HsaINT1041027 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165113816-165115575:-
Coord C1 exon
chr2:165115455-165115575
Coord A exon
chr2:165113971-165115454
Coord C2 exon
chr2:165113816-165113970
Length
1484 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAC
5' ss Score
8.14
3' ss Seq
TAACTATATTTGATTTTTAGGAT
3' ss Score
8.93
Exon sequences
Seq C1 exon
AAATTAAATGCAACCAGCTCATCTGAAGGAAGCACAGTTGATGTTGTTCTACCCCGAGAAGGTGAACAAGCTGAAACTGAACCCGAAGAAGACCTTAAACCGGAAGCTTGTTTTACTGAAG
Seq A exon
GTAAACAAGCTCTGATGTGATTAAATACAATCTCCCCTTGTTCTTTACGGAGACTGAATATGCCTCATTTAAAAAAAAAAATTTATGAAACGAGGTGTGGTGGCTTATGCCTGTAACCCCAAAATTTTGGGAGGCTACGGTAGGAGGATTGCTTGACCCCAGGAGTTTGAGACCACCCTGGGAAATGTAGTAAGGCTTTGCCTCTACAAAAAAAAAAATAAAGAAAGAAAAAATAAATTAGCTCAACATGGTGGTACATGCCTGTAGTCGCTGCTACCTCAGCCACAGCTGTATCTTAGAGCTTTTGCAGGGAGTCGAGGCTACAGTGAGCCATGATTATGCCACTGCACTTCAGCCTGGGCAATAGAGCAAGACCCTGTCTCAAAATAAATACATAAATTAAATTAAATAAGAAAAATATTTAAAATAAATAGTGAAGGCATGTTTATCTTTATTTTCCTTTTTTGTCTTTTAAAAAGTTAATCTCTCTAGATTTCTGGATTATACTTATGGCAGTGACTATTCCTGGACAGTTAAAATGATCTGATAGGTCTTTTTGTTTTCTCATTCTCCATAATGTGAGGAAGCTGACCCTATGAGATAAATGGCATTCTAGAATGTCATGTCATTGATATTGTAATCCCTTCAGAACTCCTTGGCAATGGTGTGATTTGATTTATAGATGCTACAGTAATTACATTCCCTCCCTTACAGTTCCAATGTGGTTAATGTGCTTTGGCTAGAGCTGTTTTGAGATGTAACTGTATTGTGAAGCTTTGGCAGGGAAAGCAATAGCTGTTCTCACAGAAAGCAGCACAATGTCTTGAACACAAATCAATGAATATCTATTATTCAATGTGACTGGACTTAATCAGATGAGTAGTAGCTCAGAGACTTACAGCAGAAGAGTGGATGGGAGTTAGAAATAATGCGAAAGCTAGGAGGGGGAGGACAAAGGGAAAGAGATACTGACTGACGAGCTGAGTCATAGGTGTGACTAAGAGAAGCACTGAGGCTGAAAAATAAATTAGCTTCGGAAAATTGACAGTGGCTGATGCCTGGGAAGACAGCGAGATTTTCTGTGCATGTGTGCATGAAAAGAATTAAAAACCCAGGATCACATCAAAATATGAATAAACAAATCGAACATGTAGTTTTTGCCTCAAACCTGAGAGATGCACCTGGACTATTTTCATCAATGGCCTTGAGGCAAAATAATCCTGACTGGTGGTGAAGAATGAAACCATTGTTACTTAAGCAAATCTAGATAAAATATTTCCTTGAATTCTAAGTAGCTGGCTGAGTATATAAGTCTGAGAATAATTCATTATACAGGAGGGATGCTGACGATAACTAGGAAATGAAGGAGATGGTTACCCTATGAAATGATTACCTGGAAGTGGAGTGGGGAAGGGGCAAGAAAGTTTATTTTTTCCTATTTAAGATTAAAATATATTTTTTAATTAACTATATTTGATTTTTAG
Seq C2 exon
GATGTATTAAAAAGTTTCCATTCTGTCAAGTAAGTACAGAAGAAGGCAAAGGGAAGATCTGGTGGAATCTTCGAAAAACCTGCTACAGTATTGTTGAGCACAACTGGTTTGAGACTTTCATTGTGTTCATGATCCTTCTCAGTAGTGGTGCATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.630 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.3=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(20.1=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGCAACCAGCTCATCTGAAGG
R:
CAATGCACCACTACTGAGAAGGA
Band lengths:
270-1754
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains