RnoINT0131572 @ rn6
Intron Retention
Gene
ENSRNOG00000005018 | Scn2a
Description
sodium voltage-gated channel alpha subunit 2 [Source:RGD Symbol;Acc:3632]
Coordinates
chr3:51749838-51751300:+
Coord C1 exon
chr3:51749838-51749929
Coord A exon
chr3:51749930-51751027
Coord C2 exon
chr3:51751028-51751300
Length
1098 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTCTCTGGTTTTATTTGTAGGCC
3' ss Score
9.86
Exon sequences
Seq C1 exon
GTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCTGTAATTCCAG
Seq A exon
GTAAGAAGAAGCCGGTATAAGGTGGTAGGCTCCTTATATCTCCAACTGTTTCTTGTGTTCTGTCATTGTGTTTGTGTGTGAACTCCCTATTACAGATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGCTGAGAACGTTCAGAGTTCTCCGAGCATTGAAAACAATATCAGTCATTCCAGGTGAGAGCTAGGTTAAACACAGAGGCTGACTTTAGCTGCACTGGCGCACTGCTCACAGCTTTTTTTTTTTTGGCAAAAGCCTGATTGCTTGTTGCACACTGCAAGATAATGATCAAAAGCAGGAACTGACCCATTCCGGGCTGGATAGGTTTGATTCTTGGCTTTTGACTGGTGGCTTCCTCTCGACGTGTTCTAAATCAGCCTTTGAGTTTAACAAGTTTTGCATGAGGCATTTTACAGTAACAGGCTACCTGGTTTGCATCTTACAGCATCAAGCTTTCCGCATAGAAGCTGAGATGTGAGACACTCGGGCCAATGCAAATTTGATCAGTTAGTTCGAAAACTGGCTATCTCTTTAAGAGGAGATAAGTGGCAAAGCAAGGCAGAGCATGAACGCTGCATGGGACGCGGCTTGCAGATGTCTTCCTTATTTTTGGCCCATTCTCAAGTTTTCAAAGTGCAGACGAAGCTATACCCTTGGAATTCAGTGGTTGCAAGACTTCTCGATACTCCTCTACTCATACAGATTTTTCTTAAAACAAAAAGAAAAGAAAAAAGAAAAACAAATCAGTCTGGGGTTAGAGAGTAAGACATCTGCAAAGAAAAGCAAACTGTTTACATCAGGTTGATCTTCAAGCATGAGTAACACGATCATATCTTTCGCTGTAAGGTGTGTGTGAAAACACAGTCGGCTCATTTCCATTTGGTTTTCTAATGTAAGTTCAGTTTCCATTCATTTCCACCAGCTAGCAGGCTTTTCGTGAAATTTTCATTCATCCACAAACATTAAACTAATATTGTTGGCATCCGCATGACATTTATATTTTTCAGGACAAGCTCATGATATTTTTGTTGGTAAATCCTCTGTTGAATTGTCAGTGATGACTTCCTCTCTCTGGTTTTATTTGTAG
Seq C2 exon
GCCTGAAGACCATCGTGGGGGCCCTGATCCAGTCAGTGAAGAAGCTCTCTGACGTCATGATCCTCACCGTGTTCTGTCTCAGTGTCTTTGCTCTAATCGGGCTGCAGCTCTTCATGGGCAACCTGAGGAATAAATGCTTGCAGTGGCCCCCAGACAATTCTACCTTTGAAATAAATATCACTTCCTTCTTTAATAACTCATTGGATTGGAATGGTACTGCCTTCAATAGGACGGTGAACATGTTTAACTGGGACGAATATATTGAAGATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005018:ENSRNOT00000007069:5
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(11.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(34.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTAACAGAATTTGTAAACCTAGGCA
R:
TCCCAGTTAAACATGTTCACCGT
Band lengths:
342-1440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]