RnoINT0131526 @ rn6
Intron Retention
Gene
ENSRNOG00000053122 | Scn1a
Description
sodium voltage-gated channel alpha subunit 1 [Source:RGD Symbol;Acc:69364]
Coordinates
chr3:52432167-52433820:-
Coord C1 exon
chr3:52433582-52433820
Coord A exon
chr3:52432341-52433581
Coord C2 exon
chr3:52432167-52432340
Length
1241 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TAATTTTGTTTTGATCTTAGGTT
3' ss Score
7.51
Exon sequences
Seq C1 exon
AACTAGAAGAATCCAGACAGAAATGTCCACCCTGTTGGTATAAATTTTCCAACATATTTTTAATTTGGGACTGTTCTCCATATTGGCTAAAAGTTAAACATATTGTCAACCTGGTTGTGATGGACCCATTTGTTGACCTGGCAATTACTATCTGTATTGTGTTAAATACCCTTTTCATGGCCATGGAGCACTACCCCATGACTGAACATTTCAATCATGTACTTACAGTAGGAAACTTG
Seq A exon
GTAAGTGTGCAAAAAGGTAATGTGTCTGGTCTTCAACTTTTCTGCTTAAGAAACTGTTTATTATATTTAATAGCACTCTTTCAACCACAATTCCTGCATCCCTAAGGCAATTATACCAGCTGGCTACATACTGCCTTTTTCAAAATAATGGCCTTTAGTATCTGTGCAAAAACTGAGAAATAGAACACAGACCTGTGATAATAATTAAAAAGCCAATAGTGGTGTTATTTCAGAATCTAAGGCCACATTGTTCTTTAAATGATAGCATCATTATATCCTAGTTCTAGATGGTTCAAATAAGGTCATGAGTTCTCTTTCTTATGTGTTCTTTCAAAGAATGATCAACAACACAAAAGCGTCTCCATCTTTTCTCCTTTCAGGGTCTAGGGAGTCTACGTTCTGTTTTAAAGATCTGTTCTAGATACAAATCATGAACTATTGACAGTGCCTACTGCATTTTGTACATAATATGATTAGTAAGCCCATTTTTATTGGAAGTTTCCACTTAATACTCTCCTTTTTTACTTTAAAGCATAAATTATTAAAATGTTTTCCATCGGACTCAACTTAGAAGTCTCAGTTCTTATTTGAAGAAAGAACTATCTAAAGTATAACACACACTTTATATAATATTTTAGAGAATGTTTAGGATTTTGCTGATATGGGTGTTATAAATATACATATGCTATATTGCATTTATATTTTAAAATCTCTACTATTTCTATTCTGTAAACACACTTTTAGTGCATGTGACTAACACTAATTAATGATAGTAATGAGAAAACTGTAAGACAAGATACACATGAAAAATAGCTCTCTGATTTGAAGGAAATAAAGATAAACTTACAAAGAAGATATTTATAGGCAAAATCTTGTTGAGGTTACATGAGGTCTGAAAAGAAGAATGGAATGAACATTGTCAAAATTGTACATTGATGTTCAAATTCTAATTTAGCTATTTCCTAGTTGGTTAATAATAATTGGACATTTTACATGCCTTGAAATGTTGTTTCTTCATCTGTAAATAGAATAATTCCAGTATTTACACTACCTGGTTATTGGAGCTTCTATGAACATAATGCAGTAATACATAATATGTAAACCAGTCTTGTCAAAAAAGCTTGTAGGATACTCCTAGGATCAGTAATGGAAAAAGCAGCATTAGCCTTCTATTTAAAAAATGCGTTATCCTTGAAATTATCATTATCTGATATAATTGAATAATTTTGTTTTGATCTTAG
Seq C2 exon
GTTTTCACTGGGATCTTCACAGCAGAAATGTTCCTGAAAATCATTGCCATGGACCCTTACTATTATTTCCAAGAGGGCTGGAATATCTTTGATGGTTTCATTGTGACACTCAGCCTGGTAGAACTTGGCCTTGCCAATGTGGAAGGGTTATCAGTTCTCCGTTCATTCCGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000053122:ENSRNOT00000083552:11
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(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=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:
TCCAGACAGAAATGTCCACCCT
R:
GCCAAGTTCTACCAGGCTGAG
Band lengths:
357-1598
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]