HsaINT0145783 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:165998038-165999776:-
Coord C1 exon
chr2:165999723-165999776
Coord A exon
chr2:165998176-165999722
Coord C2 exon
chr2:165998038-165998175
Length
1547 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
AAAATATTCCCCTTTGGTAGGTG
3' ss Score
6.1
Exon sequences
Seq C1 exon
GCCACATTCAAAGGATGGATGGATATAATGTATGCAGCAGTTGATTCCAGAAAT
Seq A exon
GTAAGTATTCCTTGTATTCTAAGTCTTTTTACAATATTGATCAGGTGGTAAAATTAATCGAATAAAGCATAAACGACCAAATGAAATGATTCTATCTTGATTTAAAATATTTGGGAAAAAGTGTGACAGGTAAATATTCAAGCATAGCAATGTTTATCAGAAAGATCTTACTAAGATAATTCAACACATGAATTATTTTGAAAACCAAAGTAACAAATTCATGTATTTAGTAACTAACAAATATTTTCCTTTTAAATATTTTCTATTTTGTTTCCTATTTATCCACACATTATATAATTAGTAGTAATTTTAGTGTGCGGGACCAAATTTGAAGAAATATATGATTTCTATCATTAGTTGAAATGTATAGTCACCCTCCATATTAGACAGCATGAAAAGTTATGGATATTGTTCTGTCAGCCTTAGATTACTGTGATGATTTCTTTCAAATAATCCTATTTTAAACCATATAAAAGAATGTTTTTATATGATTTTTGCATTCATAAATTGACTGGAGCCTTTACTAATGTTGCAATCACTTCTGTGACCAACAGATTCCTTTAAGTGTATATCACCAAAATATAAACCTATTTTATTTGATTTCAGCCTCTTTCAGGCTCCAAGACCTAAACTGAAATTCATGCTCATTCCAACTTTGCTCTTCAAAACTTTGTAAGATGTAGTATTTTCTATCAACCTTCATCTTTCTATTCTCAAGTCCCATCTGTTTAGTTTATCATCATAAAGAATAACCTCTGTCCCTGCAGTCTTCAACCTGATAGAGTTTGATGTTATCTTTCTTGAAGTGCATTTCAAATAGCTTTAGTTTTATGTTGAATATCATTTTGATAACCTCCAGAGTTGTTTTATTTCACTTTGTCACTTATATTTTGTTTTGTGTGTTTAGTTGGTTTTTAACTTTGTTGCTTTTAGAAGGACATGAATCTGTTAAAAAACTATAGTGACCTTTCAGTCCATTACTAAATTATAAGTAATAGCCCATTTGTTTTAAGCACAATCTAGGAATTAAATAATCAACTGAGGATTTATAAAATGGACTGTCCATCTATGTCTACTTAATCTGAAAAATTCAATAACTGTTACTTTAGGGTAAAGTGCCAAACATCTGAATGAACAACTCATTTCTTATTTGCTACATTATTTCATGCATACATGAATGACTGTTTCTAAACCTAGCCTGTAGATATTTACAGTTTTAAATTTTTTATTAATAATTTTAAAATTACTAAAATTCAGTACCTTAAAAGCTTGCAAATTTAGCACATTACTGTTCAAATGGAAGAATATTATTTGTATTTATAGTTATAAAAATAGATTTTAGAATGTCATAATAGCCATATTTTTCACATGAAAACATCCCTAAAGGCCAATTTCAGGGATGTTTTTTAGAGGTAGTTGATTCAGAAAAAAAAAAAATGCTGACATATTAGTAAGAATAATTTTTTCTATTGTTATGAAAAAGCACCAGTGACATTTCCAGCACTAAAATGTATGGTAATATTTTACAAAATATTCCCCTTTGGTAG
Seq C2 exon
GTGGAACTCCAGCCTAAGTATGAAGAAAGTCTGTACATGTATCTTTACTTTGTTATTTTCATCATCTTTGGGTCCTTCTTCACCTTGAACCTGTTTATTGGTGTCATCATAGATAATTTCAACCAGCAGAAAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285:ENST00000303395:24
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
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:
AAGGATGGATGGATATAATGTATGCA
R:
CTTCTTTTTCTGCTGGTTGAAATTAT
Band lengths:
182-1729
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