RnoINT0131729 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52590954-52591588:-
Coord C1 exon
chr3:52591484-52591588
Coord A exon
chr3:52591225-52591483
Coord C2 exon
chr3:52590954-52591224
Length
259 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAT
5' ss Score
4.46
3' ss Seq
ACTTTTGGTTTCTTTTGCAGAAC
3' ss Score
11.73
Exon sequences
Seq C1 exon
CTTGGAGGTCAAGATATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAGAAGCTTGGGTCCAAGAAACCACAAAAACCAATTCCAAGGCCAGGG
Seq A exon
GTAAATAAATACAAACACACACACACACACACACACACACACACACACACACCTTTGATATTCATTCTCTTAAGCATGTTTGTGTACTAAATTTGTAACATATTTTTAATCTTTCATAAAATTTATTTTTTATACAATATATTTGTTCATGATTTTCCCCCTCTCTCAACTCCTCCCAGAACCTTTGTATGTTTAAAATTGCAGATAATACTTTAGAATTGTGTTCAGCATTCTGTCTCACTTTTGGTTTCTTTTGCAG
Seq C2 exon
AACAAATTCCAAGGATGTATATTTGACTTAGTGACAAACCAAGCTTTTGATATCACCATCATGGTTCTTATATGCCTCAACATGGTAACCATGATGGTAGAAAAAGAGGGGCAAACTGAGTACATGGATTATGTTTTACACTGGATCAACATGGTCTTCATTATCCTGTTCACTGGGGAGTGTGTGCTGAAGCTAATCTCCCTCAGACATTACTACTTCACTGTGGGTTGGAACATTTTTGATTTTGTGGTAGTGATCCTCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCAATGAAGAAGCTTGGGTCC
R:
AATGTTCCAACCCACAGTGAAGT
Band lengths:
292-551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]