HsaINT0145820 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166166833-166168598:+
Coord C1 exon
chr2:166166833-166167105
Coord A exon
chr2:166167106-166168534
Coord C2 exon
chr2:166168535-166168598
Length
1429 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
ATTCCTTTCTCTTTAAATAGGTC
3' ss Score
11.19
Exon sequences
Seq C1 exon
GCCTGAAGACCATTGTGGGGGCCCTGATCCAGTCAGTGAAGAAGCTTTCTGATGTCATGATCTTGACTGTGTTCTGTCTAAGCGTGTTTGCGCTAATAGGATTGCAGTTGTTCATGGGCAACCTACGAAATAAATGTTTGCAATGGCCTCCAGATAATTCTTCCTTTGAAATAAATATCACTTCCTTCTTTAACAATTCATTGGATGGGAATGGTACTACTTTCAATAGGACAGTGAGCATATTTAACTGGGATGAATATATTGAGGATAAAA
Seq A exon
GTAAGATATACTCTATAAACCATTAAGTTGTTTAGTTCTCTAAATATTAAATATTATATATAATGGAAATTATCTCAATTTAGATGTGAATCAAGTGACTTAGACTAATTTAAGATGATTTAATACATATAAAAGAGATATCAAATGATACCTTATTCTATTTTTCTTATCTGTCCATTGATATAGTAAAAGTTCTCATTTGAAAATGTGTTGTCTTATACTCATGTTGAAAGTAATTTCATATTATGCCATATTAAAAAATGTTTATTTGGTAGACATTAATCAGGTTTTTCAGTCATTTTAATAAATAAGTCAGTAGTTTGAACTATTCAGTGTATTCCACTGAAATGTGTTAAGAAGACTGAGGGGAAATAATTTGGCCCTATTTGGTTGATGCAACATATGTATTGAGTACATATGCTATATCTGAAAATAGAGAAACCATTTATCAAGATGAAATAAGAATTTGTGTGCTCCTCAGAAGGTTAAGTAACCCTGATTTAGCCATTCACTTATTCATATTCTAATTAGTCCCTTTAGTGTCATCATTGTATTGTAGTTACCAGTTTAGTTTGATTATATTTAAGGTATGAACATCAGAATAAGCTTATGCCATATACTTCAGCATGATTTCTTAACATTGAGCCCAGCCCCTCTGTCATTTTTCATATGTGTGTGCATGTTTGTATGTGAATATAAAAATACGTATGTTTGCATGTGTGTGCATGTTTTCTGAGATCATCTTTGCAACTTACTGAAGTTATATGTCATGCCTTAAAAATAAAAACTAGATAGCTCTCCATAGCTTAAAAATAAAAACTAGATATACTCAGACAACATATCTCTCCAAAGAAACAAGTTTATTTTCTTCATTTGAAAGGCAGAAATCAAGCAAAAATTTCAAACAAAACACTTATTTACAGTATCATAAGAGGGAATAAATACCTAATCCCACTTCTCACAGGAAATTAAGTTAAAATTGGCGGGAAAAAATGTCTGAATCTATTTTGAGCCTGGGGAGAAAAGTATATGTAAGGTAAAATTTATTTGCATGAAAACACCTAGAAACAACAAGGCTTTCTTCTTTCTTACTTTTTGTGCCCAGCAATAGACTGGCAGCTCTTTCTTAATGTATCCCATGCAATTTGAGCTTATATTTGCAATGAATGCTGATATAAGAATGTTATCATAGTAATTCCTTCTGAACATTTTTCTTTTTAACATAGATTTGCTAACCATTTGTATAATCAAAAATGTTATATATTGATATTTGTTCAATATTGTGAAAAATCTCTTTAGCCATATATATTTATTAGTTTATCCATCTCATTATGATTGAAAACATTTGTGAGCTTTGCCACCTAAACAGGGTGGCTGAAGTGTTTTACAGGATTTTAATGATTCTTTCTATTCCTTTCTCTTTAAATAG
Seq C2 exon
GTCACTTTTATTTTTTAGAGGGGCAAAATGATGCTCTGCTTTGTGGCAACAGCTCAGATGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:7
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(34.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.8=100)
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:
GCCTGAAGACCATTGTGGGG
R:
GCATCTGAGCTGTTGCCACAA
Band lengths:
334-1763
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)