RnoINT0131560 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51798813-51801042:+
Coord C1 exon
chr3:51798813-51798933
Coord A exon
chr3:51798934-51800887
Coord C2 exon
chr3:51800888-51801042
Length
1954 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCCACTCTCACCTATTTTAGACT
3' ss Score
8.92
Exon sequences
Seq C1 exon
AAATTGAATGCAACTAGCTCATCTGAGGGCAGTACGGTTGATATAGGCGCTCCGGCAGAGGGAGAGCAGCCAGAGGCCGAACCGGAAGAATCGCTTGAACCGGAAGCGTGTTTCACAGAAG
Seq A exon
GTGAGCAAACAGTCAGGCTGTCGGGAGCCTTCTCTTGCCTCTCCATTTTTCCTGCCTCTCCATTTTTCCTGTGACCTGTCTGTATCTCTGTCATCTGTCTCTAACCACCCTCGCCTATCTGAATAAGAGTGATTCACTTATTCATTTTGTTTTAAATCTCCAACCGAAGGCATTTTTTCGGACTGTGTGTTTAATGTACATAATTGATTGCTTTTGCTTTTGAAGGTATGAGCCACCCTAAAACATGCTGCTAGTTGGTGTATTAGTCTGCTCTCTGTTGCTGTGATATAACATTCTGGCTAAAAGCAAACTGGCCAGGAAAAGATTTATTGGGCTTAAATGTCTATGTCATGGTCCACCGTGAAGGAAGTCAGCAGCAGGAGAGGAAGTCAGGAATGAAGAGGCAAGAACTGAAGGAGAGGCCATGGAGAAATTCGGCTTACTAGCTGATCTCCTTTCTTAAACAACACATGACCACAGACAGAAGGCAACACTCCACTGGGCTGTGCCTTCTCGCACCAATGATTAATCAAGAAAATGCCCCCACAGAGTTGCGTATGACCCAGTGAGATAGTAGAACTTTCTCCGTTGGGCTTCCCTTTTCCCAGATGATGTGAACTTGTGTTGACAAAAGCCTAAGCAGCACCATTGGCTCTCCGGCCTCCTAAATTAGTGACCAGGAGAGAGAGTTGGTTAGATCAGATTCATAACTGTTAAGGTTTTTAAAAAGGAAAGGAAAAGATAAGCAGCTAAAAGGCATAAGGAAATAATTCGTTATTTGCTGAGTGCTCAGACTGTACTGAATGGGTTGATAGATGGACATTTTGGTCTGACCTTGAATGTCAATCAAAGTCGAATATTTTTGTGAATTTTGAACAAAGACGAAAGATGTCAGAAAGCTGATATATACTGTATACTTTTATACGGGAGCTTTATGATCATCAGAGTACTCTCAAAAGGATTCTTTAAAGAAAACCAAAATTACACCGTTTCAGACGAGGGTCAGTTTATAGCCTGTGACTATAGTGATGATTATCAAACCACATGAAACCAGAGACTCCAAGCTGTTCCTTTGGGCTCGACCAACAACCTGGAGCTAATGCCTTGCACAAGATGCTCGGACTTGGGTGTCATTAATGTTGGTTCATATTTGCTTCTTCAAACTTCATGTTATTAATAAGATTTATACAATTCCCAAGATCTAGCCTCATCTCCGTTTTGTTCCAAAAATTCAGCAATTCAGCATTATCGATGAAATTTTATAAGACTTAAGTATTTTCTGAAACTGTAAAACTTGTTAAAAAAAATCAATCCCACTAAAACAGACATTCCCCAAGGGCAAGGTCATTTACATATTGTAGTCTTATGGTTTTCCAAGCACAGTTTTTTAATACAAACTCTCTTCAATAAATATTGAAAAGGCTTTAACCTAGTGCCTCATAAAGTACACAGAGGTGCTTAGTGCATGGCTTCAGATACTATTCAGGAACAAAACAACCCTATCATTCAATAATAGTGTATATTTACATAAATGCCCGTAATCTTATGGAAAAAAGCATGATGAAATCTTTCACAAATCTTCTGCTTAGATGGAGTTATACTATGCTATAAACTGACTAATCAGAATTCAAATGCATGTCACGTTTATGGAGGATTTACCGTGGGAGAAGGGTTGAATAGAAAGATAAACTGTGGCTTTTACTTTATGTTTTTCTGGATTTGTGTAGTTTATGATGTATTATAATACAATTATACACATATAAGATAATATTTGCTCCTTTAGCAAATCATCTAAAGTCTAGACTGCTGATGTTGATTTCTGTAAGTGGACGCCTTCATTAAAATAAGGTTGTTTGTACTGTGCTAGGAGGTAATCAGGTTCATGTTCCACCTTCCCAGAGATGCAGAAAGAGTAACTGATGACCTTTCCTTTATCCACTCTCACCTATTTTAG
Seq C2 exon
ACTGTGTGAGAAAGTTCAAGTGTTGTCAGATAAGCATAGAAGAGGGCAAAGGCAAGCTCTGGTGGAACTTGAGGAAAACGTGCTACAAGATAGTAGAGCATAACTGGTTTGAAACCTTCATCGTCTTTATGATTCTGCTCAGCAGTGGTGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.780 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=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:
TTGAATGCAACTAGCTCATCTGAGG
R:
TGCTGAGCAGAATCATAAAGACGA
Band lengths:
262-2216
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]