RnoINT0131709 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142608217-142609402:+
Coord C1 exon
chr7:142608217-142608438
Coord A exon
chr7:142608439-142609338
Coord C2 exon
chr7:142609339-142609402
Length
900 bp
Sequences
Splice sites
5' ss Seq
AAAGTAGGT
5' ss Score
6.84
3' ss Seq
GCTTCTTCCCACTTTTCTAGCAA
3' ss Score
8.37
Exon sequences
Seq C1 exon
GCCTGAAGACAATCGTGGGCGCCCTAATCCAGTCCGTGAAGAAGCTGTCGGACGTGATGATCCTGACAGTGTTCTGCCTGAGTGTTTTCGCCCTGATTGGCCTGCAGCTCTTCATGGGGAACCTTCGAAACAAGTGTGTCGTGTGGCCCATAAACTTCAACGAGAGCTACCTGGAGAACGGCACCAGAGGCTTTGACTGGGAGGAGTATATCAACAATAAAA
Seq A exon
GTAGGTGTCCCCTCCTCAGCAAGAGGAAAGCTTCACCCAAGGTTCCTGTCAGACCCCCTGTAGAGCTAGCAAGAGTGGTCGGGCCCAGAGGCACAGCACAGCAGATGGAGCCTGGGAAGCCATCCCTGTGACTCCAGGGCAGAACCGCATGGGAGCTCTCATGTCCTCTGTCATTACTTTGTCTTGTTTTATCTTATTCTGAGGCGTATGTGAAACCACTAGTCACTCGAGAGAAATAAAATCAATTAAGTAGCCACAAGGAAGTATTGCATAGGAGGTCTCAGGGACAGTGCCTTCTGATTTAAAGTAGGGCATGGGAACCAATGACTGGTGAGGAGTTTTAGGACATCTTGATAAAAATGTTACAAGGATAAAAGGGCAAATTGTGTACAGGGATGACGATCTCGGAAACTTACTTTAGACCAGTGTCTTTCAGCCTGAGGGTCACCACCCCTCGGGGGGCGGGGTCACAACTCAGATATCCTACATATCAGACATTTACCTCACGATTCATAACAGTAGCAAAATTACAGTTATGAAGTAGGAACGAAATAATTCTAGAGGGTTCCCACAACACGAGGTGTCGCAGTGTCAGGAAGGTGTGAGAACCGCTGCCTAAGACCCCCTGATTCAGCAGCAGAAGGTGGCATGCGGAGCTGAGGAGTCAAGTGCAGGTGGGTGTGGTGTCACCTCAAGGGCTTCAGGGTTAAGTTCTTAGTTCTAGCTGCGTACAGGAGATCATTAATGGGAGGGATTCTCCTCAGCTTCCTGCTGCTGGGAAGGGTTTATATGAGCTAAAATCAATAGCGGCTTCTGCTGGCATGCCGGGGCGCACGTAACCGTATTCTCTCATTCACCGGAATCTGCCTATTCACTTCCTGCTTCTTCCCACTTTTCTAG
Seq C2 exon
CAAACTTTTACATGGTTCCTGGCATGCTAGAACCCTTGCTCTGCGGGAACAGTTCTGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:6
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=FE(29.5=100),PF057587=Ycf1=PU(19.4=72.0)
A:
NA
C2:
PF0052026=Ion_trans=FE(8.4=100),PF057587=Ycf1=FE(7.5=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:
GCCTGAAGACAATCGTGGGC
R:
CCAGCATCAGAACTGTTCCCG
Band lengths:
286-1186
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]