RnoINT0131601 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51600846-51602029:-
Coord C1 exon
chr3:51601938-51602029
Coord A exon
chr3:51601119-51601937
Coord C2 exon
chr3:51600846-51601118
Length
819 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
ATATAGTTCTCTCTTCCAAGGTT
3' ss Score
5.78
Exon sequences
Seq C1 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACGTTCAGAGTTCTCCGAGCATTGAAAACAATATCAGTCATTCCAG
Seq A exon
GTGAGAGCTAGGTTAAACACAGAGGCTGACTTTAACCGTACCACATAATATTGGAATTGCAACCCCTCCGTTCATTGGCCATGGGGCCTTTTGCTCAAGTCTGTCACATTCAAGAATGCCAGACAGTGTTTCAATGTTGGGTCAGTTCCTTTAACATGTTGATAATTTCAACTTTCTTCATAAAGCCAGCCTCTGAGTTTAACAGAAAGTTGCATGAGATATGCACATATCATCGACAAATGTTTCTGTAATCCCTCTCCTGCATTTAAGATGTACGTCTTCTCTCCTGCATTCTGACAAAGCTTTGCTGTCATGCCCTTAACTGACTGTCCTGTATTTTACCATTTGCTCCAGATCTATTTCAAAAATAGATCATTTTTTCATAAAGGAGAAAAGGCTATAGGGCAGCATGTGTGTGGCATGGGATCCTTATGGCCTTAAAATTCTTTTTGCCTTGTAATTCACTGCTACTTGCAGGCCGGCAGAAAGAATGGGTTGAGAGAAACAGCTTCATGAAACGCAAAAATTGAAAGAAGAAGCAATTTAGTATTCCACATGTTTGGGGCAATACTTGATATCACTTGGTATCACAGAACCTAAAGATTTGTGAACATTGGTTCAGAACCCTCTGGCAGCATGGTGTTCACATAGAAGCGATCGGCTTTCCATCTGTTTGCAAGTCATGAGACTGTACAAAAAGCTTTTGTGTCCATGTAGCCAAGCAGCCATTCATGGAGGGTGTAGAATGTGTGCATTTATTAAGAAGAACTCTGTTCATATATTGCTCTTCTAAGGTGACATATAGTTCTCTCTTCCAAG
Seq C2 exon
GTTTAAAGACCATCGTGGGGGCCCTGATCCAGTCCGTGAAGAAGCTGTCCGACGTCATGATCCTCACCGTGTTCTGTCTCAGTGTCTTTGCTCTAATCGGGCTGCAGCTCTTCATGGGCAACCTGAGGAATAAATGCTTGCAGTGGCCCCCGAGCGATTCGGCTTTTGAAACCAACACTACTTCCTACTTCAATGGCACAATGGATTCAAATGGGACATTTGTTAATGTAACAATGAGCACTTTCAACTGGAAGGATTATATCGCAGATGACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:7
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(11.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(34.0=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:
GACAGAGTTTGTGGACCTGGG
R:
TCCTTCCAGTTGAAAGTGCTCA
Band lengths:
342-1161
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]