MmuINT0139662 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65524841-65526516:+
Coord C1 exon
chr2:65524841-65524904
Coord A exon
chr2:65524905-65526374
Coord C2 exon
chr2:65526375-65526516
Length
1470 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CCTCTCTAATGTAATTACAGCCA
3' ss Score
4.1
Exon sequences
Seq C1 exon
GTCACTTTTATTTTTTGGAAGGACAAAACGATGCTCTGCTTTGTGGTAACAGCTCGGATGCTGG
Seq A exon
GTAAGTTGTATCTCTGTTTGACACTCAGTCGACCTCTGTAATCTGCCACATACTGCACACCTGGTCCCTACTCAGTCCCCATTCAAACTCCTCTAAAAATTATCCTTCATGCTGACTCACAGAATAGCCAGGATACGTGTGGATTCTCACCTCCTTCACACACAGAGAAGCAGCAATTATTGTTCCATACTAGGTCACATCTAATCTTCTAAATTAGCACACTGGAAAATAGACACTCAGAGTCGATGCATTAGAATTCATAATCACAGACCAGAAAGTGTGATTATTTATTTAAGCTAATCCTATCTCCATGGCTTAAAAAAAAAAATCCATGAAGGTCGTGTCACCTTGAAACACAAGGTGACAATCTGCCTACCATATTTCAGCAAAGCAAAGTACATAAAATAGACTGGAGTTTCCTCATACATTCAAATTCTGACTCTACCATACTTAGTCATTTGGCTTGCCCTGTGTTTTTCCCATGTACAAACTGTCACTGTAATAATTCCACTGATTAAATATGTTAGTGAATGTATGGCTACAATAGAGAAGTTTTAGTTATGCTTAACACTGTGGTGATATTTGTAACTAAGAAACGTCACTCATGTGATAGGTAAGGCAAGCATTTTAGTCCCCCAAATACTGGCACAGTACTAAATGCTTTCTATACAGTATCATATAGAGTGTTTGCATGTGGGTAGTTTTTTCTTGATGTTGTTGTTTTGTTCTGTATTTGTTTTGAGACCGGTCCTTTTATTAGTCAATTCTAGCTGAGGAGGTTCCTGAGGACTAGCAAGGCCAGTTCACTCAGCCCAGAAATGTCAGTCACAATACTGATGGTAGCTGTGCTTACTCAGCAAGTAAGGTGATGCTATGGAATCCACACTGCTCAGTGTCATTCTCTCCTTTCGGGATGTTTATCATATCTTCTTCTCTCTACCCTAGTTTGCACACACACACACACACACACACACACACACACACACACCACTCATATCTCAAGACATCTTCAGTGAAAATTGATTATATTTCTATGCATTTATTTATCTGATCACACCCATTGTCCCAAAAGAAAATGTTCAAAATATGACTATCTTGAAGGTTGGAGAGATGGCTCAGCAGTTAAGAGCACTGACTGCTCTTCCTAAGGTCCTGAGTTCAAATTCCAGTAACCACATGGTGGCTCACAACCATCTGTAATGAGATCAGATGCCCTCTTTTGGTGTGTCTGAAAACAGCTACAGTGTACTTACATATAATAAATAAATAAATCTTTAAAAAGATATGGCTATCTTATATACATGTATGGTAAGTATATTACAATTAGGAATTAAAGGAATGCCACCTAGTGCAGGATACATGCTAAATAAGCCTGTACAAAATAATTCACATCAAGTAAAATGGAAAACAAAAAACAAAACCAAAAAACAATGGATTCAGATACTTAGTTCCTCTCTAATGTAATTACAG
Seq C2 exon
CCAGTGTCCGGAAGGATACATCTGTGTGAAGGCTGGGAGAAACCCCAACTATGGCTACACGAGTTTTGACACCTTCAGCTGGGCCTTCTTGTCCTTATTTCGTCTTATGACTCAAGACTTCTGGGAAAACCTTTATCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:7
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(7.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100),PF0253517=Zip=PU(12.6=43.8)
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:
TGGAAGGACAAAACGATGCTCT
R:
CAGCTGATAAAGGTTTTCCCAGA
Band lengths:
191-1661
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: