RnoINT0131704 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142676400-142678550:+
Coord C1 exon
chr7:142676400-142676504
Coord A exon
chr7:142676505-142678279
Coord C2 exon
chr7:142678280-142678550
Length
1775 bp
Sequences
Splice sites
5' ss Seq
TTGGTAGGT
5' ss Score
7.03
3' ss Seq
TTTCTGTCTTTCCTCTGCAGAAC
3' ss Score
13.21
Exon sequences
Seq C1 exon
TTTGGAGGTCAGGACATCTTCATGACAGAGGAACAGAAGAAGTACTACAATGCCATGAAAAAGCTGGGCTCCAAGAAGCCACAGAAGCCCATCCCCCGACCCTTG
Seq A exon
GTAGGTACAGTGGGCAGGCTAACAATGGCACACTATACATCTGTTTGGAAAGAACACACTAGGGCTACTACAGAGGAAGAAGTGACTGGCTGCCTGGTGCTGCCTGGTGCTGCCTGCTGGTTCTCTCCTAGATGCTCAGTAAGAGCTCAGCAGCCGTGATTAGGAGTGAATCGGGTTTGCATTAGTGCTTGGCCCGTGCCTGGAGCCCTCCTATGAGACAGCACGCTGCCAGAGGTGAGCGAAGGAAAGTGATCCCTCCACTACCTGTTCAAGGCAGGATTCGGTAGTCAGGCATGGTGGCACCAAGGCAGGACTGTCACAACGTTAGAGGCCAGCCTGAGCTACATAGTGACATCACCTTTCAAATAACAAAAGCACTAAGGTTTGGTCAGTATTTTCACAGCTGCTGTGCCCTAAAACATGGTGGCAATAAGGATGTGGCAGCAGCGTGCTAACATCCCATAATCAGGAAGCAGAGGGGAGGTAACGAGAGCTGGCTCCTCCTCCTCATTCCTTCTGGACCCTCCCCTACCCCACCCCGCCAGTGGGATGGTGCTTAGTGATCTTCGGTCCAGTCAACCCTCACACTGGACCTTTTGGAGAGAGCGCTGTTCTCTTCCTGTGCGGCTTTTCACCTTGTCTAGAAATGGAAAGCAGCCGGAAAGCCTGTTTTCCCAAGCTCCGTGCTTGCTAAAGTATAAAGTCACGAGGTCATAAGGCGGCTGTGACTCACACCTTTAATCCCAGCATTCCAGAGGCAGAGACAGGTGGATTTCTGAGACCACCCTGGTCTACCAAGTGAGTTCCAGGACAGCCAGGGCTGCACAGAGAAACCCTGTCTCAAACAACAATAACAAAACCCACGTGGAGCCTGCTGAGCTAGGGACGTGTACTCCTCCCGCATAGGAGCCAGGTGTGGCTGCCAGCACCAGGAAGGGTCACCAGCTCACAGACACCTGGAGCTCCAGCTGCAGGGTCCAGAGCCACATCCCCCCTCCAGGCACCCATGTGCACATACCCTATGCATATACTAAATGTAAATAAATCTTGGGATGGGGGAGGGTTCAAGAAGGGTTTCTCTATGCAGCCCTGGCTGTCCTGGAACTCTCTCTGTAGACAAGGCTGGCCCTGAGCTTAGAGATCCACCTGCCTCTGCCTCCCAAGTGATGGGGATTAAATGCTACCACTGCCCAGCTATGAATCTTTAAAACATGTTATTTATAAATATTACAAATGCTTGCATTCATACACACATATATGCCAGTAACGCCAGCACTCGGGAAGCTGAGGAAGAAGGACTGCTGTGAGTTCCAGGCCAATGTGGGCCACACAGTTAAGTTGCAGGCCAGCCTAACTACAGAAGGAGACCCCACCTCAGACTGATGGACTATGTTTGGAGTCTGGGCGAGAGGCAAGGATGAAGTCCACTTTCTGACTTAAGAACAGTGAAAAGGGAGGAGCTGGGTGAGGTCCTCAGGAGGTGCATGGTGAATCCAGTATGAGTGCAGCACCCTTTGTCTCTGGAGTAAAGCAGCCACTGGGGCTGGAACAGCATCAGGACGGAGAAGACCCTCAGCTGGGGTGGTGTTGCTCAGGCCAACAGAACAGTACTTGAGGACACTGAGGCCAGCTCTCCTGAAGAGGGCTCTGTGGGCGCTCCAGACAGATGACAGCAGGTACTGTCACCGAGAGGGCAACAAGGACGCACCAGGAGCAGAGCAGCAGCCCATGGGTCTAAAGGCTTCTGTGAACCTGTTTCTGTCTTTCCTCTGCAG
Seq C2 exon
AACAAAATCCAAGGGATTGTCTTTGATTTCGTCACTCAACAAGCCTTTGACATTGTGATCATGATGCTCATCTGCCTTAACATGGTGACAATGATGGTGGAGACAGACACTCAGAGCAAGCAGATGGAGAACATTCTTTACTGGATTAATCTGGTCTTTGTCATCTTCTTCACCTGCGAGTGTGTGCTCAAAATGTTTGCCTTGAGACACTACTATTTCACCATTGGCTGGAACATCTTTGACTTTGTGGTGGTCATCCTCTCCATTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.5=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACATCTTCATGACAGAGGAACAGA
R:
TGGAGAGGATGACCACCACAA
Band lengths:
357-2132
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]