HsaINT0145990 @ hg19
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167160748-167162430:-
Coord C1 exon
chr2:167162302-167162430
Coord A exon
chr2:167160840-167162301
Coord C2 exon
chr2:167160748-167160839
Length
1462 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
ATTCTGATTTAATTCTACAGGTA
3' ss Score
8.93
Exon sequences
Seq C1 exon
GTACACTTTTACTGGAATATATACTTTTGAATCACTTGTAAAAATCCTTGCAAGAGGCTTCTGTGTAGGAGAATTCACTTTTCTTCGTGACCCGTGGAACTGGCTGGATTTTGTCGTCATTGTTTTTGC
Seq A exon
GTAAGTACTTTCAGCTTTTTGAAACGGCAAATTTATGAAAATCTCAGGCAGCACAGTGTTCCAATAACAGCAAACCTCTGGGGTCTGATTTTTCCAGCATGGAATGTCTGTATTTAAAGGAAAATGGAAGCTATATGAAAGCTAGTCATTGATAGGCAAATACTAAATTTTTCAAAAAGACTATCTCCCACTCAGAGGTATGTGACATCATTGAGATTGATCATCTTCCTCCATGCTCAGCACTTGGATGGATAGTCTATGCAGTGCCAATTAGGTTTACACTTTTTCCAAGTTCTTGTTTAAAAATGAATAAAACCTATAAGAAGCACACAAAAAACTCAGGCCTTTAAATACAAGTACAGTGCTCTTTATATTACCCTGTATTATTCAATTATTTTATATTTTTGTATTAAAATATAAAAGTATATATTTGTAAAAGAGCTGTCACTGCTTACTAAGCCTAAGATTAATGCATTGTATACACATTATATATACACTCAGTTTATTTTCAAGGAAAATATTACATTACAGTATAATTTTAATTTATTCATAATTGTTACTCTTTTCCCAAATGTATTTATCAGAAAAATGGATTTTTACAATCTCATATCTAGATATTCTATTTTCCGTTAATGACTTTGAATTATCAAAGTAATCCAGGTTCACTGGAGCCACCTAGACAATACAGAAGGGTCTTAAGATTCCTAATATCCGATTCCTTCATCCCTGCCTAACCTCTTTTCCATCAGGCTCCCTCCTTTTGAGGTCACATATGATGGGGCAGTTCCATCTGCTACCTGCTGCTAAGAAAACATTGTGCAAAGAAGACTGCCTCTTCTCATAGGTCTCCTTTTTTTCCTATTGGTACAATTCAAATACTACAAAATTCACAATTTTAAAGTATACAATTCAGTGTTTTTCAGTATATTGACAAACTTGCGCAACATCACCACTACCTAATTAGAGAAGTTTAACAACCCCAAATAGAAACTCTGTACTCATTAGCAGTCACTTCAATTTCCTTCTCTCCCTGGCCCCTTGGAAACCACTCATCTATGTTTTATCTCTATGGATTTGTCTATTTGGATTTTTTTATGAATGGAAATATCAAACAGTATGCAGCCTTTTGTGTCTGACACTTAGCATACTATTTTCAATGTTTTATAAAAAATTAAAAGTCTAAATTACCATAATGTTAAGGGTCCAACAATTGAAACATTTAGTTGTTTACGCATTTAAGTGTATGAATCCAATTTAATAATATATAATATCTGTATTTTGTTTGCATCAAATGAGTCAAATCAATGCTAATTAAATTAAGTTAGTTATGATAGCAAAAAAGACTTGCAGAACTATACATTTAAAATAGAAGCCCCAAACGTAGAAAATACCTTGACTAAAGGCTCAGGTAAGTATCATAGACTCTATCTAAATTCTGAATAATTCTGATTTAATTCTACAG
Seq C2 exon
GTATTTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTATTGAGAGCTTTGAAAACTATTTCTGTAATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-SCN9A:NM_002977:5
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(17.3=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(12.5=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:
TGAATCACTTGTAAAAATCCTTGCA
R:
GGGATTACAGAAATAGTTTTCAAAGC
Band lengths:
192-1654
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)