RnoINT0131733 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52656582-52657861:-
Coord C1 exon
chr3:52657770-52657861
Coord A exon
chr3:52656795-52657769
Coord C2 exon
chr3:52656582-52656794
Length
975 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TTTTCCCCCTACATTTTAAGGAC
3' ss Score
9.55
Exon sequences
Seq C1 exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
Seq A exon
GTAAGACGTGATTGGTGTGGAGCTTTAGGCCGCTCAACTCCAGCTGTTTGGGAGTTTTCTTTGTCTGTGTGTGTGTTGTCACTGTGTCTGTGTATAAACTCCCCTATTACAGATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTCCGAGCATTGAAAACAATATCAGTCATTCCAGGTGAGAGTGGGGTTAAACACAAGGGCTGACTTTGACTTCTTGGAGAAAAGAATTTTCTTCCATAATTCGAACTAAATTGCGTTCCTTCTGTTTTCATTGCAATTTTTATTTAAAAAGTCAGCCATTGGGTTTAATCAGTTGCATGGGTCTTGGAGAAGGAAGGTGACCATTTGGCTCACATCTCCACTTGAAATTTTTCCTCCTGCCAAAGTATTGGTTTTCTACTTTTTTAGGAAGGAAAATTTCAACTAAACTGAACATCGTATGATTAATAAAATAGGAAATATCTGCATGTAGGCATTGCATGACATTGTTTTATTGCTTTCTGTTTTTTTTCTTGAACAGTTTACCAAGCTATTTCTTACTTGAGAATTGGTTCAGTACATGTTGTCACTATGTGCTTTGATTAGCTTCTTACATTTTTAGTTCCATTATGTAGAGGTGGTTTGTTTGACTGATGTTTACTGAATTAGTAGTTACAAAACAATTATATTTGTGAGTGTGGATATGGTTTCAGCATCCACCTTACTTAACAATTGAACCTGATAATTTCTTGTAAATACTTTACTAATTTTAACCACTTGCTGTAGTCCATAGAAACAAGTTTACAGATCCACCTTTTGGGACCTAGAGACCTCTCTGGGTTCAGTTATTTGAGGTCATTGACTTGACATAATGCATGCATTCCCAGTTAGGCTTGTGTTTTGACTTGTTTCCCGTTGAGAGCCTTTATGTCATTATGAACGCCTCTTTTTCCCCCTACATTTTAAG
Seq C2 exon
GACTAAAGACCATCGTGGGGGCCCTGATCCAGTCAGTGAAGAAGCTCTCTGACGTCATGATCCTCACTGTGTTCTGTCTCAGTGTGTTTGCACTAATTGGACTACAGCTGTTTATGGGCAACTTGAAGCATAAATGTTTCAGGAAGGAACTCGAAGAGAATGAAACATTAGAAAGTATCATGAATACTGCTGAGAGTGAAGAAGAATTGAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:6
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(12.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(28.6=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:
TTTAACAGAATTTGTAAACCTAGGCA
R:
TTTTCAATTCTTCTTCACTCTCAGCA
Band lengths:
302-1277
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]