HsaINT0145806 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166221653-166223881:+
Coord C1 exon
chr2:166221653-166221773
Coord A exon
chr2:166221774-166223726
Coord C2 exon
chr2:166223727-166223881
Length
1953 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TTTTTTCCCACATATTTTAGACT
3' ss Score
8.79
Exon sequences
Seq C1 exon
AAGCTAAATGCAACTAGTTCATCTGAAGGCAGCACGGTTGATATTGGAGCTCCCGCCGAGGGAGAACAGCCTGAGGTTGAACCTGAGGAATCCCTTGAACCTGAAGCCTGTTTTACAGAAG
Seq A exon
GTAAGCAAAACAATAACATATGTGGTCTTGAGTATCCTCTTTTCTACCCATTTTTTCCTATTTATTTAAATGTCTGTTTATTTGTCTACCATCTATTATCTATCTATCTGTATCTATCTATCTATCTATCTATCTAGTAATCATCTATACCTATCCAACAACTGTACATTTATTTGTTTTTTTTTGCATTTGCTGTTTGAAAAAAAATGCAACTTTTTAAAAGGCAAAGTTTAATTTATGTAATTAGATATTTTCATTTTTATGAATCATTTTTAACTCTAAGAAATTATTAACTGGCTTTTCTGTGGCCTTCTAAAATATCTTACAGGAGAGAAAGCCAAATCACACACATCTCTCTTTAGTTTAAAAATTCAATAAATAAGAAAGTGAGAGAAGTAATTTATTATGTACTATTTTGTGATATTATAATGGGTAATAATTGATAAGTGTACATTTAAATTTGTCCTTGACTGAAACAGCTCCTATTTCAGTCAAGGTCAAATATTTTTTATTATTTCTGAAAAAAGATAGATCATAAAAATGCCAAAATATACTATGAGTCATATGATATGGGGCAATATGTCACTGGAGTAATCGCAAAAGGATTTTCTGAAGAAAGCTAAAATTATGTAATTTGAGGTATGGATCAGTTATATATTGTAATAGCAATGCTGTGTATCAAACCACCAAAAACCCTGGGCTCTAAGCTGCTTTTCTAGTTTTGACTCCTATTTCCTTCTGTGTAACTCACAGACTTTCTTGTCACTAAGTTTTACTTGTATCATTGTTTCTCTATTCTTACAGCTTCATTTTCTACATATGTCTCTTATATATCCTTCAAGATCTAGTCTCAAATCCATTTCCTCCATAAAGCTCAGAAATTAAAGTTTACCAGAAAACTCTCATAATACTTTGTTTTGTGATAATTGTTGCTTTCCATAACTATAGAATTGTAGACAAATTGCCCCAACTTAAAATGTACATTCTTTGAGGACAAGGCTATGTTTTACATGTTATAGTATTACAATTTGTTCTATGCAATTTTTTGACAATAGTAGATACTCAATAAGTATTTGTTGAAGAGCCTTTGATCTAGCAATCCAGAAATTATACAAAGGTGTTTATTGGATTGTTATTGATAATGGCCAGATTTAAAGCAAACGAAGTATTCAATAATGGTGGAATTGGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCAGGCAAACATGGTAAGACCCCATCTCTACCGGGCGTAGTGGTATGTGCCTGTAATACCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGACAGAGGCTGCAGTGCATGAGCCGAGGTCAGGCCACTGCACTCCAGCCCGGACAATAGAGTGAGACTCCCTCTCAAAAAAAAAAAAAAAAGGTGGAATAGTTATATTAATTATAGTAATCATATTTAGAGAAATATTATGAAATCTTTCACAAATTTATTTACTTATAATAAAGATGGGAAATAGTTATACCATTAAGTGAACTAATCAGAATTCAAATATGTAAAGTGTCCATATAGAGTGGAATTACACTCATAGGATAAGGACAGGATGGAAATACCAACTTTTGGTAAGTTTATTTTCTTTTTGGTTCTTCTATTTTTTATATATTGTGTTTTTGTAATGTAATCCATTATAGTAGTGCTATAAACATAAAAATAAATATTTATTAAACAAATGATTAAAAAGCCATATAGATGATTTTAAGATAGCTTTTGTAAGCGGAAGCTATCTTAAAAATTAATGTTATTTACAATGTATTATCAGGTAATAATGTAAATGAATCTCCCACCAACACAAATATACCTAATCAAAGAGTAATTTTTTGTCTTCATTTTTTTCCCACATATTTTAG
Seq C2 exon
ACTGTGTACGGAAGTTCAAGTGTTGTCAGATAAGCATAGAAGAAGGCAAAGGGAAACTCTGGTGGAATTTGAGGAAAACATGCTATAAGATAGTGGAGCACAATTGGTTCGAAACCTTCATTGTCTTCATGATTCTGCTGAGCAGTGGGGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.780 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTAAATGCAACTAGTTCATCTGA
R:
TGCTCAGCAGAATCATGAAGACA
Band lengths:
264-2217
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)