RnoINT0131702 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142674737-142675286:+
Coord C1 exon
chr7:142674737-142674790
Coord A exon
chr7:142674791-142675148
Coord C2 exon
chr7:142675149-142675286
Length
358 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TCTCTTCTGTCCTTGGACAGCCA
3' ss Score
8.36
Exon sequences
Seq C1 exon
GCAACCTTCAAAGGCTGGATGGACATCATGTATGCGGCTGTAGATTCCCGAAAG
Seq A exon
GTAAGGACACGCATGGTGAAATGCGGCCAGCTTAGATGATAGAGAGCAAGGTGTGTGGTAGATCCATCAAGAACCACGTAGTGGGGAAGAGTAGAGGGCCGGAAGTGTCTCCTTGGACACTAAGTGCTTGTCCGGTTACTTGACCCTGGTGGCACTGACTACCCTACCCTCCTGCCTGCTCCCTGTACCGCATCCCATAGGTGACAGTGCCTTTGAAGGACAGGTAGAGCGTGAGAGGGCAGAGAGAACCCAAGCTTGTCAGCCACACAGAGGGAGGGCTGGTGGCTTCAGTATGTTGGAGTCAGCCACCTGACGACCCAGGGATTGACCTGAGTCCCTCTCTTCTGTCCTTGGACAG
Seq C2 exon
CCAGACGAGCAGCCTGACTACGAGGGCAACATCTACATGTACATCTACTTCGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTCAACCTGTTCATCGGTGTCATCATCGACAACTTCAACCAGCAGAAGAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:23
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.2=76.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTCAAAGGCTGGATGGACA
R:
CTTCTGCTGGTTGAAGTTGTCG
Band lengths:
182-540
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]