RnoINT0131692 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142650181-142653394:+
Coord C1 exon
chr7:142650181-142650422
Coord A exon
chr7:142650423-142653220
Coord C2 exon
chr7:142653221-142653394
Length
2798 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCCCGCCTCCACTTCCTCAGGTG
3' ss Score
8.96
Exon sequences
Seq C1 exon
CAGAGCTGGAAGAGTCTCAGAGAAAGTGCCCACCGTGCTGGTATAAGTTTGCCAACACTTTCCTCATCTGGGAGTGTCACCCCTACTGGATAAAACTGAAGGAGATCGTGAACTTAATCGTCATGGACCCTTTTGTAGACTTAGCCATCACCATCTGCATCGTTCTGAATACGCTATTTATGGCAATGGAGCACCATCCCATGACACCACAGTTCGAACACGTCTTGGCCGTAGGAAATCTG
Seq A exon
GTAAGATGGAGCAGGGTCTCCGATGGACGACTTGAACGTGGTTTCGCGGCTGCCGGGCTTTTCCTGGTGTGTGTGGGAGGGGGGGAGCTGGAATTTAGTTAACAAGGAGGTGATAGTTAATTGGAGACAAGGGTATCTATCCACATACCCTGCCACCCGCGCTTCTGCCAGGCACCTTCAGCTGCGCCTTCCCTGGAGAACTCTGAAGATGCCTCTTAGAGCTGTTGGCAGGAAGCCAGCTACAGTGGCCGAGTGGGAGACAGGACAGCGAGTTGGTCCAGCGCCTGCGGCAGATCTAATGGGTTGGTTTTGGAGAACCCCTCATCTGTTTCTCGTGCTTCTCAGAACCCCTCCTTTCTCAGCCCCCTAGATGAAGGGCTTCCCATGATGCACAGAGTGCCCTACACTGCCTGTACTGTGGGATCTTACCTCCCATATGCTGTTATTTATGGGGAACGTTCAATTTCCTCTCCCATCCAACTTCTGGGCCATCTTCCAGTTTCTGCCAAGTTTCTTGTACTGTTAAATCATATATTTAATTATATTATTTAGAAGAGAAAAGTATGAAGTTTTAAAACATCAAAAAGTCATGACTTTGGGTTATGTTCTCCTTCTTTAGTACAAAGATGGGACCCAGGCTCGAGCTCCAGCACCCAGTGCTGGGGGGCTTCAGCACACGTGTGGTACCACCGGCCTGTTAGCATCCCGAACACTGCCCTCCATATGAGAAGTCCTTCATCCTTCCTAGACCGACAGCCTGCACAGGCCTCCCTGCATGTGTACCCTGCTTGACTCTTGAGGAATCATCCGAGCCCTCCCGGACACATCTCTCACACCTCCGCACCCCGTAGGCTTTCTCTGAAACGGAAGCTCTCTTCGTCCCCCTCAGACCCTGACTCCTCACATTGCGACACCCGTCTGTACCACTTTCCAGACACTCACTTCCACCTGGCTCAAACTGGACCACACACACCTTCACCCTCCTGTTCTCTCAGAATGGGCCGCTTCTCTTCGGGGACACCTTCCCTACCTTACACGGGGCCTTCCAACCTGCAGGGGCTCTCTCTCCCTTACTCGTGTTCTCCCTGCTGACATGCGATCTTTGCCCTGCTTAAGCTCCCATTCTCTGCCAGCCCCACTTCACCCTTCAATGTGGATACATTCTCATCCCTCTTAGACCTTGGTGCCAGTGTAGTGTAGCTATCCAAGGCAGATCGTAGCGGATCTCTAGTAGCCCTTCCATAGTGGACAGAAGCCCCGCCCCCTGGCTCTGAAGCCCCGCCCCCTGACTCTGATAGCCATGCTGTTCATCTGCATGGTGGTCTCAGTCCTTGAGAACTGGCTTCTGATGCTGGGAAGCACATCGCAGAGGTGCCCCGCTTAGCCCCAAAGGCTAGAACCAGCCCTGGCCTGTGGATTAAAATACTGTTGCATAAAAAGTTCTCTGTAAAAATGTAGTAATCATCTGGGCAGTGGTGCATACTTTCAATCCTAGCACTTGGGAAGCAGAAGCAGGCAGCTCCCTCATTCAAGGCTAGTCTGGTCTATTGAGAGAGTTCCAGGACAGTCATGGCTTTAAAAAAAAATTAATAATCAGTAAGAGTCATATGGGGTTGGGGATTTAGCTCAGTGGTAGAGCACTTGCCTAGCAAGCGCAAGGCCCTGGGTTCAGTCCCCAGCTCCGGAAAAAAAAAAAAGAGTCATATGTGGGTATCCTGCCCTAAGGTATACCCTTGTCACAGCATCTGTCCTGTTAGTTGATATTCTTCCAGCATGTTACTTTCCTAAGGCCTAGGTGACAGGGATAGCCCCAGAAAATGCACAGTGATCTATGGGGCATAAGCAGCAGGGAAGAAGGGAGTAGTTCTCGCATACAGCAGCTGCAGATGAATCGGCTGTTATACTGAGAGGTCAGAAGGAGGCACCAAGTGTCCCACAGTGAGGGAGTTCCTTGAGTAAGCTTCATCCAGTGACAGTAACAGGCAACAGAATGGATCAGGAAGACCATGCAACAGCTGAGATGGACTTGTGACAGCTAGGAAATTAGGCCCCAGACATTCTGTATTGCGATATATATGCATTTAAAACTGAGAAAGATCATAGGAAATGGTAGTTACATGCAAGGCAGGGAGACTGTGGACTTCCTGCTCGTTTTAGATGCTTTGGACAATATATGATTGCTTTTAGTACTTAAACCATACCATATGACTAGGCCTGGTAATATGTAATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGAATGATGGTGTGTTGTGAACAATTATTTTGCAACTATTACTTCCTTACTTCCTTTTATTGATGTGTGTGTTTATACAGTGATTAGTTAAGAGCAATTAACAAAACCCAGCACCTCCAACACTTACCTTTCTTTGCCATAACCATCAGTCTTCTCTAGCTACTCTGAAATATGGATACATTGTTGCTGATTATAATTACTCCCCCATAAAACTAGACCACCAAATACCTGCCAGCTTTTAAAAGGCGGTGGCCTTCTATCCTGTTCTTCATATTGCTTGAATTATTTCTTAATCACGTGCCACCCAGTATGAACGAAAGAGATGGAGGTGCCGGGGCCGAGCACTTCATTCAAACAAAAAGGAGCCTGTCCTGTATCAATCCGGGTGCCCATGGGGACATCCAGGCCTTGGTGGCCTGCAGCATGGAGGCCGTAGCTGGCTCTTGATTCGTGGGTAAGTTGTCTTGAAAGAGATAAGGTGTGTTCTTTCTGGTGTCCCCTCCTCACCTCCCGCCTCCACTTCCTCAG
Seq C2 exon
GTGTTCACCGGGATCTTCACGGCGGAAATGTTTCTGAAGCTCATAGCCATGGACCCCTACTATTATTTCCAAGAAGGCTGGAACATTTTTGACGGATTTATTGTCTCCCTCAGTTTAATGGAGCTGAGTCTCGCAGATGTGGAGGGGCTCTCAGTGCTGCGGTCTTTCCGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.029 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF119333=DUF3451=PD(6.9=21.0),PF0052026=Ion_trans=PU(1.6=3.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=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:
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]