RnoINT0131736 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52642380-52644447:-
Coord C1 exon
chr3:52644306-52644447
Coord A exon
chr3:52642587-52644305
Coord C2 exon
chr3:52642380-52642586
Length
1719 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCTCTTTTTTGTCCCCCTAGACT
3' ss Score
11.63
Exon sequences
Seq C1 exon
GCAGTGTCCAGAAGGCTACATCTGTGTGAAGGCTGGCAGAAACCCGGATTATGGCTACACGAGCTTTGACACATTCAGCTGGGCCTTCTTGGCCTTGTTTCGGCTAATGACTCAGGACTACTGGGAGAACCTTTACCAACAG
Seq A exon
GTGAGCAGCAAGAGAAACACTCATCTCTGAAGACCATCAGTGTCTGGTGTATGTCGTCTCCTGCCTTATGAGCTACCGTAATTGCTGATGCTTTCATCTTCTTTCTGCAGACGCTCTGGGACTTCTGCTGTGCATTATTAAAATTACAGACAACTTCCTTGGCTGATAGGAGAACAGATAGTTCTTAAGTCATCAATAATTTTCTGCTGTGTTCTGAGCAGCGTTAATTTTTAGGTCTTCCATCTTCTCCAGTGTATCCATTGGGTCCAACGTAAAGAGCACAGGACATTGCAGTTCTCTAGAGATACCTTTGCAGACTCGGCACATTTGTCACATGCCCACGCTGTCTGGACCTGTGAGACTCTCCTGTAATGGGCCCACAATACTTTAGTGTTGAACACTTATTTATAACACACTCTCAGTTCTTCTCCAAACTTTCCTTTCCCATGTCAACTACTTCCTCCTCTGGACTTCATGCTCCTTTAAATATTTCTTAGCTTACGATACCAACCGCCATATTGTAACTGTCCTTTCACACGGACATCTTCTCTAGCAAGGTGCTTGCTGTTATGGGCTCTGTGTATTTATTATAGATTTCTCAACACCCAATCCCCAAAGGAAAGTGGTTGAAAGGGCTATTCTATTATTCCATGTAACAGTGAATTTCTTTTCTCAGATTTGCTACAAGCTTGTTTTATATTTACTTCTGTGAATATTATAGATGGTTACAAAATTATATAAAAAGACCCTTTGTAGGAAGATAAACATAACTGAAATAATTCAGGGGTAGAAATGGAATCTCAGAATGCTGTACTGCTGGCCTCACGTGCTTCATCTTGCTTCATCCTCTAACAAACATATCTAGTGCTGTAGTTGTGGGTTATCATAGCAGTCCCCAGTGTAATAACGTAGAAAAGAAGGCCATTTTAACCCCCAATTGAAGATATGTAAATAAAGCCACTGACATAATTTTAGGCATATTTAAGTTGATATATAGAAGCTAGACTTTCTTACACATTGGTATAACCTTTGCAGAAAGTTAATGAAAAATCAAAATGAATGTTTTCATTGATCTAATACTTCCAGTCTTAGCAATTTATTCAAGAGAGAAAAACAATCCTTATGATAGAGTGATAGAACAGAGGACTGAGTAGATAAACATTAGGTGTATCTACGGTAGATAAGTTTTACTAATATCTCTGCACTATTTTGAGTTAATCTAAAAATGCATTGCATGATAGAAGATATGCTGCATTTAAAATTATTAATGGTTATGCCAGATTAAAAAAATAAATATCTATGAGGTCAATAGATAAATTCCTTCCATAGGGTACCTCTGTCTATGTCAAAGTGTGATACTATAATTTATGCATTAAAAGGGGAAGAATAAAATCTAACAATAAAAGGGGCCTGTTCTAAAAAGTTAAAAGATAGCATGGGAGGTCAAGTTAGTGTTAATTTCAATAATGTGGAAAATGAAGAGTTGTTATATTATTATGTTTCATTCTAAGGAAGAATCAAACCTTAGTATAGCTGTGCCTTTTCTATGAAAAAGTTTAATACTGATTTTTCTTTAAAGATATTATCTTCATTTATCTTTCTATAACAAAATTATACAAAAATGTCTGTTTTACATGTTTATTATATACCAGCCAAAATTTTAAAAAGGTGAATTGTTTGTATTATTAAAGTAACCATTTCTCTTTTTTGTCCCCCTAG
Seq C2 exon
ACTCTGCGTGCTGCTGGCAAAACCTACATGATTTTCTTTGTCGTGGTTATTTTTCTGGGCTCCTTTTACCTGATAAACTTGATCCTGGCTGTGGTAGCCATGGCGTATGAGGAACAGAACCAGGCCAACATCGAAGAAGCTAAACAGAAAGAGTTAGAATTTCAGCAGATGTTAGACCGACTCAAAAAGGAGCAGGAAGAAGCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:9
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=0.014
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(19.0=100),PF0253517=Zip=PU(10.1=39.6)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.5=44.9),PF0253517=Zip=FE(36.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGTGTCCAGAAGGCTACAT
R:
CTCAGCTTCTTCCTGCTCCTT
Band lengths:
349-2068
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]