RnoINT0131568 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51817508-51819386:+
Coord C1 exon
chr3:51817508-51817778
Coord A exon
chr3:51817779-51818664
Coord C2 exon
chr3:51818665-51819386
Length
886 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGA
5' ss Score
9.14
3' ss Seq
TGGCTATCGTCTTTTCATAGGAA
3' ss Score
8.06
Exon sequences
Seq C1 exon
AACAAATTTCAAGGGATGGTCTTTGATTTTGTAACCAAACAAGTCTTTGACATCAGCATCATGATCCTCATCTGCCTCAACATGGTGACCATGATGGTGGAAACGGACGACCAGAGTCAGGAGATGACCAACATCCTGTACTGGATCAACCTGGTGTTCATTGTCCTGTTCACGGGCGAGTGTGTGCTGAAGCTCATCTCCCTCCGCCATTATTATTTCACCATCGGCTGGAATATTTTTGATTTTGTGGTAGTCATCCTCTCCATTGTAG
Seq A exon
GTAAGACAGGGGGCTGGACCCAACAACCCAAGAGTGCTAGGTGAGTGGGCAAATGGCAGTAACCGCGTACATGGGATGTTCAGGCAGATATGAAACTCCAGGAGACCTGGAGTGACATAGTGAGACACTCTCTCAAAAAACAAATGAAAAGATAAAGGTAAATTAAGAGTAGTTAATACTGATAGTCTATCATTGAAAGCATTAGAGATTTTTTTTAATCATTTCAAATTTTCAGATAAAGCCTGGAATTCCATTCCTTTGTTTGTTTGTTTGTTTTCTTGTTTGGTATTTCATCTGTTCATAAAATTATGTGTTTATTTTTTTTTCTTTTCACTATCTTGTCTCAATTTAAAAACCAATGACTATAATTTGCATTATCTCCTGTACTCAGTCATATTCCTATCCTATAGATAACTACAGCTTTGAATGAACAACTAACCCTCAAACTTAACCCTTTAAAATTATTTTCGTTGTTAATTCATAACTACAATTTTTCTACTATTATGAATTGCAATGTAAATACCTTTGTTTTCGATGGTCTTAAGTGATCCCTATGTTCAACCCCCATGGGTTTGCAATTCATAGGTTGAGATTTAAAATAAAAACCTCAATGATATAACACCAAACATACCAATGTCATTTTACTGAATAAATATCGCACTTTATTTGCATGCACAATACATATATACATATATAACCATAGACATATATATACATTATATATGTATAACTAACTGTATTAGGTAAAATTATTAACAAATGTATATGTATTGGTATTTATTTAATTCTTACATGTGTAGTTCATAAACTGGATAGTACTTATCTTAATCATATAAACTTCTCTTGGCAGCAGTCATTAACGATATTGGCTATCGTCTTTTCATAG
Seq C2 exon
GAATGTTTCTCGCGGAGCTGATAGAGAAGTATTTCGTGTCCCCTACCCTGTTCCGAGTCATCCGCCTGGCCAGGATTGGACGAATCCTACGCCTGATCAAAGGCGCCAAGGGGATCCGCACTCTGCTCTTTGCTCTGATGATGTCCCTTCCTGCGCTGTTCAACATCGGCCTCCTGCTTTTCCTGGTCATGTTCATCTACGCCATCTTTGGGATGTCCAACTTTGCCTACGTTAAGAGGGAAGTTGGAATTGATGACATGTTCAACTTTGAGACTTTTGGCAACAGCATGATCTGCCTGTTCCAAATCACCACCTCTGCCGGCTGGGACGGACTGCTGGCCCCTATACTAAATAGCGGACCTCCTGACTGTGACCCTGAAAAAGATCACCCTGGAAGCTCGGTGAAGGGGGACTGTGGGAACCCATCTGTGGGGATTTTCTTTTTTGTCAGCTACATCATCATATCCTTCCTGGTGGTGGTGAACATGTACATCGCTGTCATCCTGGAGAACTTCAGCGTCGCCACCGAAGAAAGTGCAGAGCCTCTGAGTGAGGACGACTTTGAGATGTTCTACGAGGTCTGGGAGAAGTTCGACCCTGACGCCACTCAGTTCATAGAGTTCTGCAAGCTTTCTGACTTTGCAGCTGCCCTGGATCCTCCCCTCCTCATCGCAAAGCCAAACAAAGTCCAGCTCATTGCCATGGACCTGCCCATGGTGAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:25
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=0.045
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.4=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.1=69.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGACGACCAGAGTCAGGAGAT
R:
GAAAAGCAGGAGGCCGATGTT
Band lengths:
349-1235
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]