RnoINT0131711 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142610370-142611744:+
Coord C1 exon
chr7:142610370-142610511
Coord A exon
chr7:142610512-142611537
Coord C2 exon
chr7:142611538-142611744
Length
1026 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
ACTTGGCCTTCATCTTTCAGACC
3' ss Score
10.55
Exon sequences
Seq C1 exon
GCAATGCCCAGAGGGATTCCAGTGCATGAAAGCAGGAAGGAACCCCAACTACGGTTACACCAGCTTTGACACCTTCAGCTGGGCCTTCTTGGCATTATTCCGCCTTATGACCCAGGACTATTGGGAGAACTTATACCAGCTG
Seq A exon
GTAAGTACGGCCTCTCTTTCTTTAGTGATATTGTCCTCACGGGGTTATGAGGAGCTGGGGACTGTCTGTGTGACACACCCACAGTGAAGACGTTAGGTGGGAGCCCTTGGGATGATGAATTCAGACAGCTCTTAGCCTGGTTTCTTGGCTGTTTAATCATGGTCAGCTGTGGAAGCTCACATCCTGACCCCCTCAGAGCACCCGCTTCCTCTCAGGTCAGGTTGCTCTCCGCACCCTGACTGCATCGTCTTCTGGATCTTCTGGTATCAGGACATTTGTTTAAGCAGCAGCAAACACTCATTTGTGCAGGGCATCTTCCTGGGTATTAAAACGAGGGGGAACTCTATCCCTGGGACCCTGAAGTGTGACTTAATATTTTTAGAGCTATACTGCATCTGGGCTTGTTCAGGTATGCAGTCCCCGTCCTATAATGACTTCACTGTCCTGTAATCCACAAGTCATAATGAGGAAAATCGGTGTCGATTGCTAATCTTAGAAATCCAGACGAGCCATTGTTTTTTTCTCTGGCTGGTGATGCTAGTTAGAAGATTAAAAAAAAAATAAATCTCCCCTTGCAAAAAGGAGCCTCTTCAAGAGAAGCTTCTGTTTCCAATCCCCAAGTCAGCCCTTACAGTTGAGCATAACAGACAGTAAATTCCACTAAGTGCTGGCTGATTGAAAGCATCAGGATGAGCTAGGCCTGTGCTGCGGGTCTGTGATCCTGGCACTCAGGAGCCGGGGGCAGGAGGATCACTGGGAGTTTAAAACCAGTTTGATTCACACAGCAAGTCCCATACCAGCCAGGGCTACACTGTAAGACCTTTTCTAAGATAGACAGACAGAAACAGAATATCTTTCTATGAAAGCAAAATCCAGGAGGCATTTCCCTCTCACAACGGAAGCAAGAGTTAAGCATTAGGAAGAGATTTGACCACTGGGATACGGGGTGGGTGCAAGGCACCACGCAAAGGAAACTCTGACCTCCTCAGCTGGCGACACGCTGAGAACTTGGCCTTCATCTTTCAG
Seq C2 exon
ACCTTACGAGCCGCTGGGAAAACGTACATGATCTTCTTTGTCTTGGTCATCTTCGTGGGTTCTTTCTATCTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTATGAGGAACAGAACCAGGCAACACTGGAGGAGGCAGAGCAAAAAGAGGCCGAGTTCAAGGCAATGCTGGAGCAACTCAAGAAGCAGCAGGAGGAGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:8
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=0.072
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.7=100),PF057587=Ycf1=FE(16.8=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.4=44.9),PF057587=Ycf1=FE(24.4=100),PF0043013=ATP-synt_B=PU(72.1=89.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAGGGATTCCAGTGCATG
R:
CTGTGCCTCCTCCTGCTGC
Band lengths:
342-1368
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]