MmuINT0139574 @ mm10
Intron Retention
Gene
ENSMUSG00000034533 | Scn10a
Description
sodium channel, voltage-gated, type X, alpha [Source:MGI Symbol;Acc:MGI:108029]
Coordinates
chr9:119613521-119616800:-
Coord C1 exon
chr9:119616700-119616800
Coord A exon
chr9:119613792-119616699
Coord C2 exon
chr9:119613521-119613791
Length
2908 bp
Sequences
Splice sites
5' ss Seq
TTGGTGAGC
5' ss Score
7.43
3' ss Seq
TCTCTCTCTCTCTCTCTCAGAAT
3' ss Score
12.46
Exon sequences
Seq C1 exon
GGGGCCAGGACATCTTCATGACAGAGGAGCAGAAGAAGTACTACAATGCCATGAAGAAGCTGGGCTCCAAGAAACCCCAGAAGCCCATCCCACGGCCTTTG
Seq A exon
GTGAGCCCCTGGGTTTCTCTCTCCCTGAGCAGGTTTGCAAATTAATTCATCCTAAGCCTGGGCTGAATGGAAGCCTGGCCAGCTCTGTGTGGGGAGATCTGGGGTGAGTTTAGAGGTGGAAGTGATGAGGCTCCCAGGCCCCAATAGTGAGAAGTTTAAATAAAGTGAAAGCAGCTCTGTGGGTGCGTCCGTCACGCTTGTCTGATGAGTTCTGTAACGCCCAACAACCTTAGGCTTCCATGGTGGCCTTGGAAACAGTAAAAAATAGTAAGGGTGGTTAGGATTTCTACCCCATGGTGTGGCCCTCCTATGGGTTACTCCAGTGAGTCCAGGCTGTCAGGACATTTACAGGGAGGAGAGAGCTGTCACGTTCAACACACTTTGTGTGTCGATAATGAGAATCGATTTGTTGCTATCTAGAATCTGGTCAGAAGTATCAGATCAGGAATGAACCGCAGGGGGTTCCAGGCTCTGGAATGGCAGGGGCACCTTTAAAGTCCCATAAGATGAAGATAACTGGGTTTGGGTGAGTCTGTGCAAGAGTGTGCTGGGCTTCCTTAAGATGGACACACACACACACCCTCACACACACATTTATATACATCATATCACATACACATGTGCACAAGCACCTGTGCGCACACATCAGTGGGTGAGAACAACCTCAAAGTTAACAGATTCAGGTGGAAGCTGAGTCCAGCCAGTGGGACTCAAGTGAGAGGCTAAGAAGCAAGCAGCTGAGCTCCAGGGCCTTCGCTGGCCTCACACCATCACTGAGCTCCCGCAGAAACCAGAGCCCTGTGTTTGAGCCACTCCTTAGAGTAAGCGAGCTTTTGATGTTTCTCTCCAGCCTCTCCACACTTCAGCAGCCCACAGGCCACTGGAGATTCTTCCTCTCATTATCCCTGGGAGTGGGTGGGCTCCATTTCAAAAACTGTCCTGTAGATACAAAGGTATGGAGCTACTGTTGGAATTCCAGGCAACATGGTCTGTGTTCTGGCCAGCATTTGTAACCTGATACCACCTGCACAGCTACATAAGCCTGATCCTCCCTAATGCCTGGAACCAAAAAGGAAACGCAAGGGGGATTTTTCCTACCTTATCTGATATTACTGGAAATTTTAGGGTACAAGCCTGGCTCTGGCAGACCTAACAAGTGGGACTCTAACTCCCATCCTCAAAGTGCTAAGTAGAGAGACAAGTAAGACTGGAAACCAGAGAGAGGAGATTATTCAACATGGCCACAAATAAAGAGAAAGAAATAAAGAGATCACAGATGCCCAAGTCTATCCTCTAAGTCCTGATTTGAGTTTTAGGTTGAAATAGACAGTGGGAGATATGCATAGGAAGCCCTGGTCAAGTATGGTCCTGCCTGTCACTGACCGGTCACTAACTTACTTCCAGTCTATCCTGCAGCCTGACCGGTTGCCAAAACTGCAAAAAATCTCTTCCTGGGAGACAAGCTCCCCTCTGGCTGGCACAGGACTTTGCTCTTCTATTCCTTCACCCAGCATGAGACTCCTAGGGAAATTCAGTTGCTCAGGGTCTGTGTACCAGTAGTCTGATGGTCAAACGGAGGGGCACAAAGGCCTCCACTCCTCCCAGGACCAGCTTTCTTTCCATCCAGCATCTGTCTCTGGAATGTTCCACCGATGTGTTTGGGAGCCGAGCAGAGCATTGGCTGAGACGCTGTGTGTGGGTGTTGCTCAGGGCAGAGCTAACACAGTACCACAAAATGATTTCCCAAAGCATGCAGGCACCGCACCCCTTGCCTCTGGTAAAGCCCACATTCTGAATCTTGTCTTCATTGTTGGGAAAGCTAAAGGCTCTACGAGACTGGGTGATTTTATTCTGTAGTGCTCTCTCTTACAGAAATCACAGAGTAGGTTTCACATACTCCACATTATGAGAAAATGATAGACTCCGGGCTATCCTGTTGTCAATCACCCTTCACCGTCCCTGAGGGCACAGAGCGTGATGTGAGCCCTGCCCACAGGCTGAGCTTGGAACAGCCAAAAGTTGGGCTGCCTACCCTAATCTGATGCTTGCATAGTTTGAGTAGAAGTCATGTAACCATGAACGGGCCTCTATATTTTTCCTCTGCATTTTCAGTGATGACATGGGAAGGGCTAAGTGGCTTAAGCCAGTAGTCACACACAGAGCCAGGTCCTCTCTGGTCTGATTCTCTGCTCTAACCCAGCAGGGTAGCAACCCTGCCCCCACTGTGAAGCATCAGCAGGGATTGGCTTTGCAGGAGCACTTCCCCCCACCCACTTGAAAGCTTCTGGAAGAATCCTGGCAGGTTGTTCACCCAGACCCTTGTGGCCACACACATGGAACCCTGGACACAGTATCCATCCAGTGAGAGTTATAGATATAGTGGACACTAGTCAGGTAGCTATCAAATGTTGAGGTATTTAACTCGCAGCTGCTCGTTCTGTCTTCTGTTCCCTCAATTTCCTGAGGACCTTCTGCATGGAGGGCACTATGCAGATGCTAGAATTCAAACTGTAAGCAAGATGGACGCAGGAACTGCCCTCAGAGAGGCTGCAGTTTGGTGATAGAGGCAAATAACTTGCAGAAACCACACACTGTCAGCTCATAGGCTGGAGGGCTTGCAAAGGGAGGAAGAATCTAGACTGGAGCCAGAGGAACCCTCGTGCCTAGGAGTTGGATACTGGAGACTGAAACAGCCTGGCCTGAGATTTCCTTCTCTCTCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCTCCCTCCCCCTCCCCCTCTCCCTCTCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCTCTCTCTCTCTCTCTCTCTCAG
Seq C2 exon
AATAAGTACCAGGGCTTCGTGTTTGACATTGTGACCAGGCAAGCATTTGACATCATCATCATGGCTCTCATCTGCCTCAACATGATCACCATGATGGTGGAGACCGACAATCAGAGCGAGGAGAAGACGAAGGTCCTGGGCAGAATCAACCAGTTCTTCGTGGCCGTCTTCACGGGCGAGTGTGTGATGAAGATGTTCGCCCTTCGGCAGTATTACTTCACCAACGGCTGGAATGTGTTCGACTTCATTGTGGTGATTCTGTCCATTTCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034533:ENSMUST00000214408:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.3=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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