HsaINT0145980 @ hg19
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167163466-167168316:-
Coord C1 exon
chr2:167168009-167168316
Coord A exon
chr2:167163585-167168008
Coord C2 exon
chr2:167163466-167163584
Length
4424 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CTTTCTTTTTCCTCCTGCAGACT
3' ss Score
12.64
Exon sequences
Seq C1 exon
GCCTCTTATGTGAGGAGCTGAAGAGGAATTAAAATATACAGGATGAAAAGATGGCAATGTTGCCTCCCCCAGGACCTCAGAGCTTTGTCCATTTCACAAAACAGTCTCTTGCCCTCATTGAACAACGCATTGCTGAAAGAAAATCAAAGGAACCCAAAGAAGAAAAGAAAGATGATGATGAAGAAGCCCCAAAGCCAAGCAGTGACTTGGAAGCTGGCAAACAGCTGCCCTTCATCTATGGGGACATTCCTCCCGGCATGGTGTCAGAGCCCCTGGAGGACTTGGACCCCTACTATGCAGACAAAAAG
Seq A exon
GTGAGTTTATTTTGACTTCAGTGGTCAGTTTCTGTTGGCTTCCTTCTGTATAAAAATTATTTTAAATTGAGATTAGTGAAATTTAGTGAATAACCATATCATGACCAGAATGTTAAATTAAATATATATATATATATATATATATATATATATATATATATATATATAGGATATTCAGAATCTGTACTTTTTCAAATTTTTCATTGAAATTGGCTCTGGCATTGGCATACTACTTTTAATTTTTTTTTTTAATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTGGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCCACCCCACCACAGTCCCTAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATTTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTATTCTTGTGATAGTTTACTGAGAATGATGATTTCCAATTGCATCCATGTCCCTACAAAGGACGTGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGAGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTGTTTGCTATTGTGAATAATGCCACAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCTTTTGTCAGATGAGTAGGTTGCGAAAATTGTCTCCCATTTTGTAGGTTGCATGTTCACTCTGATGGTAGTTTATTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCCTGGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAATGTTTAAGTCTTTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTGTTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGTGGCGTTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGCTGTTTGGGTTACTGTAGCCTTGTAGTGTAGTTTGAAGTCAGGTAGCGTGATGCCTCCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGCGATGCGGGCTCTTTTTTGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAGTTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTGTAAATTACCTTGGGCAGTATGGCCATTTTCACGATATTGATTCTTCCTACACATGAGCATGGAATGTTCTTCCATTTGTTTGTATCCTCTTTTATTTCCTTGAGCAGTGGTTTGTAGTTCTCCTCGAAGAGGTCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGAAGCAATTGTGAAATTTAGTATAATGTTTAGTATAACATAGTATACATTGTTTAGTATAATTGTTTAGCATAACATTTTTGGACATGACACAGTGATCTGCCAAATTTTATAATCATACCTATTTTTTCCTGCTAATAATTAACTCTCATGTGTATGCAGACCCAAAAATCACTTAAAAGTTTTTAATGAGAATGAAAATTGCTAATTTCAATTTTAAAATACCAACAATTCTTTTTATTAAAATTTCAAGTATAAGGTAACTTGATCTTGCCAATACTATGTAGTATGTTGTGATTTTTCATGTTAGCTCAGATGACCTCCGGTTTATAAAGTCTCCCTGATAATTTTGACAGTCATGTGACCCTGTTCCCTCTTCACTCTCATTCTTCCCCCTTTATATTTTTCTGTATGATATCTGTCACATCTTGCCTTATATTAGTTACTTTCTTCTTTTCATTTTTCTAGGAAGTTCCTTGAATACAAAACTCATGCCTTATTTTTGTTCAAACTCCTTTTCATTACCTGTTATGATATAGTTTCTGACTATACATGTATTAGTCTTTTTTTTTTTTTTTTTTTTGAGACAGAGTCTCCCTCTGTTGCCCAGGCTGGAGTGCCGTGGCGCGATTTTGGCTCACTGCAAGCTCCGCCTCCCGGGTTCACGCCATTCTCCCACCTCAGCCTCCAGGGTAGCTGGGACTACAGGTACCCGCCACCACACCTGGCTAATTTTGTTTTTGTATTTTTAGTAGAGACGGGGATTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACGTTGTGTTCTGCCCACCTTGGCCTCCCAAAGTGCTGGGAACACAGGCGTGAGCCACCACGCCCGGCCGTATTAGTCCATTTTTACACTGCTATAAAGAACTACCTGAGACTGGGTAATTTATAAAGAAAAGAGATTTAATTTACTCACTGTTCTGAATGGCAGGGGAGGCCTCAGAAAACTTACAATCATGGTCGAAGGCAAAGGGGAAGCAAGGCACATCTTAACATGGTGCAGGAGAGGGAGAAAGAGGAGGGAAATGCCGCACTTTTAAACCCATCAGATCTCATGAGAACTCACTCACTCACTATCATGAGAACAGCACTGGGGAAACCGCTCCCATGATCCAATCACTTACCACCAGGTCCCTCCCCTGAGACGTGGGGATTACAATTCAAAATGAGATTTGGGCGGGGACACAGAGCCAAACCATGTCAATACAATTGCAGAAAGAATGGATGAATAATTTTTTAAAAATACAGTCTACTGAGATTTAAGACAAAAAGGATTGTACTTGAGGACTAGGTATTAATTTTAAAATAATTTTCCATGTAAAAGTGAATTTTACATTAAATTGTATTTAGATAGAACTGATACAGTGAAAGGGAGCAGGAAAATAAAAGGACACCTGAAAACAATAGACTCTGATTTGTTTTCTTGAGGGAACGCTGCCGCATACAAATAAAAAGCCTGACTCACAGACTTACCTCCTGAATACGGTGAGAAATGCTTATTGCCAGAAACCCACTGATAACCCTATATAAAATTTAGAAAGTCAGTGTCTTTCAGCTAACACAAGTCATCTTCCTGCCAACCGGAGAAAAATAAGGCTGGGATTTGAACTTTGTCTTTCTGATTTCTAAGCCAATGCTTTAGGTTGCTTTAATATTTTGTTGTTACTGCTGGTTGTTTTTATTTCTTAACTGAATACTAAAGCTATGGAAAAGGACACTTATGGAATGGCTACAATAACATTTCAAGAATGTTTGCTTCTATTCATATCGTTTTTTAAATTACCGTGGTTAGTAAGTGAGGAATCCTCTTAATTTAAGTCCCTTTTAAAAGCTAATATTAGTATTATAACTAAAATAAAGAAATTGAACTCAGTGATTGGAAGGATTCTTCCAACTCTGACGTTCCTTCAACTTAGGAAAATATTTTTTGAAATAACTCATATTTTGGAACATGTGCTGCTAACCATAACAATTGCCAGCAAGTATTAAAATTCTCAAGGTTTTATGATAAAAATATTAGAGATAGCTAGTTTCTATTTGGCTTTCTTAAAATGCAGTGTAATGGAAGGGAAAGAAGTTGTACTTTAAAATAACTTAACCACAGTTATTGTTACTGGTGAAAGAAAATGAAAAATATGAAATACAGTATTTTGAAAGCTCTAAGCAATACATGCTAACAAATAGCTCAATTTTTAAAGTTACTATGAAGAAGTGGACTTGGAGTTCATTGGCCAAGGTGACATTGATAGATGCGTTGATGACATTGGAACCACATTGCTGGAGTCTGATGGCAGTGTTTCTTCAATATAACACTGCCATGTAGAAAGGTAAACTGCTGATATTGATGTGAAAAATTGATATTTTGGATTCTCAATTTCATCCTTTCTTTTTCCTCCTGCAG
Seq C2 exon
ACTTTCATAGTATTGAACAAAGGGAAAACAATCTTCCGTTTCAATGCCACACCTGCTTTATATATGCTTTCTCCTTTCAGTCCTCTAAGAAGAATATCTATTAAGATTTTAGTACACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-SCN9A:NM_002977:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.384 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)