HsaINT1041008 @ hg38
Intron Retention
Gene
ENSG00000168356 | SCN11A
Description
sodium voltage-gated channel alpha subunit 11 [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr3:38871445-38872294:-
Coord C1 exon
chr3:38872193-38872294
Coord A exon
chr3:38871709-38872192
Coord C2 exon
chr3:38871445-38871708
Length
484 bp
Sequences
Splice sites
5' ss Seq
AAGGTACAT
5' ss Score
7.87
3' ss Seq
TTTGCTTTTGTTTCCATAAGGTG
3' ss Score
7.18
Exon sequences
Seq C1 exon
GTCTCTGTGACCACCCTCATTAACTTAATGGAATTGAAGTCCTTCCGGACTCTACGAGCACTGAGGCCTCTTCGTGCGCTGTCCCAGTTTGAAGGAATGAAG
Seq A exon
GTACATTCTGCAGAAGAATGGGTAGAAGTTCAGTTAACAGAGAAAGGTGGAAAGACCAACAGTTCTTTTTGGGCTGAGATTTCCTTAAATTGCCAAGCTTTTCCTGGGTTACTTCCCAGCCTGCCCAGTGCTTAGAATTTGAGGGGTAGAGAAAAGCCTAAGATATACTTTCTACCCTAAAAGCTTCTGTGACAGCCAAGATGAGCTGTAGCTTTGCCTCAGAATCCTGGGGTAGGTGTCCATAAGTCTCTAACACTGTCATCACCAGGGCACTTCTCAAGGTATCCTCAGTGGCAACAGAGAGGACCCATTATGTAGGGAGCTGAGAGCAGGGCTTGTCATGGGGATGGGGCACATGTATGTGGAGATTAAGGACAGAGCTCCAAGAGATCAAGCCCTGCACATCAGGCCCATGCTGAGAAGTTGAAGAGCCTGGTGCATCCTACCCATCTGTTATGGTTTTCTTTGCTTTTGTTTCCATAAG
Seq C2 exon
GTGGTGGTCAATGCTCTCATAGGTGCCATACCTGCCATTCTGAATGTTTTGCTTGTCTGCCTCATTTTCTGGCTCGTATTTTGTATTCTGGGAGTATACTTCTTTTCTGGAAAATTTGGGAAATGCATTAATGGAACAGACTCAGTTATAAATTATACCATCATTACAAATAAAAGTCAATGTGAAAGTGGCAATTTCTCTTGGATCAACCAGAAAGTCAACTTTGACAATGTGGGAAATGCTTACCTCGCTCTGCTGCAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168356:ENST00000302328:20
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(15.3=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCTGTGACCACCCTCATT
R:
GCGAGGTAAGCATTTCCCACA
Band lengths:
353-837
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains