RnoINT0131590 @ rn6
Intron Retention
Gene
ENSRNOG00000005007 | Scn3a
Description
sodium voltage-gated channel alpha subunit 3 [Source:RGD Symbol;Acc:3635]
Coordinates
chr3:51556176-51557627:-
Coord C1 exon
chr3:51557507-51557627
Coord A exon
chr3:51556331-51557506
Coord C2 exon
chr3:51556176-51556330
Length
1176 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTATTAATATTGCCTTTTAGGGT
3' ss Score
10.8
Exon sequences
Seq C1 exon
AAATTAAATGCAACCAGCTCTTCTGAAGGAAGCACAGTTGATGTTGCTCCACCCCGAGAAGGTGAACAAGCAGAAATTGAACCTGAGGAGGACCTTAAGCCAGAAGCTTGTTTTACTGAAG
Seq A exon
GTAAAGAAACTCTAACTTATTGAAATCTCCATCCCTACAGAACCTGAATAAGCCTCGTTTAAAAGAGATGTAAAAAAAAAAATGGGGAGGGCATGTTTATTTTGTTTTCCCCATTTCGTCCAGCCTCAGATCTTAAAATTTCCAGATTAGACTACAGCCGAGGCTGTGTCTGGACAAATGAGAAAGTGTGCTAAACACACACGTTCTTTTTGCTGTTTCTTCCTTTTGCTCTTGTTGTCCGTATCATCCAGAATGTAGTATCATTTGAGATGCACAGCATAATGGACTGTCACATCATGGACGTGGCAGTTCCTTCAAAATGCATGAGGAGTGAGATAACTGGACTTATACAAGCTATAGCAATTATACCCACTCTTCCCAGTTGCAATTTTGTCTAATGTGTGCTCTAGCCAGAGCTGTTTGGAAATGGCGCTGTGCTGTAGAGTGTTGGCATGCCGCCATGTGATTCTCCCAGTGACCAACTCATCTTGCACAGAAATCAATAAAGATTTATTGGTTCATTGCGGTTGGATTCGATGTGACAGGTAGTAGCTGGGAGAGAGCAACAGATTAGACAGAAATTGGAAGTCATATGACGTCTAGGAGGCAGAGGGGAAGAGAGCAGAATAAGAGGCAGGGACTGCAAAATGAGTCATAGGTGTGACTAAGAAAAGAAGCAAGGCTGAATAGAAATTAGCTTGAGAAAACTGACAGTGGCTGACACCTAGGGAGACAGTGGGGTTTTCTATGCTTGAAAAGAAGGGAGAGAGTACCCAGGGTCACATGGGAAGATGAGTAAACAACTTACATATCTGTCTTTGCTCCCAAACCAGTGAGATGAAAAGGGACTTTATTTTCCTTAGTGTCCTCAAGGCAGAGAGATTTTAACTTGCATTGAAAAAAAATAAGCCATTTTTTTAACTCAAGCAAATGTATGGAAATTCCATCGATGCTAAATCTGTAAGTTTAAGTGGGACTCATTATATGCTAAATCTATAAGTTTAAGTGGGACTCATTATATAGGAGAGTATTGCAACAAAACTGGGCAGTAAAGCAGCCAGTTAACTATGACATGAACTGGGGTTAGGGTAAGGAAGAAGGAAAAATGTTATTTCTCTTCATATTACTGTTCAAAGTCTATTTTTCCTAATTTATTTTATTAATATTGCCTTTTAG
Seq C2 exon
GGTGCATTAAAAAATTCCCCTTCTGTCAAGTAAGTACAGAAGAAGGTAAAGGAAAAATATGGTGGAATCTTAGGAAGACATGCTACAGCATTGTGGAGCACAACTGGTTTGAAACGTTCATTGTGTTCATGATTCTCCTCAGTAGTGGCGCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005007:ENSRNOT00000006646:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.756 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.3=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.1=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCAACCAGCTCTTCTGAAGG
R:
CAAAGCGCCACTACTGAGGAG
Band lengths:
270-1446
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]