RnoINT0131535 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52443605-52445712:-
Coord C1 exon
chr3:52445584-52445712
Coord A exon
chr3:52443697-52445583
Coord C2 exon
chr3:52443605-52443696
Length
1887 bp
Sequences
Splice sites
5' ss Seq
CGCGTAAGT
5' ss Score
9.93
3' ss Seq
GTGTGAACTCCTCTTTACAGATA
3' ss Score
8.92
Exon sequences
Seq C1 exon
GTACACCTTCACAGGAATATATACCTTTGAATCACTAATAAAAATTATTGCAAGGGGCTTCTGTTTAGAAGATTTTACTTTCCTTCGTGACCCATGGAACTGGCTGGACTTCACTGTCATTACATTCGC
Seq A exon
GTAAGTGCCTTCTGTTTTGGAAACTTGACAGGAAAGAGTATAGTTGGGTTTGCTGTCCATGCTCAGGTTTTAAACAACCTGCTTCAACGGTAAAACATGCAGGTATGATTTAAGCACGACTTTTAAGAACTCTAAGTCTTAATGATTACCTCAAAAGGGTAAGCCCATTCCACCGCTCCATGAGAAGTAGCGTCAATTGCAATATCAATTAAAATCTATCAAAATGTCATAGTGCTGGTCTTCTCATACAAACACTAATAACACCGAAGCATAAATTATTTATCCCTTAAGCTGAAGGATGGTTATAAAAGTTCACACAGTAAAATTTGTACTGGTCCAGCAAATACGCACTGGCCTTTCAAACTCCTGTTGTGCCCCACCCCCATGGTTTCTTTTGTTACCTTTGTAGAATAGTAGAAAGCAAGTAGTCACACTGGAAAAAAAGATCATAAGATGTAAAAGGCATTTGATACATTGCAAATTAAATAAATTGTTATTTCCTGAGCAGACACACCCTGCTTCTATTTCCTTTCTGACTCAAGTTTTATTCCTCGGTCTCCATCTCTGTCTCTGTCTGTCTCTCTGTCTCTGTCTGTCTGTCTGTCTCTTTCTCTCTCTCTCGCTCTCTCTCTCGCTCTCTCTCTCGCTCTCTCTCGCTCTCTTCCGCTTTTGTACTCTCTCTTCCTCTCTCGCTCTCTTGCACTCACTCTTGATCTCCTTTTTAGGGTCTTTTTTATTTTACTCAACACAAACCTTTTCGATGTACGCCGAGTTGTACGTTCAGTCCTCACTTTCCTGTCTTCTCCCGTTTGCTAGTCACAAATCACGCCCTTCCATGCCAGGAAGAGAAGCTGAAAATGAGGGGTAGCTGTTCAAGAATAGCCAAAAGTAGGTATGGAGGACAGTGGATTAACACCACTCTCCCCAGCTGGGTAGCTGACCTTCTGGGCATCGGCAGTTGTGAAGAGATAGACAGGAGAGGAGATAAGCTCGGAATAAGCTCGGAAGTGCAAATACAGGATGTCCGGTTCTAATTATATAACTTCATATCAGATTGGAATATGAAATCTGTTCCCATGCTCTTCAGCCACAACTTTCAGGGCAGTATTTGGGACTTCTCGTTCTTGAGAATAATATAGAAATAACAGTGGCAGAGCAGTTTTGGGCCACATAAGATGCTTTTGTTAATTTGTCCAACTTCCATTTAAAAGTTACATTAGGAAATGCTAATCTTGAATGGTGGGACAATAGGCAGTCTGTTACAATAGATAATTTCTGTTGGGTGATTTCTTGTATTCTTTCTTTCTTTTTTTTTTTTTATTTTTTTAGCCTAAACCATAGCCTGTGGCTTTGGTTTCAATTAATTAATTAATTTAATTAATTTTTCCAATTCACATAGCGTGTTTCTACCTTGCTTTCCAAATGGCATCAGGAATGCCTATTTTTATGAAATTTACATTTAGTTATGGTATTTATTATGAAAATAAGGCTACATTGGTGAAGTCTAAATTTTAATTTGCAACTTACGCTACTATCATTTAAAAGCAGCAAAAGATCTTCATAAAATACCAGATTAAAAACTGGAGTCTTAGGGTTGGGGATTTAGCTCAGCGGTAGAGCGCTTGCCTAGCAGGCGCAAGGCCCTGGGTTCGGTCCCCAGCTCCGGAAAAAAACTAAAAAAATACTGGAGTCTTGTAAATCTTAAATAATTTACTGGTAAGTACCAGAATTTGTAAACCTGGGTAATTTTTAGCTCTTGGCTCATATAGAGCATTGAGTCTAAAGACGGTTTCCACAATTCTAGCTATAAATAATTAGTATAAAGTGTACTAACGAATCATTCTTTGCGTCCTGTTATCGCATCTGTGTGTGAACTCCTCTTTACAG
Seq C2 exon
ATATGTGACGGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTTCGAGCATTGAAAACAATATCAGTCATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:2
Average complexity
IR
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(16.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACACCTTCACAGGAATATATACCT
R:
TTGTTTTCAATGCTCGAAGAACTCTG
Band lengths:
206-2093
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]