HsaINT0145844 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165097252-165100424:-
Coord C1 exon
chr2:165100302-165100424
Coord A exon
chr2:165097525-165100301
Coord C2 exon
chr2:165097252-165097524
Length
2777 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
CCCCTCGCTGTCTCTTCTAGGTG
3' ss Score
13.04
Exon sequences
Seq C1 exon
GTTTCTTTGGTTAGCCTGGTAGCCAATGCTCTTGGCTACTCAGAACTCGGTGCCATCAAATCATTACGGACATTAAGAGCTTTAAGACCTCTAAGAGCCTTATCCCGGTTTGAAGGCATGAGG
Seq A exon
GTAAGAAGAATAGACACTCTAATTATTCATGTCAAAATTACATGTAGGTAATGATTTAGATAGAAAAGGGTGCCATACTCTTCTGATATTTATTTCATAGAATTACAGAATTAGAGCAAAAATCTTAGATATCACAAAGCCTAGCCTTCTGAAACTGGAGTTTATTTAAACAGGCTCTCAGAATTTTGGGAGGACAGAACTGAGACTAGCATCCAGGTCTTCTTGTCACAGTTCAAATATGTTTCTACAACACTCAAAAACCTTGGACTGCCAGTTGTTTCTTTTCATTGCTTACACCCCTTGAAATGACTACTGACTACTGACATTCATCCGTGGTGGGGAGTTTCTTTCTCTCAATAGTTTGATTCCTTCAAAATTACTGGCAATGAATGAAAGGTAAAATGGGTTTTGTGTGCTTTGCTTCTTGAATTAATATCAGTAATAAAAATTATTGCATAAGGAAACAACATTGAATTTTAGCCTCTAACAAATTGCTAAATAACATCCAAAGTGAAGGGTTAAGGTAATTAAGCATTTCAGGCAACCTCCAGAGTTTTTTGGTTTTTTTGTTTGTTTGTTTGTTTTTAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTCAGCTCACTGCAACTTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGTGCCCGCCACCACGCCCGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACTGTGTTAGCCAGGATGGTCTCGATCCCCTGACCTCATGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACGGGCATGAACCACTGCGCCCAGCCCAGAGTTTGTTTTATAGATCTTTTTTTCTAATTGAGCATTCTGAATAAGGTTCACTTTTTCTATAGCAGTTGTATTTTCCTCCCCAGCTCTCTTCCTTAATATGTATATTATGCATCTAAACATAAAATCACACTTTATTATAGATACCACCCATTTGCCATGCCCCTCGGTAGAATTCAGCACAAAGGCCAGTTTTGTTTAATCTGGCTTGTGAGTGCATGTGGATATTTAATTTAGTCTAGGTGATAGGGCTTTCATGTTAGGATGTTAGGAGATGGTTGGTTTGGGGCAATAAAAATATTTCAACCTTGACTTTAAAGTTCACCCATCAGGGAGAATTAAGCCACTCTCCAGACTCTCCAGAATCATTGTAATCAAAGAAATATTTGGTTTTTACATTGTAATTTCATTTCCTTGCTAATGCTAAAGAAAGTTAGACAAGATAAAATTCATAAAAATTACTATACAATTTCAAGTTCTTTTCAAACCAAACTTTTACCATTACTCATAATACTTAAGCTCTCATTTGGTTCCATGTTTCCTATTAACAGTTCATTTATGAGGGGAGATAGCAACTGAGCAAAATTTAAAACTTATAAATTTTCTCTAATCTGAAAAATATTCAAAGTTTAGAATTTTTAATTCAGTCATATAGCACAATTAATATTCCAGATGCAAATTATGATAATGTATTATGCATTTACTTGAAAACAGGAGAACCTGTGGTGGTGTGTACCAAACTTGTCCAACCCGCCTTATTTTGTTATTGTTGTTGTTCTATATTGTTTTAGGCTACTAACAGCCTGAAGCCATGGTTTTTAGTTTCTATCTCTAGTGATAAGTGGAAAAGAGGGATGAGGAAGGGACTTTACGGGCCCAGCCAGAAACAGAAACTAAGAACCCAGTGAATGCATTCTCTCCCTGGCAAGTATAATGCATATGGCTTAACTTCCAAAAGAAACAAAATTCAAGTAGCATAGGAAATGTTTACAATTTTGGATTTCTGGTTTTGATGTCAATTTAAGATTCCTTGGTATTGATTTCTAAAATAATGTTTGCAGTATTTTAAAATAAAACAATACTTTTATTTAACATAAATGATTAACAGAATGGTCCAATATGAACTAGATTAGACAAGAAAAATTACTGTTGACTTTCATAAAGATTTCAAAATACATCTTAATATCTTCTGAATTTAATGAGAAGTGAATGAATTTTCCTCTCATGAAATAGGTCAGCCTGGGTTGATGAAGTAGCATGTGCTCCAAAGTGAACATTTAAGAGATTGTGAAGTAATAATAATGGGAACTTATCCAGTACTGTTACGACCAGATATAAATTCCACTTTTTCCCCTAACTTAATAAACCTTTTTATTGAGATTTACTAACAGGGGGAAAAAGGGACCCAGTAAATTCCTAATCCTGTTCTTCGTAGTCATAAAAAGTTAACTTGATCTGAGAATATAGATTTAAGGCATTTTTAATACTTTGTTTATTTGCAAAGGGTTTGTTTACTGGCTTTTTCAAATTATCATTCATTCATTAACACTCTTGAAAATTAAAATGTATTACTGAAAGATGATTATTTTTTCTGTTGGCATTTAATGCATCTTTCTATTCTTTTTTCCCCAGCATACAAACATTTTCTGACTCCATCTTACTATACCAGGTTTTTAATGATTTCTTTTCATACTGTAGCATATTTTGCTTTCCTTAAAACCTTAGCTCTTTAGTTGTGTCATTGTTTGTTTTCCTTCAAATATGTGCTAGAAAAATTAGAAGAAACAACTTGTCCACCTAGATTTTTATTTAACTCTTTTCAAGCACATATTAATACTAAACAAATACATTGAAGGAATGGTTTCCATTCAAAAGGTTTGTAAGCTATGTTCCCCTCGCTGTCTCTTCTAG
Seq C2 exon
GTGGTTGTGAATGCTCTTGTTGGAGCAATTCCCTCTATCATGAATGTGCTGTTGGTCTGTCTCATCTTCTGGTTGATCTTTAGCATCATGGGTGTGAATTTGTTTGCTGGCAAGTTCTACCACTGTGTTAACATGACAACGGGTAACATGTTTGACATTAGTGATGTTAACAATTTGAGTGACTGTCAGGCTCTTGGCAAGCAAGCTCGGTGGAAAAACGTGAAAGTAAACTTTGATAATGTTGGCGCTGGCTATCTTGCACTGCTTCAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:22
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(17.7=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(39.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- Autistic and control brains
- Pre-implantation embryo development