-119768402
Length
1358 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
GTTTTCTACTTCTGTTTCAGGCG
3' ss Score
9.9
Exon sequences
Seq C1 exon
GTTGTTGTCAATGCCCTCATGAGTGCCATACCTGCCATCCTCAATGTCTTGCTGGTCTGCCTCATTTTCTGGCTCATATTTTGTATCCTGGGAGTAAATTTTTTTTCTGGGAAGTTTGGAAGATGCATTAATGGAACAGACATAAATAAATATTTCAACGCTTCCAATGTTCCAAACCAAAGCCAATGTTTAGTTAGTAATTACACGTGGAAAGTCCCGAATGTCAACTTTGACAACGTGGGGAATGCCTACCTTGCCCTGCTGCAAGTG
Seq A exon
GTAAGTGCTGTGGCTGTCTGCGTCCAGGAAGAGGGAGCTTGGAAAAATACAAATGACTAAAACCACAATGACTCCACAAAGGGAGAGGTTGGATCCTAGTCCTGTCTACAGGGTGGGGGCGGGGCAGAGTTTTTTTCACCAACTTAGTTACTTTTCTCATTACTTTGACAAAACACCTTAGGCCGTAGTTACTTTTCTGTTGCTGTGATTAAAGACCCAACAACAACAAAAAAAGAAAGTTTCTTTTAAAAGTCTTTCTTAGATTTTATTTTAGCTTATAGCTCTAAAGCGAATTCAGTCCATCAGGGCTGGGAGAGCATGGTGGGAGGAACAGGAAGCTGGCTATCACGTCTCACCTATACACTACATACATCTACAGGCATGCTGTAAATCCTCAAATCCCAACCCCAGTGACACACTTCCTCCAGCAAGTTTCCACTCCCTAAAAGTTCTATAATCTTCTCCAACTGAACCATCAAGTGGGACCAAGTATTCAAACACAGGAACTGGGGTGGGGGGCATTTCCCATTCAAACCACAGCACCTGGAAAAAGCAAATTAAGGCAGGGCTAGTTTTGCACATGCTTTGAGAGACTCGACCACCACGGTGGGGAAAGACATGGTGGTGAGAATTGTCTAGATGCAGCGGCAGGAGTGTGAGGAAGCTGGGCCCACGGGCTCTACCGTCTGGAAGGAAGTGGGTAGAAAGAGACAGAGATACCGGCGGGGTTTTTTGTTTGTTTGTTTTTTGTTTTTTTGTTTTTTTTTTTTTGTTTGTTTGTTTTCGTTTTACTCACCATATCCTGATGCTCATCCAAGATGAGTCTGCTGTCAATTAAACGTCCTCAGAAACACCTTCACCACAGGCCCTGATGCGGGTCTGGGTGACTCATGCATAGTAACGCCCACCCCTGCTTTAGGGTTTTACTCTCCTTGCTTTGTCTTCTGTGCTACCTTGCTTGCTGTTCAGAGCACCCGCCAGAAGGGGGAGCCTTTGGTGCAGCTCAGGACATTGTCAAGAGCTCTCTTTTCAAGTAGCAGCAGCCAGGTGTTGGCCAGGTAGCACAGAAAACGTGTGCTATCAAAAAGAACCTTGCCTGGCTCTTCCCAAGGAGCCTATTGTGTAGACATTGATTTTGTTTTTAAGCCATTAGTCTTGGGAGAAAGAAGAAGACGGAGGTTAGGCACAACACCCCTCCTCACATCCAGACTGTTCATTCTCGAGGACCTCTCTCTAGGGCAGGAAGGAGAATCAGCTAACACCCACCCGCCCATGGGGCTCGACAAGTTTCTGGGTGGCATGCTTCTGTTGATGAAAAAAGTCTACAGCTGTGTCCAAGTTTTCTACTTCTGTTTCAG
Seq C2 exon
GCGACCTATAAGGGCTGGCTGGACATTATGAATGCAGCTGTTGATTCCAGAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034115:ENSMUST00000070617:22
Average complexity
IR
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(40.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.8=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
TGTCAATGCCCTCATGAGTGC
R:
CCCTCTGGAATCAACAGCTGC
Band lengths:
319-1677
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