HsaINT0145951 @ hg19
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52162649-52163769:+
Coord C1 exon
chr12:52162649-52163119
Coord A exon
chr12:52163120-52163651
Coord C2 exon
chr12:52163652-52163769
Length
532 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGG
5' ss Score
6.35
3' ss Seq
CCTTTTCCTTGCGTGTCTAGAAA
3' ss Score
9.22
Exon sequences
Seq C1 exon
GTGCTGAACCTGTTTCTGGCCTTGCTCCTGAGCTCCTTCAGTGCAGACAACCTGGCTGCCACAGATGACGATGGGGAAATGAACAACCTCCAGATCTCAGTGATCCGTATCAAGAAGGGTGTGGCCTGGACCAAACTAAAGGTGCACGCCTTCATGCAGGCCCACTTTAAGCAGCGTGAGGCTGATGAGGTGAAGCCTCTGGATGAGTTGTATGAAAAGAAGGCCAACTGTATCGCCAATCACACCGGTGCAGACATCCACCGGAATGGTGACTTCCAGAAGAATGGCAATGGCACAACCAGCGGCATTGGCAGCAGCGTGGAGAAGTACATCATTGATGAGGACCACATGTCCTTCATCAACAACCCCAACTTGACTGTACGGGTACCCATTGCTGTGGGCGAGTCTGACTTTGAGAACCTCAACACAGAGGATGTTAGCAGCGAGTCGGATCCTGAAGGCAGCAAAGAT
Seq A exon
GTAAGGTCCCAGCCTAGAAACAGCCTTGATCCTGTGTGAGAGCAAACAGGGTGCTGTCAGCCTTGGGGATTGGTTCAGCTATGGGCTTGGTAGAGAGATTCTGGAATAACCAATTTACTTGGAGAACTAATTCCACCATCCCAGTATCATTCTAGGCCTTTCCTAAATGAGGTGGAATCCTAAGATGATCCTGGACCCACCTGTGTCACTTCTGGATCATCTGGGTCAGAGGCTGGGATAAGCCCTCGAGTACTTCCCTGCCATTCATCTGAGTTATAGCCCTGAAACCAACCTATAGCCGCATTTAGCTTTGGGTGGGTCATTGCCGTCCGTGAGTAGGTTTTGATGTTATATCCCATCTGGACAGAAGTTTTGGGGGCCCGTGGATATGGTTTGCTTATCGCGAGTTGTAGTAAGAATTCTAGAGAGGAGTCAGAGCTGGCCCCTCATCCCCACCAGAGGCAGAGTTCTCAGTGTGGAGTGGGCATGTTGCCTCAGAGCTGCCTGATCTCCCTTTTCCTTGCGTGTCTAG
Seq C2 exon
AAACTAGATGACACCAGCTCCTCTGAAGGAAGCACCATTGATATCAAACCAGAAGTAGAAGAGGTCCCTGTGGAACAGCCTGAGGAATACTTGGATCCAGATGCCTGCTTCACAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-SCN8A:NM_014191:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.223 A=NA C2=0.575
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
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:
AATCACACCGGTGCAGACATC
R:
GTGAAGCAGGCATCTGGATCC
Band lengths:
347-879
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)