RnoINT0131545 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52434549-52436358:-
Coord C1 exon
chr3:52436011-52436358
Coord A exon
chr3:52434682-52436010
Coord C2 exon
chr3:52434549-52434681
Length
1329 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CCTTGGCATTTGCCTTACAGGGA
3' ss Score
8.79
Exon sequences
Seq C1 exon
TCTCTGTTGAGCATTCGCGGCTCACTGTTTTCCCCGAGACGCAATAGCAGAACAAGTCTTTTCAGCTTCAGAGGGCGAGCGAAGGACGTGGGGTCTGAGAATGATTTTGCGGACGATGAGCACAGCACCTTCGAGGACAATGAGAGCAGGAGAGACTCTCTGTTTGTTCCCCGAAGACATGGAGAGCGACGCAACAGTAACCTCAGCCAAACCAGCAGATCCTCCCGAATGCTGGCGGGGCTTCCAGCAAACGGGAAGATGCACAGCACAGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGCGGACCCTCGGTTCCGACATCGCCAGTTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATAATAGATAAGCCAGCTACTGATGACAATGTAAGAAAGTTTTACATAGTTCAGGCATGGCTGGCCTTTGACTGCTGCACCAGCCAGTGTTTCTACAGAATGGAACTCTTGAGAATGATTCCTGGTTGGTCGAGCTGAGAATGCATCTGCATCTTGTAGCACCTTTACTAGACTAACCAAATAATGGTAGAGCCTCGGCACTCCTTGCACAAACCTGAATGCATTACCTACCGTATATGCTAAGGATTAATTAAACAATAATTACTGCCTTGGATGATTTGCTATGTACCCATACTGAATTTACATATGGAGACAACACCCCTAATGCCCTCTTATACGAGTAAATGGATGACGTTGAGTTTAAAGGGTGTATAGTAAATCTTCCCCACCAGACTCTTCAGTTTATCTGGGCTTTAGTTCAGATTTTTAAAAACACTGTGCATAGATAGCTTCATCATTACCTAAATTTCTAAGGTTCATATTTATATCTCACTAAAAAAATGCTGATATAGGTATTCACAAAACCAGTCTACTCAGAGACACCAATAAATTATTAATCCAGATAAAATAATTGATGGTGTAATGAAGGAATATTGTGTTTGTTGATGTACATTCAGACAATAACTTTCTAAACAAAGGCTGCTTCCTCCTAACTGTTCACTCACTTGGAAATATATCAGCATGATGAGGCATGACTCGGTATAAATTAGGTGACTTATTGCTTTGGGACCCTGGATGAAACTGTTGCCCCTGCAGCATGTGTATGGATTAGCATACACATTGAAATAAATGACTACATGTCTTATACCTAGAGAATGAGATGACAGCTAAGTATGTTGTAGTCTTTGGTATATTCTTAAAATGAAATGGCTGCTTTCTCGAAAGTGAAAAATGGCTTGACCATATGTCGGATTTTAAGGCATTAGGATTTGACAATGTGTTCATTAATTGAAAGCAAGAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGACAGATAGACAGATAGACAGAGAGATAGATATAGATAGTTATAGATATGCAAAGCTTTATTAATTATATTATGATGTTTTCATATTTCATAAGATTATAAAATCAAGAAAATCAAGGGGTCAAAATTTTAAATTTTCCTTTACAATTACATGGTTAACAGTTTGGATATTCCAGGCTAATGATTCAATAAGTCACCAATATCTGCCATTGGCCATTAAAGATGAATATGCATGACGCATGCGTTTCATGAAAATCACTGTCTCCATTTATCTCTATGCTATGATGCTCAAGCTAATCCTTTAACACCTTGGCATTTGCCTTACAG
Seq C2 exon
GGAACAACTACTGAAACTGAGATGAGAAAGAGGAGGTCAAGTTCTTTCCATGTTTCCATGGACTTTCTTGAGGATCCTTCCCAGAGGCAAAGGGCAATGAGCATTGCCAGCATCTTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.708 A=NA C2=0.244
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(12.2=19.0),PF119333=DUF3451=FE(51.1=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGATTTTGCGGACGATGAGCA
R:
CAATGCTCATTGCCCTTTGCC
Band lengths:
353-1682
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]