RnoINT0131703 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142675149-142676504:+
Coord C1 exon
chr7:142675149-142675286
Coord A exon
chr7:142675287-142676399
Coord C2 exon
chr7:142676400-142676504
Length
1113 bp
Sequences
Splice sites
5' ss Seq
AAGATAGGT
5' ss Score
2.1
3' ss Seq
CCTCTGTGTTCTCTCTCTACTTT
3' ss Score
3.19
Exon sequences
Seq C1 exon
CCAGACGAGCAGCCTGACTACGAGGGCAACATCTACATGTACATCTACTTCGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTCAACCTGTTCATCGGTGTCATCATCGACAACTTCAACCAGCAGAAGAAAAAG
Seq A exon
ATAGGTTTCCTCTCTGCTGCCAGCGGCTGAGGCCAGCCCAGATGAGAGGCTCTCTGGCCTTGTTTCTAGAGAGAGGATGCCCCTCTTCCTCTGTCTCTCTTTGTCCTCTGCTCCTCTCCCTTGTCCTCCCCGTCCCCCTCCCCCCCTCCCTCCCTCCCTTCCTCCCTAAAACTCAAAGTGCCACCTTATGGTAAGGCTGTCCCACTGTCCAGACACCAGCCCCAGACAACCCCTTTTGTTTGAGGCTGAACTTTGCAGTGTGTGGTTTACAACATTTCCCTGAAGTTTTGTGTTCTTGAGGCCACTCCTGGTGGGACTTTCTGCCAGAAGGAGGGACAGAGAAAAAAGATAGTACCATGGGGAGACTTGAACCTGGCACCCGTAGCACAGTGGAAGTGGAGAGGGCGTCCTCAAAGGATTCACTTCCTGTGGTAATGGTTCTTCTAAAGCACACTGGAAGACTGACTTAGACTTACCTTGTTCTCTTACAAGTTTAGTCCATGCAGGGAGTCACAAGAATTCTAAGCTGCCTTTTTATACCACAAGTTCCAAATTTTGAATTTCATAAAAAGTGAATTTGCTGTTTGCTACACTGAAAGATCCTTTTTGTGATGTTTGGAAGGGCCACAGGGCATGGTGCACACAGGGCATGGTGCACACAGGGCATGGTGCACACAGGGCATGGTGCACACAGGGCATGGTGCACACAGGGCATGGTGCACACAGGGCATGCACACCTTCGATACCAGCACTCAGGAGGCAGAGGCAGGAGATTCTCACTCCATAGGCCATCCAGGATTACACAACGAGACCCTGTCTGGATAAAAATAATTTTTCCCATTGGTGTGACTGCCCTCTGGTCCCTTGCTCTCTCTACTTCCTGCTCTGAAAGCCTGGAGTCAGACAGTCCTATCTCACGACTTGGCCTGGAAGATTCCAGACATCTCCACTGGAACTGTCTCTGACTGTGGTAACTGCCCCAGGAGTGCTCCCTGTGGGAGTCCATGCCACCACGATGACCTCTGGAGGGAAAGTAGTCTCTCCTGGTTTCAGTGGTGCTCAGCTGCACATCCAGAGCCGGTTGTAATTGTCCCCTCTGTGTTCTCTCTCTAC
Seq C2 exon
TTTGGAGGTCAGGACATCTTCATGACAGAGGAACAGAAGAAGTACTACAATGCCATGAAAAAGCTGGGCTCCAAGAAGCCACAGAAGCCCATCCCCCGACCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:24
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=PD(15.2=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGACGAGCAGCCTGACTA
R:
GTCGGGGGATGGGCTTCT
Band lengths:
238-1351
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]