RnoINT0131706 @ rn6
Intron Retention
Gene
ENSRNOG00000005309 | Scn8a
Description
sodium voltage-gated channel alpha subunit 8 [Source:RGD Symbol;Acc:3638]
Coordinates
chr7:142595606-142596280:+
Coord C1 exon
chr7:142595606-142595693
Coord A exon
chr7:142595694-142596151
Coord C2 exon
chr7:142596152-142596280
Length
458 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
GCTGTCTGCATCCCCGACAGGTA
3' ss Score
9.45
Exon sequences
Seq C1 exon
TTTTCAGCATGATCATCATGTGCACCATCCTGACCAACTGTGTGTTCATGACCTTTAGTAACCCTCCAGAATGGTCCAAGAATGTGGA
Seq A exon
GTAAGTGACCCTTCCTCGGTTTGTTTCGTAGACCCTAGTCCTGTTACTTACTCCACAGCTAATCTGGGGGGAGGGTGTTGTGTGGGAGGTGGGCCGCTGAGGGTCATATGGAGTCTAGGAAACAGTGAGTTCTAGAAAGGCGGTCTGCTCTGGAAGGACACCCTTCCCCTCATAGCAGAGGGTTTGCCATCCTGTGTCACCCGAGGCTAAGATAGCTCTGGGGGCCTCTGTGCCTGTTCCAGAGTCGTCCTTTTATGTTCTTCAGAGCTCAGGGCAGGCCTAGCGCAGCATCCCAGTTGCTTCAGGCTTGTCACCAAGCTTCCTCCGGTCACTGCCATGTCACCACGCCCTAAATGTCTTGTCTGTGTGGTGAAGGCACACCCCAGGCGAGTGTCATCTTAAAAGGCTCATTCCAAGTTTCCACCAGGAATAACCTCAGCTGTCTGCATCCCCGACAG
Seq C2 exon
GTACACATTCACAGGGATTTACACATTTGAATCACTAGTGAAAATCATCGCAAGAGGTTTCTGCATAGACGGCTTCACCTTCTTACGAGACCCGTGGAACTGGTTAGACTTCAGTGTCATCATGATGGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005309:ENSRNOT00000008160:3
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=PU(0.8=6.7)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.1=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:
ATCATCATGTGCACCATCCTGAC
R:
GCCATCATGATGACACTGAAGTCT
Band lengths:
206-664
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]