RnoINT0131731 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52659144-52659863:-
Coord C1 exon
chr3:52659775-52659863
Coord A exon
chr3:52659273-52659774
Coord C2 exon
chr3:52659144-52659272
Length
502 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
CAATGTACTCTTTCCTTTAGGTA
3' ss Score
9.81
Exon sequences
Seq C1 exon
TTATTCAGCATGCTAATCATGTGCACAATTCTGACGAACTGCATATTCATGACCTTGAGCAACCCTCCAGAATGGACCAAAAATGTAGA
Seq A exon
GTAAGTACTCATTAGTATATATGAGACTGGGATTAAATGCTAATTTTCAAGCATTCTTTTTCCTTCCAGAAGTTTAGAAGTTGAGTCTATAAAACAGTGTTTTGTATCCTCTCCTGGGTGCAATTTTCTTTTTAGTTCTCTCTCTCCTCCATGTTAACTCACTGGCGGTAGGGTTGAAACATCAGATACCACAGTGTTTCTTGAACTTATCTTTCCCGTTCATAAATATGATATGCATCTCATTTTAGTGACTATATTGTTTTTAAACTCTCTATTGGGATTCTCTAGATGGATCCAATACCTATGTCTAGCCGATAAGGACATTTTAAGAGCTCCTGGAAATCCGTTGCACAATGTACTTTATGAGGTAGAATGATCCGTACACCAAAAGCAGCTTCCAAGAGATGCCTTCCTGTTATTAATCAGCGATAATAAACTGTAAAGATTTTAATGAGACACTACTCATTTCACAACTAATATCTCAATGTACTCTTTCCTTTAG
Seq C2 exon
GTACACTTTTACTGGGATATATACTTTTGAATCACTCATAAAAATCCTTGCAAGAGGCTTTTGCGTGGGAGAATTCACCTTCCTCCGTGACCCTTGGAACTGGCTGGACTTTGTTGTCATTGTTTTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:4
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=PU(0.8=6.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.3=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:
CATGCTAATCATGTGCACAATTCTGA
R:
AAACAATGACAACAAAGTCCAGCC
Band lengths:
206-708
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]