HsaINT0145993 @ hg38
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium voltage-gated channel alpha subunit 9 [Source:HGNC Symbol;Acc:HGNC:10597]
Coordinates
chr2:166293231-166294662:-
Coord C1 exon
chr2:166294599-166294662
Coord A exon
chr2:166293373-166294598
Coord C2 exon
chr2:166293231-166293372
Length
1226 bp
Sequences
Splice sites
5' ss Seq
AGGGTATGT
5' ss Score
8.34
3' ss Seq
ATGTTCTTTCTCGTGTGTAGTCA
3' ss Score
8.19
Exon sequences
Seq C1 exon
AATATTTTTATTACTTGGAAGGATCCAAAGATGCTCTCCTTTGTGGTTTCAGCACAGATTCAGG
Seq A exon
GTATGTAATATTTGTTTTCTTTTTAGTCTAAAGGCTGAAAGAGAAGGAAAAGAATGTTCAGTCAGTTTGCAAATTAGTCTTTGATTCTATATTGCTTTTTATATATTTCATGGTATTATTTGACTCATTCTGTCCCACAGCAAATCCAGTCTTTAAAATGTTCACAGTTAATGCATACTCTTGAAAGCAAGACTTTGAGACAGTGCTCGAATTAACACAAGACAGAAGTCATATAAATCTTAAGAAGGTAGAAAATGTTACTTCTAGAAAACTCCACCAAAAGTTGGTTGGATAATTTCAGGTCTTCTTTCTGGAAAACGAAGAGTCACAAAGTCTATTTTTCTTTCTACTCCCAAGTTCCACTCATTCTCCAATTAAATGTGACTCATAGGTGACTGAATGTCATGTTTTGGCCACTCTAAGCAAAGGGATTCCTTGGACTTGGGTACACATATTTTAAGAATATTGTATATATAAGAATATTGTATATATTCAACTGTCCATCTTGCTGCTTCTCTCTTACACCAACTTCATTTTGTAGCATCAGCTGCATAAGCTCTTGCTTTTCCCCCTATGCAGACATCTATTCATCAGGCTCTGTGTACACTGGCAACATAGGAATAAACTGGATAAGGTTGCTGTTCCCAGAAGAATCTCAGAATATTGTATTTATTTAATGGCATCAGGAAAAACCAGTCCACCAATTTTAGAAAGAAAAAAGTCTTAAAGCTGCACATTTTTATGAACTTAGACAATTACTATATTTTGACTATTATTGACTCTAATCTATTCCAAGAATTATACAGACAGAAAGAGCTTTGGTAACAGCCTACATATCAATATTTACTGAACCAAGAACTATCACAAAACGTCTGTTGAAAATTTCCATGTTTTAATGATGATGATGCTAATGGCAGCTATGATTTATTAAACACTTTCTATGTGCAGGATGTAAGCTAAGTAATTTGTACACATTATCTTATTTAAACTTATTACAAGTCTTATTTTCTTGAGGTAGATGTTATTATCCTATTTTCACAGACAGACTTATGCCTTGAAGAATTTGGTAAAGTCACTAAGTAGTCAGTAGCCAAATCATGTATTCTTAATCCTTATTCAATATTGTCCCCCTATAGAAGAAACCTTGAGTTTGTAACTTTTCAGTAAGGCTATTTAGCTTGTGTCCTGAAGACACTCTCACCTATAATGTTCTTTCTCGTGTGTAG
Seq C2 exon
TCAGTGTCCAGAGGGGTACACCTGTGTGAAAATTGGCAGAAACCCTGATTATGGCTACACGAGCTTTGACACTTTCAGCTGGGCCTTCTTAGCCTTGTTTAGGCTAATGACCCAAGATTACTGGGAAAACCTTTACCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432:ENST00000409672:8
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(8.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(19.0=100),PF0253517=Zip=PU(11.2=41.7)
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:
CCAAAGATGCTCTCCTTTGTGGT
R:
CTGTTGGTAAAGGTTTTCCCAGT
Band lengths:
182-1408
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