RnoINT0131556 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51780703-51782842:+
Coord C1 exon
chr3:51780703-51780941
Coord A exon
chr3:51780942-51782668
Coord C2 exon
chr3:51782669-51782842
Length
1727 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGA
5' ss Score
8.85
3' ss Seq
CAGCTGCGTTGCTCATATAGGTC
3' ss Score
7.45
Exon sequences
Seq C1 exon
AACTTGAAGAATCCAGACAGAAATGCCCACCCTGCTGGTATAAATTTGCTAATATGTGCCTGATTTGGGACTGTTGTAAGCCATGGCTAAAGGTAAAACACGTTGTCAATCTGGTAGTGATGGATCCATTTGTTGACCTGGCCATCACCATCTGCATTGTGTTAAATACGCTCTTCATGGCCATGGAGCACTACCCCATGACTGAGCAGTTCAGCAGTGTGCTGTCTGTTGGGAATTTG
Seq A exon
GTAAGACTCCTTGATGGCTCATCTTCCTACAGATTGCTTTTATTAATTTTATGTTTCACGGTCAAATAAGATGTCAACTAATCGACTATGTTCACCAAAGACACCAATTTTTTTTTTTGCATCGGTTTTTAGCAATGAAAATAGGTTGCTACTTAAACTTAGTACAAAGGATTTAGAGGTTTTAGGTGTATTTTGATTTAGAAATGAATCTAAATTGCTTTTGTACTATAATGATAACTACAGCCAAGCATAATGACACATACCTGTAATCTCAGCCATTGGGAGACAAAGGCAGGAAGATCACAGATTCTAGGCCATCTGTGCTACATAGGGAGATCCTACCCCAAAGCAGACGAAGAAAGAAGCAAAAGCAAAATTAGGGCCATCCAGGTGGTTCAGCAAGAAAGGGAGCCTTCAGCAAGCCTAATGACCTAAATTCGACACTTGACCCCAAAAGGTGGAAGAGAATCTACTTCTCTTAGTTATCCATTGACTGTCACATACATACCATTTTACAGAGATGCTCCCTCAAACACATAAGACAAATAAGTAAGTGAAAACATTATTTAAAAACAGGATTATGCTGTGAATTGTGGGAAAAATATGTGTGTAACATATATACATATTTGCACATACATAACATTTATACATATAGTATGAAATGCTAACTTCTCATGAGTCTTATAACAAATGCCTTAAAGCATAATATACTTCTTAGACGTGAAATATATATATATATGTATATATACATATATATTACTTTATTTCTGATAGATCTCAAGTGAGTCAAATAATAAAGTATGTTCAATGAACACACTGATATATCAAATTCTGCATTAAATATCATATGCACTCCATCCCTTTCTGCCCCTCCTCCACTGACTATCTCAGTGGACAACATTTTGATTTAACCGTTCACTTGTGGAAAAAGAGATTGTGGAACAGGAAGTGTGGAACTGGAAGTTCCTGAAGGAACTTTGTTCAATGTTTAGTGACCTATTAGGTACATACCTTTTTTGTAGCCTGAGGAAATTTCACAAGAAACAACCTGTTTGACTTATAATTAGCCATCGCCTTAGTCTTGAATTGGTCTCCTGTGGTTTATTGTCATGTCTTCAAAAAAAAATTATGATCCAAGTCTTTTTTAGCAAGCCTAAGCTTTTGGTTAGTGTAATAGTTATTCAACTACTACAGTTAGCTGAGACACGGTAGCTCAGCTACACCTATGTTTATTATTGCTTGTGTGAAGCCTCCTTAGCTCCAGTTTCTTCTGCAGAGTCATGAAAAGAGACCAATCTATTATACTTCGCAACTGAAGTCTGTGCTTCTGGGCAAACACTTGGTGATGTTTTAGAGGACAAGAGAGAGAGATCAAGCAAAATGTGTCCAATGCGTTTTTTTTTTCTTTTTTTTTTTTTCGGAGCTGGGGACCGAACTCAGGGCCTTGCGCATGCTAGGCAAACTCTCTACCACTGAGCTAAATCCCCAACCCCGTCCAATGCGTTTTGAGAGTAGCAAAATCAGGGTGTTCATTTCATTATTTGAATGATTAAACCTTAAGTATTGGGAACAATTATAAATTGTGTTGAATATAAAACATGCAAGGGCGTCCATTTGTTGAATGCAAACCAACCTTTAAAATGCAGAATATATGTTTGACCTACCGTTTGTTACATTACCTCCTTTTGTGAGCAGGCATTCTGTAATCAGCTGCGTTGCTCATATAG
Seq C2 exon
GTCTTCACTGGGATCTTCACGGCAGAAATGTTTCTCAAGATAATAGCCATGGATCCATATTATTACTTCCAAGAAGGCTGGAATATCTTTGATGGCTTTATAGTGAGCCTTAGTTTAATGGAACTCGGCTTGGCGAATGTGGAAGGATTGTCAGTTCTCCGATCATTCCGGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 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:
GGGACTGTTGTAAGCCATGGC
R:
GCCGGAATGATCGGAGAACTG
Band lengths:
345-2072
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]