HsaINT0145808 @ hg38
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium voltage-gated channel alpha subunit 2 [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:165295773-165297135:+
Coord C1 exon
chr2:165295773-165296090
Coord A exon
chr2:165296091-165297016
Coord C2 exon
chr2:165297017-165297135
Length
926 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
TGTTGTGTTTTCTTTTTCAGACG
3' ss Score
12.15
Exon sequences
Seq C1 exon
CACTTTCTTATGCAAGGAGCTAAACAGTGATTAAAGGAGCAGGATGAAAAGATGGCACAGTCAGTGCTGGTACCGCCAGGACCTGACAGCTTCCGCTTCTTTACCAGGGAATCCCTTGCTGCTATTGAACAACGCATTGCAGAAGAGAAAGCTAAGAGACCCAAACAGGAACGCAAGGATGAGGATGATGAAAATGGCCCAAAGCCAAACAGTGACTTGGAAGCAGGAAAATCTCTTCCATTTATTTATGGAGACATTCCTCCAGAGATGGTGTCAGTGCCCCTGGAGGATCTGGACCCCTACTATATCAATAAGAAA
Seq A exon
GTGAGTTCTTAGTCAAGTTGCCTTCACTGCCTATTTACTAATTGGTTCTGGGCTAGTCCCAGGGATGATGGTGAAGAAGGCTGGCCTCCTTCCCTCTGTCTAAAGTATCACTAAGATGCTGGATGGGCCTGACCGTGTAATGGACCAATGATCCTAGAAGTCTTTTGGAAGCACTCATTTGAACCTGCATTTGTGAGACAGGCAGAGAACTGGTGAGGCATCCTCCAGCGCGGGAATTAAGGAAGGACAAAAGCCTATTCACCTTCTTGAATACAAATTATATGCTTAAACCAGTGTAAATTGACCCTGATTCCCTAATAATGTTGAGAAGCAAAAACTGTAAACTAGGAGTCTATTTAAATTTTATTTTTTATATTTGCAGGAGTAGTATCTAAATTCCTCTTTATAGTCTCTAGCTCTCCATAAGTCACTTTGATCTTCAGTGGGTTTAATTATTCCTTTATACCATACTTTCTCCTTTCTATTGCTCTCCACAGAAGGAATAATAGCAGGTGACTTGTAGGTGCCAAATAAGATTCTGAGCAAAGAACACACCTGGAAAACCTTGAAGTTCTCATGAGAAAATTTTCTAACCAAAAAAAAAAATCAAAGCCTCAATTTTGTGCTTTATGTGAATTATAAATGCGGTTTTAAAATACTTACATTAAAACTTGATAAAGTTGCTAAGAATTCCTATGGCATTGATCACAAATTTTCTTAATAATCCTCATGTCATTTATCAAATTTAGGAAAGTTTATAGTGCTCAGAAAAAAAAAGCATCTATCTTCATGTCATATGATGGTAATTATTATGTTATACACTATTTTACAGGGCAATATTTATAAATAATGGTTTTACTTTTCTCTTAAAATATTCTTAATATATATTCTAAGTTTTATTTTATGTGTTGTGTTTTCTTTTTCAG
Seq C2 exon
ACGTTTATAGTATTGAATAAAGGGAAAGCAATCTCTCGATTCAGTGCCACCCCTGCCCTTTACATTTTAACTCCCTTCAACCCTATTAGAAAATTAGCTATTAAGATTTTGGTACATTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531:ENST00000283256:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.348 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(12.8=92.5)
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCAGGATGAAAAGATGGCA
R:
AAATGTAAAGGGCAGGGGTGG
Band lengths:
350-1276
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development