RnoINT0131695 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142657739-142658590:+
Coord C1 exon
chr7:142657739-142658209
Coord A exon
chr7:142658210-142658472
Coord C2 exon
chr7:142658473-142658590
Length
263 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGG
5' ss Score
6.35
3' ss Seq
TCCTCTTCCTTCCTGTCTAGAAA
3' ss Score
10.07
Exon sequences
Seq C1 exon
GTGCTGAACCTATTCCTGGCCTTGCTTCTGAGCTCCTTCAGCGCAGACAACCTGGCGGCCACAGACGACGACGGGGAAATGAACAACCTGCAGATCTCAGTGATCCGGATCAAGAAGGGCGTGGCCTGGACCAAAGTGAAGGTGCACGCCTTCATGCAGGCTCACTTCAAGCAGCGGGAGGCGGATGAAGTGAAACCCCTCGACGAGCTGTATGAGAAGAAGGCCAACTGCATCGCCAACCACACGGGCGTGGATATCCACCGGAACGGCGACTTCCAGAAGAACGGGAACGGAACCACCAGCGGCATCGGCAGCAGCGTGGAGAAGTACATCATCGACGAGGACCACATGTCCTTCATTAACAACCCAAACCTGACCGTCCGGGTGCCCATTGCTGTGGGCGAGTCTGACTTCGAGAACCTCAACACAGAGGATGTTAGCAGCGAATCAGACCCTGAAGGCAGCAAAGAT
Seq A exon
GTAAGGTCCCAGCCAAGAAAACCAGCCCAGCGCCCCAGGGTCAGGCTAGGTCTCCCCTTGGGGACCGAGCTCCCTGGGCTAGTCCAGATTTAGTTGCATGGATTCTGGAGTCAATCAACCCTTTAGTTTGTCCCTGCTCTTAATCCACCTGACCCCGCGGTTAGTGTCTGTCTGTGCGTGACCCCTAGCTGAGGTCACGTACACATGATCACGGGACATGTTCCTGCACAGCTCCCTGACCCATCCTCTTCCTTCCTGTCTAG
Seq C2 exon
AAACTGGACGATACCAGCTCCTCAGAAGGAAGTACCATCGACATCAAGCCTGAGGTGGAAGAAGTTCCCGTGGAGCAACCTGAGGAATACTTGGATCCGGACGCCTGCTTTACAGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.223 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=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:
CCCTCGACGAGCTGTATGAGA
R:
CTGAGGAGCTGGTATCGTCCA
Band lengths:
300-563
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]