HsaINT0145967 @ hg38
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium voltage-gated channel alpha subunit 8 [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr12:51701144-51702914:+
Coord C1 exon
chr12:51701144-51701207
Coord A exon
chr12:51701208-51702772
Coord C2 exon
chr12:51702773-51702914
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:ENST00000354534:8
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(8.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(18.7=100)
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