HsaINT1041009 @ hg38
Intron Retention
Gene
ENSG00000168356 | SCN11A
Description
sodium voltage-gated channel alpha subunit 11 [Source:HGNC Symbol;Acc:HGNC:10583]
Coordinates
chr3:38870691-38871708:-
Coord C1 exon
chr3:38871445-38871708
Coord A exon
chr3:38870745-38871444
Coord C2 exon
chr3:38870691-38870744
Length
700 bp
Sequences
Splice sites
5' ss Seq
GTGGTAAGT
5' ss Score
10.36
3' ss Seq
TTTTTCTGCTTTTGTTGCAGGCA
3' ss Score
11.3
Exon sequences
Seq C1 exon
GTGGTGGTCAATGCTCTCATAGGTGCCATACCTGCCATTCTGAATGTTTTGCTTGTCTGCCTCATTTTCTGGCTCGTATTTTGTATTCTGGGAGTATACTTCTTTTCTGGAAAATTTGGGAAATGCATTAATGGAACAGACTCAGTTATAAATTATACCATCATTACAAATAAAAGTCAATGTGAAAGTGGCAATTTCTCTTGGATCAACCAGAAAGTCAACTTTGACAATGTGGGAAATGCTTACCTCGCTCTGCTGCAAGTG
Seq A exon
GTAAGTACAGTCAGTATGTTTTTCACTCTGAGGAGAAAAACCTTCAGAGAATCATGAATTGTTTCTCAGCTAATAAAAATGCAGTGACTCCATTGTGATAATAGAAGCAAATCCTAATTCCTTATATGAAAGCCAATGCCTTCTGGAATTGTCCTCTACTGAGCATCTGCAACTTCATTGACTGCTGAGCCTCAGCTTCCTAGTGATGCCCCTTTAAGGATCTGTACATCTCACCTTGTCCTGTATGGCACCTTGCTGGCTCTCCACATCTCCAGGCAGAGAGGAGTGGAGCCTCAGGTGTAGGTCATGACACTTTGAACAGTTCCCTGTTTAAAGCACAGTTGCCAGGTCTTGAACAGGCAGTGCAAATACATATGGCATCAGAAAAGAACCCTTTAACTCTTAGCCAGTCTCTTTTCAGCTGTTGGGCCACAGCTTCAGCCTCTCTGGTAACTTTTAAGGTGGAAATTTCTTGTTTTTAAACTTTGTATCTTGTACAAATGAAGAAGAAGAAAAAAATCCAAGACACACACCCTTGAGTTCCCTTCTACTGTTCTTTTATTTGAGCATCCTGTCCTAGAAGGTTGGGGTATCATCTTATATATTCAGCCCACTGGGCCTCACCTGCTTTTCCATGCCATGTATCTGTTGATGGCAAGTCTACATTTGTATTATTCATGTTTTTCTGCTTTTGTTGCAG
Seq C2 exon
GCAACATTTAAGGGCTGGATGGATATTATATATGCAGCTGTTGATTCCACAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168356:ENST00000302328:21
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(40.3=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.9=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:
GTGGTGGTCAATGCTCTCATAGG
R:
CTCTGTGGAATCAACAGCTGCA
Band lengths:
318-1018
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains