HsaINT0145819 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166165862-166167105:+
Coord C1 exon
chr2:166165862-166165953
Coord A exon
chr2:166165954-166166832
Coord C2 exon
chr2:166166833-166167105
Length
879 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCTTCTGATTTTGTTTGTAGGCC
3' ss Score
9.32
Exon sequences
Seq C1 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTCCGAGCATTGAAAACAATTTCAGTCATTCCAG
Seq A exon
GTGAGAGCTAGGTTAAACACCGAGGCTGACTTTAGCTACAGTGGTGCTACAATCACAGCTTTTGTGCAGAAGCCTTGTTGCTAGTTGCATATTGCAAATAAATATGTAAAAAAGCAAGAATTGGTACATCATTTTTTGGATGGATTTGATTCTTTGCTTTTTACTCGTTGCTTTCTTTAAAACTATTCTAAATCAGCCTTTGAGTTTAACAAGTGTTGCATGAGGCATTTGCAGTAACAGGCTACATGGTTTGCATCCTATAACATCAAGCTTTCCGCATAGAAGCTAGACTAAGAGACATTCAGACTGATGCAAATTTGACAGTTTAGGCCTAAAACTGGCAATCTTTTAAGCTGCAGATAAATGAAAGAGCAAGGGATAGCATGAGTGCTGCATGGGGCTCAGATTTCAGATGTCTTCCTTTTTTTAACCCATACTCAAGCTTGCAGAATTCACAAATATATAACCTCATAATTCATCGACTTCAAGATTTCTTACTACTCTATTCACATAGACTTTTCTAAAACCAATAAGGGGTTAGGGAGTAAGACATCTGCAAATAAAAGCAAAATATTTACACAAGGTTGATGTTTAAGCATGAATAACAAAATCATTCTTTTGCTCTAAAGAGTGTTTGGAAATACACATTTGGTTCATTTCCATTCACAGTTTTCTAATGAACATACAAGTTCTGCTTTCATTCATTTTCACCAGCTAGCAGGCTTTTCATGAAAATGTTATTCAATCACAAACATTAAACTAATATTGTTGGCATTCTGCATGACATTTTTATTTTCCAGGACAAGCTCATGATATTTTTGCCGGTAAAATAGCTGTTGAGTAGTATATTTAAATTCCCCCTTCTGATTTTGTTTGTAG
Seq C2 exon
GCCTGAAGACCATTGTGGGGGCCCTGATCCAGTCAGTGAAGAAGCTTTCTGATGTCATGATCTTGACTGTGTTCTGTCTAAGCGTGTTTGCGCTAATAGGATTGCAGTTGTTCATGGGCAACCTACGAAATAAATGTTTGCAATGGCCTCCAGATAATTCTTCCTTTGAAATAAATATCACTTCCTTCTTTAACAATTCATTGGATGGGAATGGTACTACTTTCAATAGGACAGTGAGCATATTTAACTGGGATGAATATATTGAGGATAAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:6
Average complexity
IR-C
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTGACAGAGTTTGTGGACCTG
R:
TCCCAGTTAAATATGCTCACTGTCC
Band lengths:
342-1221
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
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)