HsaINT0145967 @ hg19
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52094928-52096698:+
Coord C1 exon
chr12:52094928-52094991
Coord A exon
chr12:52094992-52096556
Coord C2 exon
chr12:52096557-52096698
Length
1565 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
ACTTCCCTTTCTTTCTTTAGGCA
3' ss Score
11.6
Exon sequences
Seq C1 exon
CAAATTTCTACACAGTTCCTGGCATGCTGGAACCTTTACTCTGTGGGAACAGTTCTGATGCTGG
Seq A exon
GTAAGTAGCTCACCTAGTTTTATTCTCTTTCCTTAAAATAATGTACCTGTTATTAGTAGGGTCAAAATAGGCAATATGTTTACTTTTCTTTGTGCTCAAGTAGTAGACCTTACAATTGCATCTGACCTATCGGTTGGCATAGATTTTCTTTGTTTCACATTTGTCTATCTAAAGTTGACATTTCACTAGTAAGTGCCTGTGCTTGTAGTCTCAAGCCAAAATGAAAGAATCCAAGGATGAAATCAATAACACCAGATAGCTTACCTGCCTCTTGGGGACTCCTCTCATCCTATAGTACAATAGAGAGCAAAGATACCATCTTAGTGATGGTTATGGATCCAAGGATGACCCAAAATATGCTTGACCTGACAGCATAGAGGAGGAAAAAGAGTAGCAACGTAGTATTTGAGTCCTGATCCTGATACTTCCTGCTCTAAGACCTTTGGCAAGCCATTTAACTTACCTGAGCCTTGGTTTTTTTCATCCATAAAATGGATTTATTTAATAAGCCATGCTCTCTCTTGCTCACAGGGTTACTGTAAGGATCCACTTACATTACATGAAAATGCTTTGTAAACAGAGGGCTTTATAAATGTAGGGTGGTAGTGTCATTTTGCAGAGTATATTGGTCCTCTAAGAACTGGTGTTTTAACATGACCACAATGTCTAGAAATCCATTTAATTTCTGTATTAGACTACTAGAGATTACATTGAAAGAAATATGAGATGAATCTAAAAGCAGGAGAAATGGTGTAACTGAGGTAACTGAAATCCCCCCTTGACTTAGGTTGTCACAGTGAGTGTAAAGAAAACAAATGATTAAGAGGAACTTCTGGCCAGGCGCGGTGGCTCACGCTTGTAATCCCAGCACTTTGGGAGGCTGGGGCAGGCAGATCCCGAGGTCAGGAGTTCGAGACCAGCCAGGCCAACACAGTGAAACCCCGTCTCTACTAAAAATACAAAAATTAGCCAGACGTGGTGGCAGGTGCCTGTAATCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCAGAAGGCAGAGGTTGCAGTGACCCGAGATCATGCCATGGCACTCTAGCCTGGGCAACAGAGCTAGACTCTGTATCAAAAAAAAAAAAAAAAAAAAAGAGGAACTTCTAGCCGTTTGTCATTTGGGATAATAGCTGAGTTAAATTTGATTGAATTGCACATTGATATGAATCTAGAACAGTACTTCTCACACTTTGGCATGCATAAGAATCACCTGGCATACCTCTTAAAAATGCAGATTCATAGATCCCATATCCAGAACTTTTAATTCCTAGTTTGGGTAAGGATGCAGGAATCTGCATTTTTAAAGACCATGCCAGGTGATTCTGACCCTAGGCTGTCCCCAGAAGTTGGTTAGCTGCTTATTTCCTTCTTCTTTTTCTTCTAATTTGTTGGCCTGGCTCTATCAATGGTTATTTATTATCTCCAAGGTCATGGAGTAAATAGAATTATGTTATTTATTATCTCCAAGGTCATGGCTGGGTGGAATTATGTTGAAAAGTCCTGAACTTCCCTTTCTTTCTTTAG
Seq C2 exon
GCAATGCCCAGAGGGATACCAGTGTATGAAAGCAGGAAGGAACCCCAACTATGGTTACACAAGTTTTGACACTTTTAGCTGGGCCTTCTTGGCATTATTTCGCCTTATGACCCAGGACTATTGGGAAAACTTGTATCAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-SCN8A:NM_014191:8
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(10.1=100),PF146251=Lustrin_cystein=PU(47.2=77.3),PF057587=Ycf1=FE(7.2=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(22.6=100),PF146251=Lustrin_cystein=PD(50.0=37.5),PF057587=Ycf1=FE(16.0=100),PF153451=TMEM51=PU(1.2=4.2)
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:
TTCTACACAGTTCCTGGCATGC
R:
TTGATACAAGTTTTCCCAATAGTCCT
Band lengths:
198-1763
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)