HsaINT0145990 @ hg38
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium voltage-gated channel alpha subunit 9 [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:166304238-166305920:-
Coord C1 exon
chr2:166305792-166305920
Coord A exon
chr2:166304330-166305791
Coord C2 exon
chr2:166304238-166304329
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:ENST00000409672:5
Average complexity
IR
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
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