HsaINT0145817 @ hg19
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium channel, voltage-gated, type II, alpha subunit [Source:HGNC Symbol;Acc:10588]
Coordinates
chr2:166164358-166165304:+
Coord C1 exon
chr2:166164358-166164447
Coord A exon
chr2:166164448-166165175
Coord C2 exon
chr2:166165176-166165304
Length
728 bp
Sequences
Splice sites
5' ss Seq
GGAGTAAGT
5' ss Score
8.57
3' ss Seq
GCTTGGCTATTTTCTCTCAGGTA
3' ss Score
7.75
Exon sequences
Seq C1 exon
TTTATTCAATATGCTCATTATGTGCACGATTCTTACCAACTGTGTATTTATGACCATGAGTAACCCTCCAGACTGGACAAAGAATGTGGA
Seq A exon
GTAAGTATAAATATTTTTCAATATTGACCTCCCTTTATGTTTCATATTGTGCTTTTAACACCTTGAGACCTCCTCAATTTCTTTAACAAATCATGCTAGCTACTGTTAACCAGACCCTGATTCAAATTCATTTCTGTCACTAAATGTCTTCTAGGACAAAGCTTGTAGTGGGCTCACTTAGTTGTGTAAATTACTGCAGTAGTTTGACTGCTATTATCTGCAGCCCTTTATCTTCTTTGTGAGTCTTATGTTCTTTTGAAGATCACCAGTGATTTACTAATATCTACTGATAAAAAGTATACCTAGTTTTTATGTTCCTTTTTTAATGACTACCACAGTTCTGTGTTACTAGTATATGTTTGATGGCTTTTAATGGTGCATATTTTATGAAATACAAATGCTTCACTCATTTTTGTATTAATACCTATTTGCTCAAATCGGACTGAATGCCAGTGTATTTCAGATTATGTCTTCATATAGAGCCACATTATTTGGATCCTTTAAATTAATTAATGTGGAAAATGCAATATACATTTATTTACAGTCAATGAGAATGTCTTTTGGAATTTAATGTTTCTTTTTTGACTTAAGCCCCACCTAAACTCTATATCGTAGGGGGACCAACCTGGAAGTGTCTAATTTTTGTTTGCTGTTTATGTCATCTTTAAGATATGTACTTGTAAATTAACCACTAGATTTTTAATGTGAGCTTGGCTATTTTCTCTCAG
Seq C2 exon
GTATACCTTTACAGGAATTTATACTTTTGAATCACTTATTAAAATACTTGCAAGGGGCTTTTGTTTAGAAGATTTCACATTTTTACGGGATCCATGGAATTGGTTGGATTTCACAGTCATTACTTTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531-SCN2A:NM_001040142:4
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=PU(0.7=6.5)
A:
NA
C2:
PF0052026=Ion_trans=FE(16.0=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:
TGCTCATTATGTGCACGATTCT
R:
GCAAAAGTAATGACTGTGAAATCCA
Band lengths:
208-936
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)