RnoINT0131552 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51737904-51739119:+
Coord C1 exon
chr3:51737904-51738170
Coord A exon
chr3:51738171-51739000
Coord C2 exon
chr3:51739001-51739119
Length
830 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TGTTGTGTTCTCTCTTTCAGACC
3' ss Score
13.55
Exon sequences
Seq C1 exon
ATGGCACGGTCAGTGCTGGTACCTCCAGGACCTGACAGCTTCCGCTTCTTTACCAGGGAATCCCTTGCTGCTATCGAACAGCGCATTGCAGAAGAGAAAGCTAAGAGACCCAAACAGGAACGCAAGGACGAAGACGATGAAAATGGCCCAAAGCCAAATAGTGACTTGGAAGCAGGAAAATCCCTTCCTTTTATTTATGGAGACATTCCTCCAGAGATGGTGTCAGAACCACTGGAGGACCTGGACCCCTACTATATCAATAAGAAA
Seq A exon
GTGAGTTTTTAGACCAGTTGCTCCCCCTGAACCCGATCTCTTTAAGATGGTGAAGAGTGTACCCCTTTCCATCTCTTAAAATATCTCTAGGATGCTGGGTGGGCTGAGAAAGCAATGGGGCCGTTGTCTTAAAGTGTTTTGAAAGCACCTGGTTGAGTCTGTGGGGGGGGGGGGGGGGACAGACATATACCGCAGAGGCCTCCTGCAATGGGGCATGGGAGGAAGACAAAGCCAATTTATTTTCCTGGATACTAATTAAACAGTAAGTTGCATGCAGATTCACCCCGGTGCTACTGCATTGTGATGAAGGGAAAAGTAGAGAAAGGGTGTGTGTGGTTTTTATACTTCTAAAGCAGTGTCTAAGATCCCCCCTATTGCCTTGAACTTGACCTAAGGCTTTGAGGTCCTCCATAGGCTCAATTATGCCTTCATCCCACAGACTGTTATTTTTCCCATGGCTCCCTGCAGAAGGTAGAACACCAGAATACATATAAGGGCCAAAACCCAAAGTTCTAGCAGTTTTCACGAGAAAATAACCTCCATGACAAAAGTTGCCGAAACCTCATTTTTAGACTGCCGAAGAAGTGAGTCAAAGAGTCGGCAAAGTTACACAGAAGTCCCGTGGTCCTGACCACAGAATTGTCTTAGTATTCCTTACCTCCCGAAGTTGCTTATCCAATTTTGCATAGTTTGCAAGAAAGAGGACTAGGGTGCTGTCCTTTGCTGGTAACTGTTGCAGCGCTGGGCATTTTAGCGGGGTCTCTTACTCTCTTCGCATATCCTGATGCAGCCTGTGAATTCTGATCTGTGTGTTGTGTTCTCTCTTTCAG
Seq C2 exon
ACCTTTATAGTATTGAATAAGGGGAAAGCAATCTCGCGGTTCAGCGCCACCTCTGCCCTGTACATTTTAACTCCCTTCAACCCCATTAGAAAATTAGCTATTAAGATTTTGGTACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.348 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTACCTCCAGGACCTGACAG
R:
TTTCTAATGGGGTTGAAGGGAGT
Band lengths:
342-1172
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]