RnoINT0131566 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51809898-51813009:+
Coord C1 exon
chr3:51809898-51809951
Coord A exon
chr3:51809952-51812871
Coord C2 exon
chr3:51812872-51813009
Length
2920 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TACCTTTCTTCATATTTCAGGTA
3' ss Score
10.72
Exon sequences
Seq C1 exon
GCCACCTTTAAAGGATGGATGGATATCATGTATGCAGCTGTTGACTCAAGAAAT
Seq A exon
GTAAGTCTACTTAGGGAACATGGCTTACTCGCATCAGTGAGCATAGCCATGTTATTGTAAATTGTTGATGGCAAAAAACCCACAGCTCTACAGTTATATAGATCAATGTATAAAGCACAACTATCTTGCTAAAGTGTGTATATTATACTATTTCTTTCAATTTTTGTTGGGGATCCAATTCTTCAGTTAGAGTTAAAATTCCTTATCATGTGAAAAGGCCTAATAGGAACCGTCTTCTAAATAACTAGTAATCAAAAAAATAGAATCTGGCCAATTTTTTCAATTTTTAATGAATATGATTTTTCTTGACTCACTGTATATTTATACATTTTTCGAAGACTTGTTTCATGTATGCGAGTGGTTTGTCCTGATTATATGTCTGTGTGTGTCATGTGTTCCTGGTGCCCAGGAGGCCAGAAGAGAGCTTCAGACCCTCTGGAAGTAGAGTTACAGGCTGTTGTGAGCCACCATGTGATTGCTGAGAATTGAGCTCTGATATATTAAAAAAGCAACAAATACTATTTTTTAAAAAGATTTATTTATTTCATGTATATGAGTGCTCTATCTGCATGCCAGACCTCATTATAAATGTTTGTGACATAACATGTGGTTGCTGGGATTGGAACTCAGGACCTCTGGAGGAAGAGCCAGTGCTCTTAACCACTGAGCCATCTCTCTGGCTCTGCAACAAATGCTTGACTACCAGGCTTCTCTCCAACTCCTGCTCATGATTTTTTTTCCCTTTCTTTTTGGTCTTTTCCTGTAATCTTAGACCTTGGTGCTTAAATTTTTATGAAGCGTACTTTCAAAATGAGATGTTAGGTTTTTCTAAAGAGGAATCCTCAGGGCAATTTTCCTTATCTGTCATAAGTTTCCTCCAGCGTTTTATCTTCCGTGAGGACGGATATGACTAATGATGACTAACAGTGGGGAAAACAGGAAACGAAACGAAAAAGCTATAACCTGATAGTGTCTCCAACCAAGATGGGAAGTGTGTGAGAGAAGGCGGGGACTTGCAAAATCTACCTTAGGAACACAGAGGAGTGTTCGCTTTGATTTTTATTACTTTCACACAAATGATCCAAAGACAGTGGCATTTTGGAATTGTTTCTGATTTTCTAGAGCCCCCAGGTTACTCTCAAAATGATATTTTCCTGTACCAGCAATTAACTCTCCATATTAAAAAAATCCCTGAATTGGTTTTTCAGCCTCATAAAAAGGGAGAATAGGATAGAAGATTGGCAGAAGCAGAAGATGCTCAAAAGCCCTGCATGGCATCAGCGATTTCAGCCGCAGGTGTTTTCTGACCCAGGAAACCAAGGGTTACCTCATATTCTCTCCTTTCATTTGCACAGTAGCCTCATGTAATTGCTACTAACTCAATGCATTACTGAAGCAGAGAGGTTCAACATATTCAACAGGGAACATTTTGGAACTCTGAATTGAGACTGTGTTACTTACAATGGTTTCTGCAAGAGCTCTTTCTACCTCCTGGATTAGTTCACTGGAAGCTATTTCTACCTTTAGCAACAGCCTACAAGGTCCAGAGCTTACTTTGCTTCTCTTCTTTTCAAACCTAGCAAAAATACTACGGAAGCCCTCACACCCAATCATATTGTAGAAGAGAAAAGCCAATGGGCCACTGGAATTTCTGACTCCTTTTTTTTTCCTTTACATTCATTTGTATTTAATGTTATTTGAGACAAGGTCTCACTGTGGAGCCTTCACTGACCAGGATGTCTTATGTAGATCAAGCTGGTATCGATTCACAGCTATCTACCTGCCTCTGCCTCCTGAGTGATGGGGTTAAAGGGTGTGACACCATACCAGGTTCTGGCTTTACTTTCATTAGCATCATCATGAAATGATGCTAATGAAAGTAAATAAGGCTAATGATGGTGGCTAGGTTGCAGAAGAAGAAACACACCAGGACTTTTGAAATACTTAAGTCGTATGTTTCTCTTACAAATAGGTAAATTCACTTAAGATTTTAAATTAGACAATTTACTCTAGTGTGTTATATTTAATTTTAAAAGGTTTGAAAATATTATTTCACATTGTTGTGCATATTACACACAGAGAAGTCAAATGATCGTCAAATAAATAGCAGTCAGTTTTACAAGCATTTTGTTGTCTTTTACTTTATCGTATGCCATTTAAAATAAGCTGGTCATGGTGCTCAGAATTGTGTCATGACATGGTAAGTTGCACTTTGTGTTCTTTCCCACCTACGATTGATTACCTGAGTTATTAGAAGTGTCCTGTGAGACTTGAACTTTTGATTCTTCCATCATCACTGATTTTCCTCCAAGATCTGGACAAGAGAGAGGATCACTGTAATGCCAACAGCAGCTACTGGAGAGAGGGGGTCAACGTGCCCACTATCAGGAAGGACAGACCCTACCAACCTAGTCATGTGTGCACACAATGTAGTTTCTAGACTACCTAGGAAGTGTGTACGATTATATCTCATGCACTTTTACTCATATTGGTACATTTGACTTTCATGAGTTACTCTTAAAACTATGGGTTTCCATTTCACAGATATGAGGACTAGGGAGAGAAAATAAATACTAACCATCTGAGAAGAGAGTAATGACACTCTAACTTTGCCACTGTGGAAGGAGTAATCCTACTTGCTTGGCGTGTTGAGATATTTGCTTACTAAGGAAAAGAACATTCCCAATATAGTGGTGTATTTGGTGAGACTGTGATAATCATTTAATCTGTTGCTTGAATGTATTTTCTTTTCTCAAGTCAGTGATTAGCCTGACAGGATTCAGCAGACCCATTAGACCTGGGGGTTCCAAAATTTTGCTTGACATTCGTCTGTTTGTTTCATGTTTAGAGATTTGAAAATTCTGTGATGTACTCCTAATGAGACTGTGGGCTTGACTGTCTACCTTTCTTCATATTTCAG
Seq C2 exon
GTAGAACTGCAGCCCAAATACGAAGACAATCTCTACATGTACCTTTACTTTGTCATCTTCATCATCTTCGGCTCATTCTTCACCCTGAACCTGTTCATTGGTGTCATCATAGACAACTTCAACCAGCAGAAGAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:22
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]