HsaINT1041026 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165139476-165140998:-
Coord C1 exon
chr2:165140651-165140998
Coord A exon
chr2:165139609-165140650
Coord C2 exon
chr2:165139476-165139608
Length
1042 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATA
5' ss Score
3.13
3' ss Seq
CATCAGTATTTGGTTTGCAGGGC
3' ss Score
5.44
Exon sequences
Seq C1 exon
TCTCTCTTGAGTATCCGTGGCTCCCTGTTTTCCCCAAGACGCAATAGCAAAACAAGCATTTTCAGTTTCAGAGGTCGGGCAAAGGATGTTGGATCTGAAAATGACTTTGCTGATGATGAACACAGCACATTTGAAGACAGCGAAAGCAGGAGAGACTCACTGTTTGTGCCGCACAGACATGGAGAGCGACGCAACAGTAACGTTAGTCAGGCCAGTATGTCATCCAGGATGGTGCCAGGGCTTCCAGCAAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTGGGTGGACCTTCAGCTCTAACGTCACCTACTGGACAACTTCCCCCAGAG
Seq A exon
GTGATAATAGATGACCTAGCTGCTACTGACATTATTCACCAATTTGAAATAATCAAAGCCTGGACAGTTTAGGCTGTCATACCGTCCTGCTTCCTCAAAATGAAAGTTGGTAAAAATAATACATGATTAATCAAAGGGAAAACAATAGAATATTGAGAATCAATTGAATTGTATGGGACCATTAGCTTTTGTTGTATGGGAATTACTTGTAAGGGACCATGGCTTTAGGTTAAAAGGGCCCCGTTTTTAGAGTCTGCTATGAAATACATATCTGCAAATTTGGTAGACCTACCGAGACAAATAATGGACATTTTCACCATCAAATCTATAAGATGTATATTCACCAAGAATTGTATAATTATCTATTCATATTCTGGAAAATTCATATTCTTAAAATTAAATATTATAACCAATTTGTTGATAATGGGCAATTTCATACAACTGTCAATATTTACAGTGCTATTTTAAAATGACTCTAAAATGTGTTGTTTTTTAATAGGATAAGATATAGAAATAATTAAAGAAATTTCAGGAAAGCACACACATTTCATCGTACATCTGTGTTTGTGCATGGAAAAAATTGGCCCACATATGTCAATATTGTCAATATAGCCTCAAAGAAAATAATTCAGCCTTGAGACTATATAATCATAATATTTATTGGGGGGAGATTGATCTGATTATTAATCATTGATAGAAGATAAAAATAATTTTCACCTGAATGAAATAAAATAATAAATGACTTTAGCATGTTTACAACAAATTTCCTTGAAAATTGTGACAGGTTAATTAAAATAGTTCTGTAATATAATTGTGTTATAAAACTGCATCCCACTGGTGAATTCCTCTTAAAGAGTACTACCTGTGATAACTTTTTTTTAAAAAAAAAACTGTTTATAACTTAGCAATAATTCAATATTTTATTCCTTGAAAATTCTTACCTGGAAAAATTGCATGTAGCATGATTTGCCAAAGAAATGCTATGTGGTGTTGTATTACTTATTGGGAAGAGTGGTTTGAGCCATCAGTATTTGGTTTGCAG
Seq C2 exon
GGCACCACCACAGAAACGGAAGTCAGAAAGAGAAGGTTAAGCTCTTACCAGATTTCAATGGAGATGCTGGAGGATTCCTCTGGAAGGCAAAGAGCCGTGAGCATAGCCAGCATTCTGACCAACACAATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.642 A=NA C2=0.222
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(50.9=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.4=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCCTGTTTTCCCCAAGACG
R:
ACTTCCGTTTCTGTGGTGGTG
Band lengths:
351-1393
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains