RnoINT0131575 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51756154-51756644:+
Coord C1 exon
chr3:51756154-51756295
Coord A exon
chr3:51756296-51756437
Coord C2 exon
chr3:51756438-51756644
Length
142 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCCTTCCACTTTTCCCACAGACC
3' ss Score
11.56
Exon sequences
Seq C1 exon
ACAGTGTCCAGAAGGATACATCTGTGTGAAGGCTGGGAGAAACCCCAACTACGGCTACACAAGTTTTGACACCTTCAGCTGGGCCTTCTTGTCCTTATTTCGTCTCATGACTCAAGACTTCTGGGAAAACCTTTATCAGCTG
Seq A exon
GTAAGAGCTGACATAAAGATTCTTCTAGGAAGTGTGAGATTCTGTGACTGAGGGAACTGCTGAGGTATCTTTTATTATTTTAGAGGAGCTTGCAACAGCGGATGTGAGATTTACAAACCTGTTCCTTCCACTTTTCCCACAG
Seq C2 exon
ACCTTGCGTGCTGCCGGGAAAACATACATGATATTTTTTGTGCTGGTCATTTTCTTGGGCTCATTCTACCTGATAAATTTGATCCTGGCTGTGGTGGCCATGGCCTACGAGGAACAGAACCAGGCCACACTGGAGGAGGCTGAACAGAAGGAGGCAGAGTTTCAGCAGATGCTGGAGCAACTGAAGAAGCAGCAGGAGGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:8
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=0.043
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.5=100),PF0253517=Zip=PU(12.6=43.8)
A:
NA
C2:
PF0052026=Ion_trans=PD(11.6=44.9),PF0253517=Zip=FE(40.7=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:
AGCTGGGCCTTCTTGTCCTTA
R:
TGCTTCTTCAGTTGCTCCAGC
Band lengths:
257-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]