HsaINT0145953 @ hg19
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52164313-52168146:+
Coord C1 exon
chr12:52164313-52164467
Coord A exon
chr12:52164468-52167972
Coord C2 exon
chr12:52167973-52168146
Length
3505 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
AGCTGCTGCCTCTCTTTTAGGCC
3' ss Score
9.09
Exon sequences
Seq C1 exon
GTTGTGTCCAGCGGTTCAAGTGCTGCCAGGTCAACATCGAGGAAGGGCTAGGCAAGTCTTGGTGGATCCTGCGGAAAACCTGCTTCCTCATCGTGGAGCACAACTGGTTTGAGACCTTCATCATCTTCATGATTCTGCTGAGCAGTGGCGCCCTG
Seq A exon
GTGAGGTCCAGGGGAGAGTGTGAGGAGGGATTGGCTGGGGAAGGGTGTAGAGAAGCCAGTGGGAAAAGGCTGAGGCCAAAGCCCAGTGGCTCTGAAAACAGATTGGCTGTGGTCCCAAGAAGAATGATCTGTTAAAGTGCTTTAGGCTGCTGCTTTGAGCCTGTGGGATTAGAATCCATACTTGTTCACATTGTGATCCTCTTAGCACTGTCCCTCTCATGTGTCCCCACTGCCTGGTTTACCCCATCCTTAGCAGCCCCTAAAATGAACTTCCCTCTCTTACCTAATACCCCAGATCTCTTGTTCTTTGCTTTTCAGTTACCCAGGATGGGAGGGAGGTGTTATTCCTCCACTTACTGTCCCTTCACAGCCTACTGGATTTAGAGAACCCATGGCATTAGCAAATGTTTAGAGTCAGATCTCTGGTACAAAGGTTATTTATATTCACATTGTCCTAAGTGCTTATTAATCAGTGAAACATACAAGGCCCTGAACACACAGGCTCCTCCACTGCTGAGACTAATTATCTTGGCATTTGCTTTTATTTTTAGCTGGGTTATAACTGAGGAGACCTGGACAGGGTGTGGTGTGAGGGAGTTGCTTGCTGGTTGAATAGTTTTGAGGACTGCCGGGACTAGAGACAGTACACACTTTCCTTAAGGGAAAGGTGAAGAATGCATAATGTTGAAGTATATTTAAAGAAGGTGGGCACATTCATGTAGGTGTGGAATCAAAGCTTAATCTGGAAGCAAAAAAAAAAACATAGCAAGGGAGAAACCCCAAATTCAGTGTTAAAGATTTTGACAGTGACTTGGGAAGTTTCACTGACTTGTGAGGCAGGAGAATAAGAAAAGCTGAGAGAGGCAGCAGTGTGTATTAAAGACAAGCCCAAGGGTGAAGAAGACAGCTTTCATGAAAAGAGGACCATGGGAAGTAAGGGGAAGGTTTACACAGGAAGGTGTCAGGATTAAAGTAGGAGGCAAAAAAGATGGCTTGGTAGCCACTGATCTGAGTGAAGGGGAGCCAGACCACCCCGCCTGCCCCTGGGCCACTTGTTGCATCAACGAGCATTCACACAACACTTCCTGAGGTGCCGCAGAGGCACCCAAAATGACAGCATGGTCTCTGCCCTTAAGAAAAGAGAGGATCAGACTAAGCCGAGTGATTGGAGAAAGGCGTTTTATTATTGCTGTCATTGTTATTCTTCAAATCTAGTGAACAAAAATCTAAACAGTATGACCCATCATTTGGCTCTTCTCTTTCCCATCTCTACAAAAAAGAATAAAGCAGTAGTGAACTAAAGGTTTTGAACTTTCTTTACTGCTCACCTTTGACAGTTTTTATTTGTCTTAATGATTAAGCAAAGGATATTTGGTTCAGTACCTGCAGACCCTGTGCAACAGTAGGCATGAGATTTAAGAATAACAAAGTGGCCCGGTCCAGTGGCTCACGCCTTAATCCCAGCACTGTGGGAGGCCAAGACGTGCGGATCACCTGAGGTTGGGAGTTCGAGACCAGCCTGACCGATATGGAGAAACCACGTCTCTAGTAAAAATACAAAATTAGCCGGGCATGGTGGTGCATGCCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGGCGGAGGTTGCAGTGTGCCGAGATTGCACCATTGCACTCCAGCCTGGGCAACAAGAGCGAAACTCCATCTCAAAAAAAAAAAAAAATAACAAAATGAAGCCACAGCTAAAATGTCCAAGAAGAAACTAGAACGTGGTTACAATGGGACTAAAGAGGGTGGGGATTAGGGCCCTCAGTGACATGAGATCAGTCTTGGGCATCTCACATACCTTGGATTATAGAAGGGATTTCCAACAGATGGGGTTAAGGGGAAACCTGACATGGAAGCTGTTGCCTTTTTGATTGAGCAAAGGGGATTTATTTGCACCGAGACCCTGAGTAGGACTGTGGAACCCATGACCCCTGTCCCCCCCACTGCCTGTTGATGAAAGTGGAGCCGGGCACGGTAGCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGAATCACGAAGTCAGGAGATTGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATACAAAAAAAATTAACCGGGCATGGTGTCTCACACCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGCGAATCACGAGGTCAGGAGATTGAGACCATCCCAGCTAACACAGTGAAACCCCATCTCTACTGAAAATACAAAAAAATTAGCCGGGTGTGGTGGCATGTGCCTGTAGTCCCAGCTACTCGGAAGGCTGAGGCAGGAGAATGGCATGAACCCGGGAGGTGGAGGTTGCAGTGAGCTGAGATCGCACCACTGCACTCCATCCTGGGCAACTGAGCGAGACTCCGTCTCCAAAAAAAAAAAAAGAGAGAAAGTGGAGCACCTGATATCCATGTGCCTCCATTTTGGAAGGTGACGCTGCAGACAACCCAATTCTATTCTTCTGGAGCTGTTCAGAGCAAGCACTTCCCATTGTATCACAGAGGACTTCCTCCCCACCTCCACAGGTTGTCCTATGCTTTAGCAATTCCCTCCTCTTGGCACCATACCTGTATAGTCCACCACTCTGCAGATGGGAATGCTCACACCACCATATAAGGGATTATCCCATTCATGAATGCCAAAGAAATAAAATAGTGATAAGATTTTCTTCACCTGAGTATCTCCCACCTGTATGACCCTCCACCCATACTGTGGTGTCAAGGAACTAAAAGGAGGAAAGATTTTGTCATTTCTTTTATATATAGTATTGGTGAGGATGTGGAGAAATTGGAACACTCATATGCTTCTGGTAGGAATGTGAAATGATGCAACCACTTTGGAAAACAGTTTGGCAGTTCCTCAAAAAATTAAACAGTTACCATATGACTCAGCAATTCCATTCCTGGGCATATGCCCTAGAGAATGAAAGCATGTCTACCTAAAAACCCATACACAGATGTTCACAGCAGCATTGTTCACAATAGAAACAATACACATGTCCATCAACTGATGAAGGATAAACAGAATGTGGTATATCCATATATTGGACTATTACTCAGCCGTAAGAAGGAAAATCTAGAGAGAGAAAGTAGGTGAGTGGCTGCCTAGGGCTAGGGGGTTGGGGGTTTAGGGGGTGATAGCTAAAGGGTGTGGGGGTTCTTTTGGAGGTAATGAAAATGTTCTAAAATTGATTGTGGTGATGGATGCACAACTCTGAATATACTAAAAGCCATTTTAAATGGCTGAATTTTATGATGTGTGGATTGTATCTCAATAAACCTATTAAAACATAAAAAGCCTGTGTAGTCGGGGAGTAAAGCGAAGGAGACAGGGAGCTGATGACAGGCCAGCCCATGTGGGACGGCTCCCTGAGGATAGCAGTGCTCCCTGTGGCCTGCTTGCCTTTAGGCACTGTCATAGGCAGCTGCTGCCTCTCTTTTAG
Seq C2 exon
GCCTTCGAGGACATCTACATTGAGCAGAGAAAGACCATCCGCACCATCCTGGAATATGCTGACAAAGTCTTCACCTATATCTTCATCCTGGAGATGTTGCTCAAGTGGACAGCCTATGGCTTCGTCAAGTTCTTCACCAATGCCTGGTGTTGGCTGGACTTCCTCATTGTGGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-SCN8A:NM_014191:19
Average complexity
IR-C
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:
PF065128=Na_trans_assoc=PD(20.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
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)