HsaINT1041022 @ hg38
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium voltage-gated channel alpha subunit 1 [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr2:166056411-166058688:-
Coord C1 exon
chr2:166058570-166058688
Coord A exon
chr2:166056501-166058569
Coord C2 exon
chr2:166056411-166056500
Length
2069 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
GTTCCTTAACAATAACCTACATT
3' ss Score
-5.77
Exon sequences
Seq C1 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCCATCTTCCGGTTCAGTGCCACCTCTGCCCTGTACATTTTAACTCCCTTCAATCCTCTTAGGAAAATAGCTATTAAGATTTTGGTACATTC
Seq A exon
ATATCCTTTTTCAAGTGATTAATATTAACTATTTGTACATGATCTGTAAGCACTTTATAGCTAAATATCAAATTAAGTTGGGAAATGTCCATATTATATAGTTTTCATCACTCTCATTTTGCATCTTTGTCATATTAGCCTCATTCTTAAAGTTCATTAATCACATAGACATTACTGAAACATGTACTCTTTAACATTTTATATATTATATATAAACATGTATTTATGTACTTTTGTTATCTTTCTAAAAACACTTATATGTATTGAATCCTACAAATCTAAAGTAAGATAACCATGTTTACCTCTACCATCTTTATACAAAGTTTGTGATGGTGTAGAATTTTCAGTGAGCAATGATATGATAACAGAAAAATCTACTTCCAGACTCAAGTTTATCCATAGTTATGATATAAAACACTTCAGTGTATCTTAGAATAAACCTTTAAGTATATTTTCTGTCAGAGAATGTCAGGAGTCTTTGGCCAGTACTTAGTTAATTCTTGAAATTTCCTGATGATTTTTGTGAAGGAAGTACTGGAATATTGGCTGAATTTCAAATTCAAGTCATGAGTTATGATGCTGCCATGCAAAACTGTTTGCTTAGTAAAGACTCCGGAAGTTAATGAGAGAAGTTGGCATATATTTCCAAATGGTCTTAAGGGATTTGGTTTCATGATTCCCATTGGTGTTAAAAAGGACTCCACGACTAAATTCATTTGTTAATCAATTTAGGAAAACAATTCACTTCTGATTGTATCTTGTTTGATAGCTTTGACAATAATAGATATTAAAATACCATTATAATTATCATAAGCTCATACTTTTTTTTAAAGGATTCTAAAATTTGAACGGCCATTCTAATTTTAATATGACAGCAAGAAATTTCTTTAGTGGTATAAATATGCTATTACTAAAATTAAAAGATTTGAAACATAAAAATCATATGATAGGGTTTTTATACTTAGGGAAGTTTCCTTGTCCCAGTTTGTATTCCTAGCGCCATCATGTGGTCATTTGATGAAAACTTTCTTTTTCAATTATGGAAAATTTTTGTTTTGGCAGTAAACTATAGTGGAAAGAATATTGGATCTTAATGTAGGAAACTTATATTCTAGTCCTGGACCCTTTATCTGATTCCTCTAGAGCTTAGTAAGGCCTTATTTCCCTGATTTTTAAAATATAGTGATAAACTAATTTTTAGGGTCCCTTTCAGTTTTATAATTCTGTTATGTCTGTTCATTTGTTTTAGCTACCACTTAGAGTATATTTACTTACGTACCGTGACTGTTCCAAGCATTTCCAATACATTAACTCATTTAATCTGCATGTAGAAATGGTTACATTACAAAATGAGTACATTATTAGCTCCATTGTAGAGAAGTAGGAAGAGATACAAGGCAATGGCACAGAGAGGTTGAGTCTCTTGGCCAACATCACTTTGCTATGTTGAATTTTAATTACATTCCCATCATGTTAAGTGTCAACCTTCAAGAATATTCACTTTTAATGTTATCGAATCCTGCTGCACTTGTATAAACTCAGTCAAAATAGAGCAACCCAACAATTAGCATCGTGCTGTACTTTGACTACAAATTGTTTTCATGCGTTGAACTGTGTTGGATAAGATGTGTTTAAGAAATTACAATATTGCAGATAAGTGGCCTTCCTCAACAATTTACTAGTTTATTCACCTGAATGAGCTCAAGTCAATACTTTCTGCTGAAAAACTGTGCAACTCCAGGTAGCACAAAAATAGTCTTCCCACTGAAGTTCTCTGGGAGGTGAATATATTGATTTAATAATAGTTGTAAAAACAACACCTTATACTGATATAATGCTTTCATATACATTACCTCATTTAATCTATACAAATACTCAGTGAAGGTGATATTATTACCCACATTTTACACATGAAGAAATTGAAATGTAAGGAGATTAGAAGACTTGCCCACAATGCATTTATCCCTGAATTTTGGCTAAGCTGCAGTTTGGGCTTTTCAATGTTAGCTTTTTGTAATATAACACTTGGATTTTGATTTTCTTTTGTGTGTTCCTTAACAATAACCTAC
Seq C2 exon
ATTATTCAGCATGCTAATTATGTGCACTATTTTGACAAACTGTGTGTTTATGACAATGAGTAACCCTCCTGATTGGACAAAGAATGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285:ENST00000303395:4
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.7=6.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
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