RnoINT0131571 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51749332-51749929:+
Coord C1 exon
chr3:51749332-51749460
Coord A exon
chr3:51749461-51749837
Coord C2 exon
chr3:51749838-51749929
Length
377 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
ACTCTGATTTAATCCTACAGGTA
3' ss Score
9.61
Exon sequences
Seq C1 exon
GTATACTTTTACAGGAATTTATACTTTTGAATCACTTATTAAAATCCTTGCAAGGGGCTTTTGTCTAGAAGATTTCACATTTCTACGGGATCCCTGGAATTGGTTGGATTTCACAGTCATTACTTTTGC
Seq A exon
GTAAGTATTTCTGTAATACTTTCTACCCTGGCAGGGTAATACTATGGAGCCTATACTGTAGTTCTCGGTGTTGGCTTCCTTTGACTCATAAAGCACTTTAATTAGTTGGCATGTGTATTTAAAAAACCTTTTCCAATCAAATTATTCAGTTTGGAAAATTAGGAATGATCCTAATAAATTATATGGCTTTGGTTTCAAATAGCTGTAAGGTAACAATAAAAAAATCCCCCAGTAACAGCTCAGTCGATGACAATACCGTTCTCCTCTAACTGGGAAATCTGATAACAACACTCACTGAAGTTGAAATGGTCTTGATTCAAGACCAACATAGGCTTAGATTTCCCAAAAGTCTGAATAACTCTGATTTAATCCTACAG
Seq C2 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:4
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=FE(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACTTATTAAAATCCTTGCAAGGGG
R:
ACAGAAATAGTTTTCAAAGCTCTCA
Band lengths:
182-559
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]