RnoINT0131726 @ rn6
Intron Retention
Gene
ENSRNOG00000006639 | Scn9a
Description
sodium voltage-gated channel alpha subunit 9 [Source:RGD Symbol;Acc:69368]
Coordinates
chr3:52596780-52597811:-
Coord C1 exon
chr3:52597530-52597811
Coord A exon
chr3:52596834-52597529
Coord C2 exon
chr3:52596780-52596833
Length
696 bp
Sequences
Splice sites
5' ss Seq
GTTGTAAGT
5' ss Score
8.3
3' ss Seq
CTAAATGTATTTTTTTGCAGGCA
3' ss Score
8.32
Exon sequences
Seq C1 exon
GTAGTGGTCAACGCACTCATAGGAGCAATCCCTTCCATCATGAACGTGCTTCTCGTGTGCCTTATATTCTGGCTAATATTTAGCATCATGGGAGTCAATCTGTTTGCTGGCAAGTTCTATGAGTGTGTCAACACCACCGATGGGTCACGATTTCCTACATCTCAAGTTGCAAACCGTTCTGAGTGTTTTGCCCTGATGAACGTTAGTGGAAATGTGCGATGGAAAAACCTGAAAGTAAACTTCGACAACGTTGGGCTTGGTTACCTGTCGCTGCTTCAAGTT
Seq A exon
GTAAGTGACTCCCTTCGCGAATACTTGGTACAGAGTGGAGGGTGTAAAATGCTGTGTAAATCTGCTACTAACTAGAAATTAAGATGCCATATGATTTTTCAAGTGGATTTAATATTTTCTCAGAGCATGTGCCCTGTAAGCTTAGCTAAAGCACACAGGTTTCTTGATTTTTAGATTTATTAATCCAGGATAGATGGTTTATTTTCCCTTGAACCCCCATCACTGCATCAACAGAAAATTGCCTTCCAAGCAGTCTTTGTGGGACTTCTATGTTTATCTTACAAGGTAATGGGAAGATCTTCTTAAAGGCACTGAGAAGCCCTGAGAAATAGAGACAAATTATTTTCTGCTCTAATGAAAAAAACTCAGTTCCACTTTTAGAAAAAGTTTCATATATAAAACGTACAAGTATTTGTAACAATTAAGAAATTCTTAATAAGGAAAAAAGCTTAGACTATGTCTTCTTAAAATATTATAGCAGTTTTCACATGTCTTTTTACATCTGAAGTAAATTATGGAGTGCTCTGATTCTAAAGCATAATCATAGCACTTTTATGTTAAGTCTACCGAGTTCTTTAAATAGAACTAAACTAATTGGATGCTACTAGTTATATTGGAAGATTAAATAGGTAAACCATATGATGATTTTAGAGTCTGAGCTTATCATTTAATTTCTCTAAATGTATTTTTTTGCAG
Seq C2 exon
GCAACATTCAAGGGCTGGATGGATATTATGTATGCAGCAGTTGACTCTGTTAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000006639:ENSRNOT00000065126:22
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(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGTGGTCAACGCACTCATAGG
R:
ATTAACAGAGTCAACTGCTGCA
Band lengths:
334-1030
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]