HsaINT0145788 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:166052852-166054766:-
Coord C1 exon
chr2:166054638-166054766
Coord A exon
chr2:166052944-166054637
Coord C2 exon
chr2:166052852-166052943
Length
1694 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
GTGTGAACTCCCTATTACAGGTA
3' ss Score
8.7
Exon sequences
Seq C1 exon
ATACACCTTCACAGGAATATATACTTTTGAATCACTTATAAAAATTATTGCAAGGGGATTCTGTTTAGAAGATTTTACTTTCCTTCGGGATCCATGGAACTGGCTCGATTTCACTGTCATTACATTTGC
Seq A exon
GTAAGTGCCTTTTTTGAAACTTTAAGAGAGAACATAGTTTGGTTTTCCATCAGTGCTTATGCTTTTAAGAATAGGTTTGCTTTACCTGTAGAATATTTTGGTGTGATTTATACATTCAAACTCTGGATTTCAATTTAGCACAACAAAGGTCTAAGTGGAATTTCACTATAGCATGAAGGCTTTGCAGTAGTTGAAAACTACAATTTTCACACGTAGCATCAGTCAGAAAATTTCACATATGCCACTCTTCCACACACACATGCACAAACACACACACATATGAACACACACAATCTAATGTCAAAACACAAGCATATTTGTAATACATCTGTGAAAATAACTTTAAAAATTACAGCCACAAAACAGTTCTATTGGCTACACAAATTTGCAATGACCTTGCTGATATTACACACAGCTTCTTTTATTGGTTTGGTAAAATAATTGAAAGTAAGTATCTACTAGCATCAAAACGATCTGACAAATCAAACTAAGAGAAGAAAGAAGATACTTGAAATATTATGTTTTTAATATATTAAATTACTGATTTCTAAGACCTGTAGAGGAATACATTCTCTCTGCCTCTTTCTGTTTCTCTCCTGACCCCTTTTCTTTCTTCTTTTCTTCTTTCCTTTTATGGCTCTCTTCATCTCTTTAGTCTGAACATAAACTTCCTTATCCTTATCTCCTATTCATATCCACTCAGTAATATGCACAGTTTATGCACCCCAATGCTTTTTTTTCTAGTGGCAAACTTCCTCAGGAAGAGACCCAGAAAAATAATAGAAAACCATTCCAGACTAAGTGAAAGTAGAGTGTAGAAGGAGGCAGCCCAACAACACTTACCCTCATCCTTCCTTCAGGAGCTGATTTTTTGGCCTCTAACAGTTGTGATGTAGTGGATAGGAGCAGGAGAGGTGGCACTGATACACTCAGGACTCCGAATGTCTGGTCTTAATTTCCTATCTGATCAGGATGAGCCAATTCTTTGCTAGGCTCTCTGGTCACAGCTCAAAAGAAGGCCTACAGGACTTCTATTTCTTAAGAACAAAATGGCAGTAACAATAGGCGCAGCATTGGACCCTCATCAAGTATTGTTCTTAATTTGCTTAACTTTTATTTAAAAGTTACACTAGGAAAATCTTATCTCATATATAAAAGCAGTAAGGCAAACTGCCTTTTCATGCCTAAATTTCTGTTGGGTGATTTCATATATTTTTTTCTAACTAAAACCCTAAACCATAGCCAAGATTTACTTTCTTTTTACAAGTTACACATGATGTTGGTTGCATTGCTTTCCAGAGTGACAACAAGGGTGTCTACTTTATGAAGTTTACATTTAGCTAATGGCCTTAAATTATGTGAACAAAGATTAATGATGGAATCTAATTCCTGATTTACCACTTATAATATTTATCATTTAAAATCACCAAGAAGGTCTTTATAAAAGACCCATGCAAGTAATATAAATCCTGCTAAAATCTTGAATAATTCTGATTTAATTCTACAGGTTTGTAACAGAATTTGTAAACCTAGGCAATTTTTCAGCTCTTCGCACTTTCAGAGTCTTGAGAGCTTTGAAAACTATTTCGGTAATTCCAGGTAAGAAGTGATTAGAGTAAAGGATAGGCTCTTTGTACCTACAGCTTTTTCTTTGTGTCCTGTTTTTGTGTTTGTGTGTGAACTCCCTATTACAG
Seq C2 exon
GTACGTCACAGAGTTTGTGGACCTGGGCAATGTCTCGGCATTGAGAACATTCAGAGTTCTCCGAGCATTGAAGACGATTTCAGTCATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285:ENST00000303395:6
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(16.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
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:
AAAAATTATTGCAAGGGGATTCTGT
R:
CTGGAATGACTGAAATCGTCTTCA
Band lengths:
182-1876
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