HsaINT0145821 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166168535-166170271:+
Coord C1 exon
chr2:166168535-166168598
Coord A exon
chr2:166168599-166170129
Coord C2 exon
chr2:166170130-166170271
Length
1531 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TTCCTCTAACCTAATTATAGCCA
3' ss Score
4.57
Exon sequences
Seq C1 exon
GTCACTTTTATTTTTTAGAGGGGCAAAATGATGCTCTGCTTTGTGGCAACAGCTCAGATGCAGG
Seq A exon
GTAAGTGATGCTTCCTACTGAGTTTCAGTCCACACTGCTCCATCAGTGTCAATAACCTGCCACCTCCCACTCATCCAGTCCCACTCACTCCTCACTCAAAACCCTCCATAAATTCTACTTCACGGTGACTCTCAGAATAGCCAGGATAAGTGTAGATTCTCACCTCTTTCACACAGTCATTTACTGCAATTATTTTTCTATGCTAGGTCACATCTAATCTTCCAAATTAGTTCAATGTAAAATAGAGAATAAAGCAGTATAATATGCATCTGAAGCTTAATAGAATTCTTAAGCACATACTTTTTATAAGTGTCATATTTTATATATACTAATGTGTTCTCCATAGCTTAAAATGTAAGATCTCTGAAAATAATGTTAATATCTGAGACATGGGGAGTATTTAGCATATTTTAGCAAAGTGGTTACAAACATAAACTGGAGAGTCTGCATAGAGTCAGACTTTGACTCCATCATATAATCTCATTTCTTCTTGCCTTCGTTTCCTTATATGACAAATGGGTATAATAATAGGGTTTTTGTGATGATGAAGTGGATTAATAAATGTATAGCTATTTAGATCGCTCAATAAGTGCTTGTAATTGTTATTATTGGGATCATGCAAATGTTTGCTATTAAGAAACATGGAGCTAAATCCTAGGAAAATTTAAAAACACAGTTAATTTTCTTTATTTAGCAAGATTTTAGAGCCACACACAAAAGTCTAATGCACTTTCTTTGGACGATGATACTGTGGACATTAGTAGCTAATACCTGTAGCAAAATTCCCAGTGATAATAGGCTTTCCATTTGGCTCCTACGATCAGTGCTATGCTGCCTTTATCTTCAGATTCCAATGATAAGTAAATCAATTGATTTTCATTCCTTGTTTGTACTGTACTAAATGCGTTACATACAGTATCTTCTTCAATGTTTGCAAATTTGTGAGACAGGTTCTCTTATTAGCCCATTCTCACATGCGAGGTGCCTGAAGATTAGCAAGTTAAGTAACTTGCCCAAGATCGTTCAGCTCAGAAGTGTCAGGCAAGACATTGAAGCCAGGTCTGCTTGATCTTCAAGGTCCTCCTATGACATTTTTACCACACAGTGTCATTCACTCCTTGCAGCATGCCCCACCTATCCTTTTCTCACTTCTTTACCCTGTTCCCACACTTACACACATTTCTGCCTCAAGACATCCTCAGTGAAAATCAACTTTTTCCTTACAGACTTTTTTAACTGCCCTTAAGTCCCAGAAGATATTAATCATGATATGATTGCTTTTATATGGAGACATAATAAATATAATAATGACAATTATGAATCACAGAGGAATCCACAAAGTAGACCTTATAGATTCTGTTATTATATAAATCAGTCCACTTAGTGCTGAGTTAAGTACTGGGTAAGGTGAGAGAAATCGGCTTTTTTCTAGTGCCTGTATAAAACAGACATTGGCATATATTAAAACAGGAAAACCAATTAGCAGACTTGCCGTTATTGACTTCCTTTCTTTCCTCTAACCTAATTATAG
Seq C2 exon
CCAGTGTCCTGAAGGATACATCTGTGTGAAGGCTGGTAGAAACCCCAACTATGGCTACACGAGCTTTGACACCTTTAGTTGGGCCTTTTTGTCCTTATTTCGTCTCATGACTCAAGACTTCTGGGAAAACCTTTATCAACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:8
Average complexity
IR-S
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(12.4=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGGGGCAAAATGATGCTCTG
R:
CAGTTGATAAAGGTTTTCCCAGAAGT
Band lengths:
190-1721
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)