MmuINT0139734 @ mm9
Intron Retention
Gene
ENSMUSG00000032511 | Scn5a
Description
sodium channel, voltage-gated, type V, alpha [Source:MGI Symbol;Acc:MGI:98251]
Coordinates
chr9:119425021-119426909:-
Coord C1 exon
chr9:119426466-119426909
Coord A exon
chr9:119425183-119426465
Coord C2 exon
chr9:119425021-119425182
Length
1283 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
TGCTCATGGGGTCTTTTCAGCAG
3' ss Score
4.56
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTCTTGGCCTTGCTGCTCAGCTCCTTCAGCGCAGACAACCTCACAGCCCCTGACGAGGATGGGGAGATGAACAACCTCCAGCTGGCCCTGGCTCGCATCCAAAGGGGCCTTCGCTTTGTCAAGCGGACCACCTGGGACTTCTGCTGCGGGCTCCTGCGGCGGCGACCTAAGAAGCCCGCGGCTCTTGCCACCCACAGCCAGCTGCCCAGCTGTATCGCCGCTCCCAGGTCCCCACCACCCCCAGAGGTGGAGAAGGCGCCCCCAGCCCGCAAGGAAACACGGTTCGAGGAAGACAAGCGGCCGGGCCAGGGCACCCCTGGGGATACCGAGCCTGTGTGTGTTCCCATCGCAGTGGCTGAGTCAGACACTGATGACCAGGAAGAGGATGAGGAGAACAGCCTTGGCACGGAGGAGGAAGAGTCCAGCAAACAG
Seq A exon
GTCAGCCATCTCCCCACCCGTCCTGACGGGACAGCCACCTGCTTGTATGGAGTCCAGAGAGCAGCTCCTAGCCTCACCCAGACTACCTCAGCAATGACACGGGGAGAGAGGAAGCCCCACGGCAGCTGGCCCCTCAGAAGGTGCCAACTCCAGCTTGTCCGTTTATGCCGTTAGTTAGTATTCATCCCTGGCTGACCTTACAGCCAGGGAACATGAGGCATAGCTCAGTATTCTTGATGAATACTTCCACCCCCACCCCCAGCTCTGCACATTGTCCAGCACCAGGACCAGCAGAGACAGATGTCCGGGAGAGAGAGGGCTACAGTTTGGTGTCCTTGCCACCCTCTCCTCCCCTCCTCCCATGACTGAGGCTAATTCTGAGATTTAAAAATAAGTATCCCTGAGATGGAGGTGTCGGAGACACCACTATCTTATCTCTCAACCTGTTACTTTTAACACTTAGGACCAGGGTCTGGCTAAGGCAGGGTGTCTGTCCCTCAGGTTTCCCTTGACCTGAGCTGGGCTCCGTATAGCTCCTGAGGTCCCTCGGTCAGGCGTAACCAGGTCCCCTCCATGTTGGTGGCCCTTCCTGACTGCTTCCTTAGCTAGCAGTAGCTGGGCCCAGCTCCGGGGTTCTGCTTTCTCCTGCCTCAGTTGGCCTTGTTGTAGGGGCGGTTGAGGGAGGGAGGGCTGGGATTATAGGACCACAGCTTCCGGTGTCTCCTGCACAGGAGATGAGAATTGGTTTCTGGCTGTTCCTTCTCTTCCTCGTCCCCTGGGACCAGAACAAACATGCCTGTGCACTTGTGCGGGTGCACGTGTGTGCATGAGTATGCTTGAGCGTGAGCGTGGGCGTGTGTGTGCTCGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGAATCGGTCCAGGCTAACTGCAGTATCTTCAGACTTTGAGAAGTCAGAGCATCCTCCTGAGGAGAGTTGATAGCAATCATAAGATGGGTATCGAGGGCCAGCTGCTCCCTTTCAGGGAGTCTTAAATATGCTGAGCTTTGGCTACGGGTCCTTTGCCCATACTTACCAGGAACCTCTCACTTACTGACCCAAGTCAGCAGAGGATGGGACCTTTAGTAGGTGGAGGTTCATGAAGAGGCCAGGAAGCAGTGGGCAGGGGCTGCAGCCCACAAGACTAGGGCCCTGGAGACCCCCTGCCCGGGTGTCTGGGCTCTGCTCATGGGGTCTTTTCAG
Seq C2 exon
CAGGAATCCCAAGTTGTGTCTGGTGGCCACGAGCCCCCCCAGGAGCCCAGGGCCTGGAGCCAGGTGTCAGAGACCACATCCTCTGAAGCCGAGGCCAGTACGTCTCAGGCAGACTGGCAGCAAGAGCGGGAAGCGGAGCCCCGGGCCCCGGGGTGCGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032511-Scn5a:NM_021544:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.547 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.4),PF065128=Na_trans_assoc=PU(47.1=83.8)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(19.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTTGTCAAGCGGACCACCTG
R:
CCACCAGACACAACTTGGGAT
Band lengths:
345-1628
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs: