RnoINT0131696 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142658473-142659324:+
Coord C1 exon
chr7:142658473-142658590
Coord A exon
chr7:142658591-142659169
Coord C2 exon
chr7:142659170-142659324
Length
579 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAA
5' ss Score
4.51
3' ss Seq
GACTCTCCCATTGCTTCCAGGTT
3' ss Score
8.58
Exon sequences
Seq C1 exon
AAACTGGACGATACCAGCTCCTCAGAAGGAAGTACCATCGACATCAAGCCTGAGGTGGAAGAAGTTCCCGTGGAGCAACCTGAGGAATACTTGGATCCGGACGCCTGCTTTACAGAGG
Seq A exon
GTAAAAGGGACAGGGAAAGGTTGTGCATGACCTGTGTGCTGTTTAGTCATGGGCGCCATTTTGGAGGCGCTGTGGCTGCCCGTGATTTTGGAGGCGCTGTGGTTGGGCGCCATTTTGAAGGCGCTGTGGTTGGGCGCCATCTTGGAGGCGCGATGGCTGCGCGCGCGCTATCTTGGAGGTGCTGTGGACGAGCACCATTTTGGAGGCGCTGTAGACTTGTGCCATTTTTGGTGCAGGTTGGTTTTTAATAAATATTTTTTAATCATTTCCCTTACTCAGTTCTGACATACAAGTTTCCAGTCTAGATTTTTTTTGTGCCCGACTGCCATTAGAAAGGCCTCCGTGGTGTGCTGTGCCTGCCTCCTGACCTGACCAGCCTCCTCCCAACCCTCTCACTGCTTCCTTGTAGTGATCTTCCTGATTCCAGAAGTCCTGCCTTTTTATTACCCTTGCAACATAGCTTCAGCGATTCTCACCATATTCAGCGGCTACCCTCCCTACTGTGGAGTGGGAGCCTGGAAAGGGACCAGTCAGGCCGCACAAGGGTCCAGTCTGACCCGACTCTCCCATTGCTTCCAG
Seq C2 exon
GTTGCGTCCAGCGGTTCAAGTGCTGCCAGGTCAACATCGAGGAAGGACTAGGCAAGTCGTGGTGGATCTTGCGGAAAACCTGCTTCCTCATTGTGGAGCACAATTGGTTTGAGACCTTCATCATCTTCATGATTCTGCTCAGCAGTGGCGCCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.575 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(17.9=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.2=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGACGATACCAGCTCCTCAG
R:
TGCTGAGCAGAATCATGAAGATGA
Band lengths:
258-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]