HsaINT0145976 @ hg19
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167128909-167133849:-
Coord C1 exon
chr2:167133493-167133849
Coord A exon
chr2:167129386-167133492
Coord C2 exon
chr2:167128909-167129385
Length
4107 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGT
5' ss Score
7.64
3' ss Seq
CTCTCCCCACCCTGATATAGGTC
3' ss Score
8.39
Exon sequences
Seq C1 exon
CTCCGAGTCTTCAAGTTGGCAAAATCCTGGCCAACATTGAACATGCTGATTAAGATCATTGGTAACTCAGTAGGGGCTCTAGGTAACCTCACCTTAGTGTTGGCCATCATCGTCTTCATTTTTGCTGTGGTCGGCATGCAGCTCTTTGGTAAGAGCTACAAAGAATGTGTCTGCAAGATCAATGATGACTGTACGCTCCCACGGTGGCACATGAACGACTTCTTCCACTCCTTCCTGATTGTGTTCCGCGTGCTGTGTGGAGAGTGGATAGAGACCATGTGGGACTGTATGGAGGTCGCTGGTCAAGCTATGTGCCTTATTGTTTACATGATGGTCATGGTCATTGGAAACCTGGTG
Seq A exon
GTATGTAACCAGATGTTCATGCATTTTAATTTCTCTGTGGAAATTATTTTGTGATGATGTGATCTATTATTTTTATAATTTTATAATTAATTATATCTACAATTATTAATTGCAAAAGAATAGTGATAATTTTAATACAAGAAAGAACAGGAAAGAGAACGAAATTTTGTATTAGTTTTCCTAGCCAAATAACCCATATTTATATTTTTCAAAATCACTGCCTATTCATTTTAAGGCAAAGGTTTCTATCTTTTTCTCTAATTTTGAAAGTGATGGCATATGCTCTCTTGAAGCTATACTAGTAAATAAAATATAATTAAGTTAATAATAACAAAAATGAAGTTAATAATGGACCAAGGCAAATGAAAGGACTGGTCCCGCACCTTATAGCCATGTGTAAGACTAGCCTCTATAGCAAGGATCAGCACCTATGCCCCACAGACCAAAGCCAGTCCAATGCCTGTTATTGTGTGGCCCTGGGAGCTAAGAATGATTTTTACATTTTTAAGTGGTTAAAATAATCAAAAGAAGAATAAATGACACATGCACATTATATGAAATGCAAATTTTAGTGTTCATAAACTTTATTCAAACATAGGAATGTCAATTCATTTACGTATCTTCTATGACTGCTTTTACATTACAGTGGCAGAGGTGAATAGCTGCCATAGAAATCGTATGCCCAATAAAGTCTAAAATATTTATCATTTGGCCCTTTACGAAAAAGTTTTCCAGCCACTGGCCTATAGCATCGCGTGGACATAGCAATCTGCCTACTTTTTGAATTAGTGTTTTCTTGGCTTGTACTTTTTTTTTATTTTTTTTCTTCCTTATACTGATTAGTGAAAACTTTCAAGCTTACAAGCAGGAGAAAATTGGGATAAAATGCTCTTCTATGAGCCACTCATCTCAATTCTCAAATCTGCCACGTTGACTTGTCACAGTTGGTCAGCTTGACATCAAATCTCTCATCAGGTATCCAGAAGGTGGGATATGGTAACAGCCATATGGTAAGTGCCTTCACTTCCCACTGAGTTGAAAAAAATTACTAAAATATTGTTGTCCTTGTAACCACCATAAAAAGAGGATTCAGAAGTCAGGACAGAAACTTACATTCATCCAGTCACACACTAAATGATACTGTGCCAGACATACACAAAGGCATTTATGCAGCACAAATTCTAGATTTTTACTGCACAAAAAATATACATCCTGGATTACCATTCTATAATTGTTGATCACCCTCAAGTTGTAGTAATAAATAAGCTTCCTAGTTTTATATAGCCTTACAAATTCCTTCCAATATGGAATGAAATGCACATTCTCTTTGTTTCTTCTTCTCTGTTTTGTATTTATAAGCTCCTATAGCAGGATTTGCTTGTGTATTTTTTTTTTTTTTGAGATGGAATCTCGCTTTGTTGCCCAGGCTGGAGTGCAATGATGTGATCTCGGCTCACCCCAACCTCCACCTCCCAGGTTCAAGCAATTCTTCTGCCTCAGCCTCCTGAGTAGCTGAGATTACAGGTGCATGCTACCGTGCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGTTTTCGTCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCAGCCTCCGTCGCCTCCCAAAGTGCTAGAATTACAGGCGTGAGCTACTGCGCCCAGCTGTGCATTTCTTCTTACAAAATTTTGACATAAAATCGTGAAATTGGGAAAGGTATAACTTGTGAAAACATGCCACATCAAAGCCAATAATCACAAATAATTTAAATGTTTATTATTTATTCAGGCAAATTCAAAGGGAAAGGCATTCCCTTGGCTCTCACCACATTTTCCACTCAATATTTTTTAGTATCTTCTCTGTGAAAAGAAAGGTATTTAGGTATTGTTTAGATAGGAAGGCATTGTTTAGGTATTATTTAGGGTGGAAGACCAAAACCAATTACCCATGGTCTAATCCTTGTTTTTAAGATGCTTATTAGGGCACAGAAAAGTGGAACACAAAAGTTATCAGACAAGGAAGAAGTGATGAGTTCTACCAATAAGGTTAAATAAAATGCTTCTGACACTTAAAGAAAGAGTTCTAGATTGAGACTTAAGGGAGGTTTTTGAAGTGGGCCTTTGAACAATGGATAATATAATATTTGATCATGGACACTGGTGTGAGAGTTATGTTTTCCTTTGAAAGGCAATATAGATTTATAGTAAAAAACAGAGGGGATATATTGGTGAGTGTTTCATTCGTGTAGAATTAGTGTTAACTAACTCATATTATTATTCTTTAATTATTAATTCTTGGCAAAGAAAGTATACAGAAGAAAATTCATAAAGTTGATAACCAACTCTTGACTAATGGAGGAACTACCAATATCATAGAATTAAAATTTAAGGAAAAAAATATATTCCTGATATAGCCTTCCACATTAGAGTTATATGCTAAACTGGCTTCTCTTTTTTTATATTTCTCTAATTTATTCTTTTGATCATTTTATTGCCAGTTAATTGAAATGGTTAAGGACCATAGGTTTAGGAAAACATTTGGAAAAATAAGTTTTAGTCAGCTCGGGTCTATATCAGGAAACTTGCGAAGACCATTAATCAAAATGAGACTTTGAATCAAGTATACATTTTATTAATATTTCTTCTCTTGTTTAACATGATAATACAAAGATGATACAAATGGACTTTATTTTGATTTGTGATACCCACTAGGTTATAGAAATATTAGAGACTTATGATTTTTGAAGGAAAGAAAGTTGTCACAGCAGCTGTTCTCAACGAAGTGAGAACCGCATGAGCCACTGCACCCTGTTAAAATGGTTTAACGCTTGAACAGATTAAGGAGACTAAAGCAGTAAAATGGACCCTCAGATCTTCACCAATATTCCTATTAAAACAAATATACACAAACATGTATTTCATAGTGAAATATACTTTTTCATTGACAACTATTAAACCATTTCAGGGATTTTTAGCAATTATCAAAATTGTTCACTATGATTCCCAGACCTCCGACCTCCAGAATTTTCTCCTAAATCAGACTTATTGAGACACACAATTTTAGCCTGCTGTCTTTACTTACATCTCAGAGAAATTGTTTTAGGTATGACCAAAATGAGGGATGAGTACCTTCTCTTCAGTTAGGTCTTACTTCGATTTTTAAAACATGAGGTAGATGATTTGGGCCATGAAAAGACTTACATCAAATGCCAATTCAATTTCCTTTTTTGTTTCCTGGATAAAACAATGTTTAAATATAATTTACAATTTACATGTTTCCTGCCCTCTGTGAACATTTTTTTTTTTTACAATGTGGAGTTGACCTGCACTTCTACTTCAGTGAGAAAAAAAAATAATTAACTCAGAAATAAAACTTTGCTTCAAGAGAATAGAAATTGTCCTGACCTTTTTTGTAATCTCTTCTAGGGCAAACATAATAGGCAATGAAGCCAGCCAATCATAATGCCATTATTGCATGTGAATCAGGTTCAAGGGGCAGGTCCTTTTCTGTGCTTTAAAAGTCACATTAAGCAGTATTCTAGCACGCTTCTTGGACAGAATATTTTATTACAGGAACTTTGTAAGTATTATGTGTTCCATTTGTTAGAACAAGTGACATTTATCTTCTGGTAAAGTGAACAAAGATCTTTAGCACAATAGAAAATAGTCACAATTGTTTTGTTCTACCTGTTTCTCACAGGTAATAAAGAGTAATGATAGATGAATGCTAGGAGAGTTTTTTGGGTTCATAAAAGAGAACTTGATTAAGGCACTACTGCTACAGAAATGAACTTAGAAATGATGTAATGATAATGGTGAGGGATCATTCTCTCTGCTCCCCATGGTAATTCTTCCTGGGTATGGCTGACCCTCTGCTGCTGAGTCTGCAGGGGCTAGTCTAGGGATACAGTGATGAGGAGTCTACCCTCGCCTCTGTCTCTCTCATGTGGTCTTATCCGTGTGTGAAAAGGTGCAGAAATCTTCGTTGCTGGTTTGTATTGTGGCCTATATTCGGAAAAGTGTACTTATTTTATTTTATTTTTTATATTTCCTGTCTCCCTATTTCTCTACCCCCTCTCCCCACCCTGATATAG
Seq C2 exon
GTCCTAAACCTATTTCTGGCCTTATTATTGAGCTCATTTAGTTCAGACAATCTTACAGCAATTGAAGAAGACCCTGATGCAAACAACCTCCAGATTGCAGTGACTAGAATTAAAAAGGGAATAAATTATGTGAAACAAACCTTACGTGAATTTATTCTAAAAGCATTTTCCAAAAAGCCAAAGATTTCCAGGGAGATAAGACAAGCAGAAGATCTGAATACTAAGAAGGAAAACTATATTTCTAACCATACACTTGCTGAAATGAGCAAAGGTCACAATTTCCTCAAGGAAAAAGATAAAATCAGTGGTTTTGGAAGCAGCGTGGACAAACACTTGATGGAAGACAGTGATGGTCAATCATTTATTCACAATCCCAGCCTCACAGTGACAGTGCCAATTGCACCTGGGGAATCCGATTTGGAAAATATGAATGCTGAGGAACTTAGCAGTGATTCGGATAGTGAATACAGCAAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-SCN9A:NM_002977:16
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=0.233
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.1=84.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
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)