MmuINT0139648 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65564385-65566597:+
Coord C1 exon
chr2:65564385-65564505
Coord A exon
chr2:65564506-65566442
Coord C2 exon
chr2:65566443-65566597
Length
1937 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TCCACTCTCACATATTTTAGACT
3' ss Score
8.13
Exon sequences
Seq C1 exon
AAATTGAATGCAACTAGTTCATCTGAAGGCAGTACAGTTGATATAGGTGCTCCTGCAGAGGGAGAGCAACCAGAGGCCGAACCAGAAGAGTCCCTTGAGCCAGAAGCCTGTTTCACAGAAG
Seq A exon
GTAAGCAAGCAGGTTGTCAGGAGCCTTCTCTTGTCTATCCATCTTTCTTATCACCTGTCTGTATCTCTCTATCACCTAACTGTCTCTGGTCACTCACGCCTACCTATTTAACAGTGATACATTTATTTGTTTTGTTCTAAATCTCAAACTAAAGACAGTTTTTTTTTCTGACTATGGGTTTAATTTATGTAATTGGTTCCTTTTGCTTTTGAACAAATGATCAACTCTAAAATGTGCTGCCACTTGGTATATTAGTCTGCTCTCCATTGCTGTGATGAAACATTCTGGCCAAGAGCAAACTCGGGGAGGAAAATGTTTGCTAGGCTTACATTTCTATGTCACAGTCCACCATGAAGGAATTCAAGGCAGGAGGCCAAGACAGGAATGAAGAGGCAAGAACTGAAGGAGAGGTCATGGAGAAATTCGGCTTATTAGCTTTATCTCCTTGCTTTCTTAGACAGCACCTGACCACAGCTGAAAGATGGCAACACTCCATTGGGCGGGGCCCTCTTGCATCAATCATTAATCAAGAAAATGTTCCACAGATTTTCATAGTCATCAATCAGTTAGTAGCATTTTCTCAGTTGTGGTTCCCTTTTCCTAGATGATGTGAACTTGTGTTGACAAAAAAGCTTACCAGCGCAATTGACTCTCTGGCCTTCTATATCAGCTAACAGGAGAGAGAGTTGGCTAAATCAAATTCATAGCTATTAAGGTTTCGAAAAAGGAGTAAGGAAATAATCCCTTATTTACTGAGTTCTCAAACTGTAGTGTACGAATTGATAAATGTACACATTTGTCTGACCTTGAATATCAATCAAAGTAAAATACTTTTTGTGAGTTTTGAAAAAAGATGAAAGATGTAAGAAAGCTGAAATATTCTGTATACTTTTATATGAGGACATTATCATCATCAGAGTACTCTCAAAAGGATTCTCTAAAGAAAACCAAAATTACATCATTTCAGAGGAGGGTCAGTTATACCCTACAACAGTAGCGATGAATATCAAACCACATGAAATTCTGAACTCCAAGCTGCTCTCAAGGGCTTGGCCAACAACCTTGAGCTAATGCCTTGCACATAACGGTCAGACATGCCTGTCATTAACTTGGTTCTTATTTCTTAATTGCTTCTTCTAACTTCATGTTATTAATAGGACTTATACAGTTCCCAAGATCTAGCCTCAAGTCTTTTATTCCATAAAATTCAGAAACTCAGCATTATTGATGAGCCTTTATAAGAAAATGTCTTAAGATAATATTTGTAAAACTTGCTGAAAAGTCACTCCCACTAAAACGGACATTCCCCAATGGCAAGGCCATTTACATAATGTAATCTTATGGTTTTCCATGTACAGTGTTTTAAATACAAAAGCCCTTAAATAAATATTATTGAAAAGCCTTTAACCTAGTACCTCACAAAGTACACAGAAGTGATTATTGCATGGCTGTGGATAATTATCAGAAACAAAACAACCCAATTATTCAATAATAGTGAACATTTACATAAATTCCCATAGTCTTTTGGAGAAAAGCATAATAAAATCTTTCACAAGTCTTATGGTTAGATAGAGAAGGTTTACTATGCTATGAAATGACTAATCAGAATTCAAATGCATGTCATGTTTATGGAGGATTTACCCATGGCAAAAGGGCAGAATAGAAAGATAAGCTGTGGCTTTTTTTATGTTTTTCTGTATTTGTATGGTTTACGACATGTTATAATGTAGTTATACACATATAAAAATAAATGCTCATTTAGGAAATCATTTAAAGGCCCCACTGCTGATGTTGATTTCTGTAAGTGGAAGCCATCTTTAAAATAAGGTTGTTTATTCTGCGGTATGAGGTAATAAAATAGGTGTATGTTCCATATTCCCAAAGATGCACAAAGAGTAACTGTTGGCCTTTCCTGTATCCACTCTCACATATTTTAG
Seq C2 exon
ACTGTGTAAGAAAGTTCAAGTGTTGTCAGATAAGCATAGAAGAAGGCAAAGGCAAACTCTGGTGGAACTTGAGGAAAACCTGCTACAAGATAGTAGAGCACAACTGGTTTGAAACCTTCATCGTCTTCATGATTCTGCTCAGCAGCGGTGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.780 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=84.6)
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:
TTGAATGCAACTAGTTCATCTGAAGG
R:
TGCTGAGCAGAATCATGAAGACG
Band lengths:
262-2199
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: