RnoINT0131574 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51754157-51756295:+
Coord C1 exon
chr3:51754157-51754220
Coord A exon
chr3:51754221-51756153
Coord C2 exon
chr3:51756154-51756295
Length
1933 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
CCTCTCTAATGTAATTACAGACA
3' ss Score
4.41
Exon sequences
Seq C1 exon
GTCACTTTTATTTTTTGGAAGGACAAAACGATGCTCTGCTTTGTGGGAACAGCTCGGATGCTGG
Seq A exon
GTAAGTTGTGCTTCCACTCGACGCTCAGTCGACCTTAATCTGCCACGTCCCACACACCTGGCCCCTACTCAGAGCTCATTCAAAGTCCTCTATAAATTCTCCTTCATGCTGACTCACAGAATAGCCAGGATAAGTGCAGATTCTCACCTCCTTCACGCACAGAGAAGTGGCAATCATTGTCCCATACTAGGTCACACCTAATCTTCTAAATTAGCACAATAGAAAGTAGATACTCAGAGCCAGTGCATTAGAATTCATAATCACAGACAAGAATGTATGATTATTTATTTAAAGCTAATCCGATCTCCATGGCTTAAAAATTAAAAAATCCCTGAAGATCATGTCACCTTGAAACACGAGGTGACAATCTGCCCACCACGTTTCAGCAAAGCAAAATATATCAAATAGACTGGAGTTGCCTCATACATTAAAATCCTGACTCTACCATATTCTGTTGTTCTGCTTGCCTTGTTTTTCCCATGTACAAACTGTCACTATAATAATTCCATTGACTAAATATGTTAGTGAATATATGGCTACAATAGAAAATTTTTAGCTATGCCCACCTCTGTTTAGAATTCATAATCACAGACAAGAATGTATGATTATTTATTTAAAGCTAATCCGATCTCCATGGCTTAAAAATTAAAAAATCCCTGAAGATCATGTCACCTTGAAACACGAGGTGACAATCTGCCCACCACGTTTCAGCAAAGCAAAATATATCAAATAGACTGGAGTTGCCTCATACATTAAAATCCTGACTCTACCATATTCTGTTGTTCTGCTTGCCTTGTTTTTCCCATGTACAAACTGTCACTATAATAATTCCATTGACTAAATATGTTAGTGAATATATGGCTACAATAGAAAATTTTTAGCTATGCCCACCTCTGTGGTGATGTTTGTAATTAAGAAACATTACATATGAAAACAAAGCCTGGGAAAGTTCAAAGAAACATTTATCTTTCCCTACTCGGTCAGATGTTAGAAGAAAAAAAAGTCGTCAAACATCTAACATTTTTTTCTGTGATAACCTTCTAGACAATGCAAGCGATACCTTTACCAAAATTCTCCTTGATGATATGGTTTACAATTGGCTCCTATGATTAAAAACAGCAGACTTTATCTGTGATTAGATCTTCGATAGGTGAGACAAGCATTGTAATCCCTCCTGCACAGCATTAAATGCTTTCCACTCATAACGAGTGTTTGCATGTTGGTAGTTTTTCCTTGTTGTTTTGTTTTTGTTTTGAGGCTGGTCCTTTCATTAGTCCATTCTGGCCCATGAGGTTCCTCAGGGCTAGCAAGGTCAGGAAATTAGCCCCAGTTGAATCAGCCCAGAAATAATGTCAGTCACAACACTGAAATAGCTCTGCTTACTTAGCAGGTAAGGTGATTCTGTGGGATCCACGCTGTTCAGTGTCATTCTCTCCTTTCAGGATGCTCACTCCTGGCTGTTATATCTTCTTCTCTCTGCCCTAGTTTCCTAGTTACACACATACACACACACACACACACACACACACACACACACACACACACACACACACATATATATATCCTTATATCCAAGGATATATATATCCCTTATATCCCAAGACATCTTCAGTGAAAATCACTTATATTTCTATGGATTCATTTATCTGATCATGTCCATTGTCCCCAAAGAAATTGTTCAAGATATGATTATCTGATGTGGATGTGTGGTAAGCATAATATTACAATTAGGAATTAGAGGAGCCTACAAGTCTTGGAAAATTCTGTCAGTCGCACAGGAAAAGCCACCTAGTGCAGTATACATAGTAAATTAGTCGGGAGATGTAAGATTTCCATAGAGCCTGTAAAAATGATTCACATCAAGCAAAATGGAAAAAAAAAAGACCAAGGAATTCACAGATGCTGAGTTCCCTCCTCTCTAATGTAATTACAG
Seq C2 exon
ACAGTGTCCAGAAGGATACATCTGTGTGAAGGCTGGGAGAAACCCCAACTACGGCTACACAAGTTTTGACACCTTCAGCTGGGCCTTCTTGTCCTTATTTCGTCTCATGACTCAAGACTTCTGGGAAAACCTTTATCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:7
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(7.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=100),PF0253517=Zip=PU(12.6=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAGGACAAAACGATGCTCT
R:
CAGCTGATAAAGGTTTTCCCAGA
Band lengths:
191-2124
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]