MmuINT0139671 @ mm9
Intron Retention
Gene
ENSMUSG00000057182 | Scn3a
Description
sodium channel, voltage-gated, type III, alpha [Source:MGI Symbol;Acc:MGI:98249]
Coordinates
chr2:65345204-65346719:-
Coord C1 exon
chr2:65346519-65346719
Coord A exon
chr2:65345337-65346518
Coord C2 exon
chr2:65345204-65345336
Length
1182 bp
Sequences
Splice sites
5' ss Seq
AACGTTAGT
5' ss Score
1.4
3' ss Seq
CATCAGTATTTGGTTTGCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACGAGCATTTTCAGCTTCAGAGGTCGGGCGAAGGACGTGGGGTCTGAGAATGACTTTGCGGATGATGAACACAGCACCTTTGAAGATAGCGAGAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACCTGGAGAGCGACGCAACAGTAAC
Seq A exon
GTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCCAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCCTCAGCTCTTACGTCACCTACTGGACAGCTTCCGCCAGAGGTGATAATACATAAACCAGCTACTAGTGACACTTTACTAAAATTGAAAAAAAATAAAAAAATTTCAGGCCTGGGCAGATGAACCTGTTCTGTGATCCTAATTCCTCCAAATGAAAGTGCTTAAAAGTAACATGATTAAGTGATCTAGAAAACAAAACAAAAAACAAACACGCAAAAAAGCAAAACAAAACAAAACCCAAACTTGATTTGTATGCAACTATCAGCTTTCTAGGTTAAAAGTACTCAAAATTTAGAATCTGAGATAAAGCACATATCTACAACTTCAGTAGATTTGTTACAAATACAATATAATGAGCACTTTCACAATCAAATCTTCATTATAAATGTTTCCCTTAAATTATATAATCATCCATCAGGTCTTATTCTAAAATGTTGTATTCTTAAAATTAAATATTATAATGACAAATGTATTGACGATGGACAGTTTTAGACATCTGTCTATATTATAGTGCTGTTTGAAAAAAAATTCCAAAATAAAATGTGTTGATGAAATAGCATATGGAAATAAAGAAATCTCAGGAAAGCACACACATTTCATTGTACATCTGTGTTTGTGCATGGAAAAAATGGCCCATATATGTCAGTATGTCAATATAGCCTCAAAGAAAATAACTCAGCCTTGAGACTATATAATACTATCCAGTTTTGTGGAAAGATTGATCTATTTCTCACTGCTATAAGTTGAAGAATAATTTGTATTTGAATGAAAAACTAATTACAGCATGCTTATAAAAAAATTCCCCCCTAAACGTTGCCATGTTGTTTAAAATGCTTGCGTAAAATAGTTGCTTTATAAAATTGCATCTAGCCAGTGAGCGCTTGTCAAAGGATCTGTGGTCTTTAAAAGAAAACATGTTTATAGAATATGATAACCTATGTAATATCTTCATGTATTATCACTTGAGTTTGTTACCTGAAATAACTTGCACGAAGCATGATTGTCCAGAGAGATGCTATATATTCTTGTGTTGTCAATGGAGAAGGGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGTACCACCACTGAAACAGAAGTCAGGAAGAGAAGGCTAAGTTCTTACCAGATCTCGATGGAAATGCTGGAGGATTCCTCTGGGAGACAAAGAGCCATGAGCATAGCCAGTATCCTGACCAACACGATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000057182-Scn3a:NM_018732:12
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.597 A=NA C2=0.178
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(46.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(0.7=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTCTTGAGTATCCGTGGCT
R:
CCTCCATCGTGTTGGTCAGGA
Band lengths:
334-1516
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: