MmuINT0139646 @ mm9
Intron Retention
Gene
ENSMUSG00000075318 | Scn2a1
Description
sodium channel, voltage-gated, type II, alpha 1 [Source:MGI Symbol;Acc:MGI:98248]
Coordinates
chr2:65553717-65555924:+
Coord C1 exon
chr2:65553717-65554073
Coord A exon
chr2:65554074-65555444
Coord C2 exon
chr2:65555445-65555924
Length
1371 bp
Sequences
Splice sites
5' ss Seq
GTCGTAAGT
5' ss Score
9.9
3' ss Seq
CTTCCTCCACTTTTTTGTAGGTT
3' ss Score
9.84
Exon sequences
Seq C1 exon
CTTAGAGTCTTCAAGTTGGCAAAATCCTGGCCCACACTGAATATGCTCATTAAGATCATCGGCAACTCGGTGGGCGCGCTGGGCAACCTGACCCTGGTGCTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTGTTTGGAAAGAGCTACAAGGAGTGTGTTTGCAAGATTTCCAATGATTGTGAGCTGCCGCGCTGGCACATGCATGACTTCTTCCACTCGTTCCTGATCGTGTTCCGCGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGCATGGAGGTCGCAGGCCAGACCATGTGTCTTACTGTCTTCATGATGGTCATGGTGATTGGGAACCTTGTC
Seq A exon
GTAAGTAGGAAAAACACTTTTCTCCTTTTCAGTCACAGATAATATGGTTTTAACAAAGTTTGATTTAAGCACATTTTATGTTTTCGGGAGAGTTATTTGGTATTGAGTTCATTTCCAGTTGTCTTTAACATCAGATTTCAGGAGCCATAGCTGATTTAGACTTCTGTCACATGCACACCCTCCAAATGTCTCAAAATTAAAATAAAACAAGAAAATAAAGTCCAATATTGGACATTATATGGGCAGAGTCATTGATACAGGTAAAAAAATATAATAGACAAAGATATTCCAGTAATAATCCTTAAGAAATTAAATCCAAAAATAATTGTGGTACTGTAATTCAATTTTCTTACAGATAAAAATTTAAAGAGTTTATCTATTTGTCATCCAAGTAAGAAATTTAAGGATGAGTCAGAGACATATAAGTGTATTAGTAAATTTCTGAAGTGGGGAGACAGAGAGCTCCTAGTATGGCCGCCAGGAGCCATGGGAGGGCAAATGACAGAAGGTCAGAATGGCCCTGACATTATCTTTCTTCTCACTGACTTTTACCTGACACGTCAGTCACGGTCATTTGCATTGGAATTTTAGCTAAAATCTTCTGCAAGTTTCCACTTTTGAACTAAAAACCTCTGCATTTAGTCCTGTCTATATTTAATTTTGATTCCGTGTTTGAATAATTGAGGGTTGTGTCAACTAAACCCTGATTTAAAAAATGATGACAGTCATGTCCCCAGCACTGCCTAATTCCTAGTAACCTACCTAGTCTATGGACTTGGAGATTCCTGGTGATACCACAAACATCACTTTTAATTCAACATAACAGCGGTGTTATTATACCACTTTGTTATATTTATAAGTCTTGCATGAACTAGTAGCATCTACAAGGTTTTTTTTTCTTAATCAAAATTAGGAGTGTTGATCTAGCAATACATATATTTTTTAATTGAATTTAGCAAGTTACTAAGGTGAAAAAGGTTGCAATGCTGCAGAGGCCAAATCATATCCAAATATATAGTTCTATGAATCAAATTACAATAAGTGTTCAGTGTCCTACTAAATACAGATTACATGTTCAAAATAACAAGCATCCAAAATAGCTATTTCTTTTACTTGTCTAGATTCCCCAAGACATAAAGTTAGTATAGAAGTTTCATACCATGGCAGCTTAGGGATTTTGAAACAAACCCAAAATAAAAAGAGTATGAGTAGTGTTTGCTATCAGCCAGCCATTTGTTTGTTTTTACTTTTCTTTGCTGTGTTCTGGGAGACCTTGTCTTTAATGGGATGTATGAAGACAATTCCACGTCTTACAACTAAAGCAAGGGACACAACAGGGTGTCTGATTGCTCTTCCTCCACTTTTTTGTAG
Seq C2 exon
GTTCTGAACCTCTTCTTGGCCTTGCTCCTCAGTTCTTTCAGCTCGGACAACCTGGCTGCCACAGATGACGATAACGAAATGAACAACCTCCAGATAGCCGTGGGAAGGATGCAGAAGGGGATTGATTTTGTTAAAAGGAAGATACGTGAATTCATTCAGAAAGCCTTTGTCAGAAAGCAGAAAGCTCTAGATGAAATCAAACCCCTTGAAGATCTGAATAACAAGAAAGACAGTTGTATCTCCAACCACACAACCATAGAAATAGGCAAGGACCTGAATTACCTCAAAGATGGAAACGGGACGACCAGTGGCATAGGCAGCAGTGTGGAGAAGTACGTGGTAGATGAGAGTGATTACATGTCATTCATCAACAACCCCAGCCTCACCGTGACTGTGCCCATTGCTGTGGGAGAGTCTGACTTTGAAAACTTAAATACAGAAGAATTCAGCAGTGAATCAGATATGGAAGAAAGCAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075318-Scn2a1:NM_001099298:15
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=0.134
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.3=85.0)
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:
CCTGGCCCACACTGAATATGC
R:
GCAAGGCCAAGAAGAGGTTCA
Band lengths:
357-1728
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: