HsaINT0145778 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:166012109-166013898:-
Coord C1 exon
chr2:166013744-166013898
Coord A exon
chr2:166012283-166013743
Coord C2 exon
chr2:166012109-166012282
Length
1461 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GTGTAACATTTTCTTTATAGGCA
3' ss Score
8.16
Exon sequences
Seq C1 exon
GCTGTGTACAAAGATTCAAGTGTTGTCAAATCAATGTGGAAGAAGGCAGAGGAAAACAATGGTGGAACCTGAGAAGGACGTGTTTCCGAATAGTTGAACATAACTGGTTTGAGACCTTCATTGTTTTCATGATTCTCCTTAGTAGTGGTGCTCTG
Seq A exon
GTGAGTGAGATTAAGAAAAGGTGATACAGCACTAATTTTTAGAACACTCTAATACTGATGACTTATTAATCCTTTGTTTCATTGTCTTAGTATCCAATGCATTTTTAATTATCCCACCTTGTATCTTCTATAGATTTACTCTATAACTCTATATTTCTGGATTAACTTTTACTATGTATGTAAATATAATTTTAAGAAGCTAATCATTAATTTTTGCTTACTATTAAATAGCCCAGAAAGTGTAGCCCTTCAGCTTATTCATTAACACCAAAGGATGTGAATATTCAATTACTCATTGTTTAATTAAAAAAAGTTATTGGAAGCCCTGGGATGGGAATATATATTCTCTGAGTTCTGACGAATTTTGTTTCTAAATGGTATTTATTATTATTATCTCTTGATGGACAGTAGTAAGTCCTTAGGGACCACTTCTCTGTCTTTTTCCAATTGTGTGCTCACTATTTTTGTGCTACTTAAGAAATAATGAAAGTTGGTAACAATAAATATTGGGCAGCATGCCCAAGAGATTCATTTAAGGATGGGTTTATCTTTATAACAAGGTGTTCACTTCATCAGAATCAATTTATTTTTATAGGAAAATTATTTATAAAACTATAAATAAAACATACAGATAGCATTTTAGGGAAACACTAACACAAAGGAAATACCATAGATAGAAAAAGAGAAAGAAAGAGAGAGAAACAGAGTTTGCCTGATTGAAATGCAAGTGTGTTACAAGTTTAACTTTTTATAATTCTAACACAGACATATATTTACCTGTAATTTTTCTGAAGAAAGAAATATTTTCTACACGCTACTTTAGAAGTCTTTCACCGTTGAAAGGAATGCATACTTAGAAGTGAAACATCGAGAGGTTCATAATAGAAGAATATATATTAGAATCTAAATGAAAAGTAATTTCATTTAATCATTGTCACACTGTATGTCTGTTGAGAAACATAAATTATTAAAAAAATAACAAACAACAACAAAAAAGAAGCAGATGAACCCAACTATTTAGTCAAATTGGAGACTGCGAAGATCAATCACAATTTCTGCTTTACAAAAGCACAAGCTTTCATTATTTCTTCAACCTCCTTTCTATAGCAAAAAAAAAAAAAAAAAAAAAAAGCCAATAGAAGGAAGCAAAATAAATGAAACAAAAGGAATACATAACTTCAAGTTGGGATGGCCACATCAGGATACAACATCAAGAACTATTTCCTGACTAAGTCAAATTAATTCATTGGAATCATACTTTTCTTTTTCTTCCACCAATAGTCTTTCCCCTGATTAAATAAGTAAAAGACCTTTGCGAGGAAAAAAAAAAAGTAACAGTAACTACTGTTTCTCTGCCCTCCTATTCCAATGAAATGTCATATGCATATGATTAATTTTTTAAATAGCTTATGGAGTATAATTATTTTTGAAAGCTAATAATGTGTAACATTTTCTTTATAG
Seq C2 exon
GCATTTGAAGATATATATATTGATCAGCGAAAGACGATTAAGACGATGTTGGAATATGCTGACAAGGTTTTCACTTACATTTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATATGGCTATCAAACATATTTCACCAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285:ENST00000303395:20
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:
PF065128=Na_trans_assoc=PD(19.7=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
GCTGTGTACAAAGATTCAAGTGTTGT
R:
TCAACAATTAAGAAGTCCAGCCA
Band lengths:
328-1789
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