HsaINT1041021 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:166073358-166077801:-
Coord C1 exon
chr2:166077710-166077801
Coord A exon
chr2:166073671-166077709
Coord C2 exon
chr2:166073358-166073670
Length
4039 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
CTGTATTCCTTTTATTTTAGGAA
3' ss Score
10.27
Exon sequences
Seq C1 exon
GTTTGGGCAATTATGAATAAGGCTGCTGTATACATCCGTGTGCAGGATTTTGTGTGGACATAAGTTTTCAACTCCTTTGGTTAAATCCTAAG
Seq A exon
GTATGCAATTGCTGGATCATATGGTAAGAGTATGTTTGGTTTTTAAGAAACTGCTAAACTGTCTTCCAAGTTGCTGTACCATTTTGCTTGCCCACCAGCAATGAATGTGAGCTTCTATTGCTCCATATCCTCATCAGCATTTAATGTTGTTAGTGTTCTGGACTTCGACCATTCTAATGAGGGTGTAGTGCTATCTTATTGTTTTAATTTGCATTTCACTAATGACATATGATGGATGTGGGGCATCTTCTTCTCATATGCTTATTTGCCATCTGTGTGTCTTCTTTGGTGAAGTGTCTGTTCAGGTCTTTGGCCCATTTTTTATTCAGATTGTTCATTTTCTTATTGTTGAGCTTTAATAATTTTTTGCATGTTTGGGGTAACAGTCCTTTATCAGACATGTCTTTTGCAAATATTTTTCTTAGTATGTGGCTTGCCTTCCTATTCTCTTGATAGTATCTTTCACAGAGCAAAATTTTTCATTTTAATGATATCAGATTGTCAATTCTTTTTTTTCATGGATCGTGCCTTTGGTGTTATATCTAAAAAGTCATCACCTGAGTTCTGGTTCCAAAATGGCAGTGAAGAAGCAAGCTGGCACAATTCCTCCTCACCATCACTCCTAGAAAACCAAAAACAAATATATAGCACTGAGAATATCACCAGAAATATTCCAGAACTCAAATATGAAGATGAGACAGTTCCAAGAAAAACAGAGAACTAAAAAGTTATCAACAAATTTAGTCAACTAGGTTTTCTCCAATATTATCTTCTAGTAGTTTTTTAGTTCTGCATTTTACATTTAGATTTGTGATCCATTTTGAATTATTTTTTGTGAAAGGCATAAGGTCTAGGTTCATTTTTTTTTTTTGCATTTGGATGTCTAGTTATTCCAGCAATACATGTTGAAAAGACTATCTTTTCTTCATTTTATTACCTTGCTTCTTTATTACAGATCAGTTGGCTGTAATTATGTGGGCCTTCTTCCACACTCACTATCCTATTCCATTGATCCACTTATCTATTCTTTTGTCAGTACCACACTGTATTGATTACTGCAGCTTTACAGTAAGTCTTAAAGTTGGGTTAGTGTCAGTCCTCCAACTTTGTTCTTCTTCAACATTGTGTTGGCTCTTTTGGGTTTTTTGCCTTTCCAAATAAACTTCAAAATCAGTTTATCAATATCCACAAATAACTGCTGGGATTTTGACAGAAATTAAATTAAACCTTTAGTTCAAGTTGGGAAGAACTAGTGTCTTTGATATATTGAACACTCCTATTCAAAGACATGGACTGTCTCTGCATTTATTTAGTTGTTCTTTGATCTCTACCTCACTCCATATAGAAAATAAATTCCAAATAGATAAAATATTTAAACTTATAACATTAAACCACCAAAATACTAAAAATACAAGAGGGAAAGGTGATACAGATGCATGTGTGTGTATGTATATATTTTATATCCTTTTTCCTACCCCTTACTGCCCATCTCTCTGGATGCCTTTCTAAGCATTATACAGTATCCAGAAGCCAAAGAAGAATTAGATAATCACCTAACAATTTTAACATTTTTAATTAAATCTTTTAAAATCTGTAGCACAAAGCACCATAAAGTCAAAAAATATACATTTTTAAAAGACCACACATCAAAAAATCAAGTGGCTAATATTTTGTCTTAAAAGATGCTATAGATTGAAAAAAATAGAAGGAAAAAATGGGCTGTTTTTAAATAAGCAGTTGCAGGAAAGAAAATAAAAAATAATTCTTAAGTATAAGAAAAATATATTCCACTTTTCTCATAGTAAGACAAATGCAAATTAAAATTATAATATGCTCTCATCTTTGTCCCTGTCAGATTGGAAATATCAAAAATATGATAACATATTATATTGGTGAGGATAAATAGGCACTCTGTTACATTGCTGTCAGGAGAATAAGTTCATACAAACTCCATAGAAAGTAGTTTTGCAGTAACTATCATAAATAAACATTCTGTACAAAGCCAAGTCTACCTTTAAAAATTAATTTTATAAATATATCCACATATATTTGAAAGTATGTGTGTAAAAATGTATTACTTGCAACTTTATTCAATATTAGCTAAAGATTGGAAACAACCCAAATACTCACATTCAGGGAATTGGTTAAATAAATTATGGCACATAACATGCAATGGAAACCCATGTAGCCAGTAATAGGTACGAGTCAAATCTATAAAAATTAAGATAAATGAACTCTAATATACATTTTAAGTAAAAAATGCTGGTGTAAAACAGTTTGTATAATAAGATTCCATTTGAATATGTATTTTAAAATAGAATATGTATACATACACTCATGTTCTAGCATATACCTATTGAATACCTGGAAATATATATGGGAGATAAGTAGTAGTAGTTGCCTCTAGGAAGGGGAACTGGGCCTGGGGAAACAAGGTAAAAAGGAGATATTATACTGCATTTTCTTTTAGATATTTGCATTTATATCATTTACATATATTTTCTATCAAAAAGCTATTTAAAAATAAAAACTATATATATACATCAGAATATTTTATTTCCCTTTTGAGAAAAGTTACTATATTTGTTATCCCTAAACTTTTATTTGCAAAAAATAAATGTTAGTATTTTCCTGATGCCTTGTAGGGGAACCAGAGTTTGTAGACAGAACATTCAGTTTTCATTGATTTACAGACAACCTATTCTTGCAGGTACTAAATAACTGCAGGTTAAGTTCTAAGAACCGCTGAAAACTTCACTTAGTAGACTAAGGGTACAAATTTAAACTTGAGTCCTCCCTTCTTTTGATCATCCACTCTGAAAAATATGGTTATAAACCTCACAACAATGAGAACCTCCTTGAAATTTGAGGTCTCTGTCCCTCACAAAATAATTATGCCTGCAATTTTCTTATTGTAGTTCATATACACCAAAGCTATAATTAACTGTACCATAGCTTGCTGACCTTAATGAGTTAATGCAGTCTCCAAATAAAATTCATGGCCAAGTGGCAGCTTAGGCTCTGGAATATTTTGGCTCAGTAATATCTGTGAAATCTGAGCTCATATTAAATATGCCTTAAAACAATACATTTGGGATTTGGCGTCTGGCATCAGATCAGGTCTGACTCTGCTGTATGGGGTTGACGGTTTTGCCTCAGGCCTTCATAATATGGTTAGCACTATAGGACTATAGAATCAGCAAGAATTTCATTATTGCTTCAGTGAAGAAAAACACTTAGTTTCTATTGAGTTTATGGCACCCTGACTTCTTTCTGATCATTTTTCTTGAAACAGGAGACTCCTGCTGTCTCCTGCACCTACAGCTATCTTCTTCCACCCCCACCTCCATCTAGCAATTTCTTTACAGCCTAGTTTTCCTCTCCTTCTTACTCACATAAATGACATTTGTCCAACCGTGGACTGTCTTTATCTTTATGTGTTCAAGTAAGCCAACCATGCATGGCTAGTGAAGTGAGCAGGACATAGTTCCAGTTGTCTCAAATCTTAGAAGAGGTTAAAGCCCAGTCAAGACAGCAATAACTATTTGATTGGTCATTAAGGTTGGTCACTGCAAACTATCCTGACTATCTTGGCCAGGAATCACTTGTCAGACCTAGAGGGTTAGATTTTATGTCCTCTCAGAGACAATTCCTTTTCCCCTCATCCTTGTTAAATGAGCTATCCTTTGCCTTTATACGCACAGTCTCCATCTTCTGGGTGTGTCACAGACTGAATAACTCATTAGTGATATAGTGTTAATTAGCCTAATGTACTTTGATTAAGGCCATATTTGAACCACTTTTAAAACTCATGGCACAGTTCCTGTATCAGTAAAGCACAAGAATTAATAAATAAGTGATGCTTAACTAAACTCAACACAGAAACCATTTGTGTTAAAATTTTTTCTTTAGAAATCACCTTTCAATTTAAGGAGAAAACAGACTTTAAATCCTCTAGCTCATGTTTCATGACAAGAATTTATTTATATTAACATCTCTTAGTCCACTCTTTAAAATATCTGTATTCCTTTTATTTTAG
Seq C2 exon
GAATTTCATATGCAGAATAAATGGTAATTAAAATGTGCAGGATGACAAGATGGAGCAAACAGTGCTTGTACCACCAGGACCTGACAGCTTCAACTTCTTCACCAGAGAATCTCTTGCGGCTATTGAAAGACGCATTGCAGAAGAAAAGGCAAAGAATCCCAAACCAGACAAAAAAGATGACGACGAAAATGGCCCAAAGCCAAATAGTGACTTGGAAGCTGGAAAGAACCTTCCATTTATTTATGGAGACATTCCTCCAGAGATGGTGTCAGAGCCCCTGGAGGACCTGGACCCCTACTATATCAATAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285:ENST00000303395:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.366
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
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
- Autistic and control brains