RnoINT0131584 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51580790-51582285:-
Coord C1 exon
chr3:51582085-51582285
Coord A exon
chr3:51580923-51582084
Coord C2 exon
chr3:51580790-51580922
Length
1162 bp
Sequences
Splice sites
5' ss Seq
AACGTTAGT
5' ss Score
1.4
3' ss Seq
CATCAGTATTTGGTTTGCAGGGT
3' ss Score
5.3
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACGAGCATTTTCAGCTTCAGAGGTCGGGCGAAGGACGTGGGGTCTGAGAATGACTTTGCAGACGATGAGCACAGCACCTTCGAGGACAGCGAGAGCAGGAGAGACTCCCTGTTTGTGCCGCACAGACCTGGAGAGCGACGCAACAGTAAC
Seq A exon
GTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCAAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACTCTCAGCTCTTACGTCACCTACTGGATGGCTCGCGCCAGAGGTGATAATACATAAACCAGCTACTAGTGACACTTCAATTGAAAAAAAAAAAATGCAGGCCTGGGCAGTTGAGCCTGTTCTGTGATCCTAATTCCTCCAAATGAAAGTGCTTTAAAATAACATGATTAATTGAATGAAAAACAAAATAAAACAAAACAAAAATAAAAAAAGCAAAAAAACCCAAACTTGACTTGTGTGGAACCTTTTTAGGTTAAAAGTATTCAAAATTTAGAATCTGAGATAAAGCATAAATCTACAACTTCAGCCGGTTTATTGCAAATACAAAATAATGAGCACTTTCACAATCAGATCTTTGTTATTAATGTGTCCCTTAAATTATACAATCATCCATCAGGCCATATTCTGAAATGTTTGTATTCGTACAACTAAATATTGTAATGACCAATGTATTAATGATGGACGGTTTTATACAACTGTCGATGTTACAGGCTATTTGAAAAAAATATTCCCAAATAAAACGTGTTGATGAGATGCCATATGGAAATAAAGAAATCTCAGGAAAGCACACACATTTCATTGTACATCTGTGTTTGTGCATGGAAAAAAATGGCCCATATATGTCAGTTTGTCAATATAGCCTCAAAGAAAATAACCCAGCCTTGAGACTATATAATAATAATTAGTTTTGTGGAAAGATTGACCTATTCCTCACTGCTATAAGTTGAAGAATAATTTGTATTTAAATGAAAAACTAATTATAGCATGCTTATAAAAATATTTCCCCTAAACTTTGCCATAGTGTTTAAAATGCGTGTGTAAAATGGTTGCCTTATAAGATTGCATCCAGCCAGTGAACTCTTGGCAAAGGATCTGTGGTCTTTAAAATAAAAAGTCTTTATAGACTGTGATAATCTATCCAATAGTGTCTTATTATTACTTGAGATTGTTACCTGAAAAAAAAACTTGCATGAAGCATGGTTTTCCAGAGAGATGCTATATATTCTTGTGTTGTCAATGGAGAAGGGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGTACCACCACTGAAACGGAAGTCAGGAAGAGAAGGCTAAGTTCTTACCAGATTTCGATGGAAATGCTGGAGGATTCCTCTGGAAGACAAAGAGCCATGAGCATAGCCAGTATCCTGACCAACACCATGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.617 A=NA C2=0.393
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(46.8=100)
A:
NA
C2:
PF119333=DUF3451=PD(0.7=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCTCTTGAGTATCCGTGGCT
R:
CCTCCATGGTGTTGGTCAGGA
Band lengths:
334-1496
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]