HsaINT0145806 @ hg38
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium voltage-gated channel alpha subunit 2 [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:165365143-165367371:+
Coord C1 exon
chr2:165365143-165365263
Coord A exon
chr2:165365264-165367216
Coord C2 exon
chr2:165367217-165367371
Length
1953 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TTTTTTCCCACATATTTTAGACT
3' ss Score
8.79
Exon sequences
Seq C1 exon
AAGCTAAATGCAACTAGTTCATCTGAAGGCAGCACGGTTGATATTGGAGCTCCCGCCGAGGGAGAACAGCCTGAGGTTGAACCTGAGGAATCCCTTGAACCTGAAGCCTGTTTTACAGAAG
Seq A exon
GTAAGCAAAACAATAACATATGTGGTCTTGAGTATCCTCTTTTCTACCCATTTTTTCCTATTTATTTAAATGTCTGTTTATTTGTCTACCATCTATTATCTATCTATCTGTATCTATCTATCTATCTATCTATCTAGTAATCATCTATACCTATCCAACAACTGTACATTTATTTGTTTTTTTTTGCATTTGCTGTTTGAAAAAAAATGCAACTTTTTAAAAGGCAAAGTTTAATTTATGTAATTAGATATTTTCATTTTTATGAATCATTTTTAACTCTAAGAAATTATTAACTGGCTTTTCTGTGGCCTTCTAAAATATCTTACAGGAGAGAAAGCCAAATCACACACATCTCTCTTTAGTTTAAAAATTCAATAAATAAGAAAGTGAGAGAAGTAATTTATTATGTACTATTTTGTGATATTATAATGGGTAATAATTGATAAGTGTACATTTAAATTTGTCCTTGACTGAAACAGCTCCTATTTCAGTCAAGGTCAAATATTTTTTATTATTTCTGAAAAAAGATAGATCATAAAAATGCCAAAATATACTATGAGTCATATGATATGGGGCAATATGTCACTGGAGTAATCGCAAAAGGATTTTCTGAAGAAAGCTAAAATTATGTAATTTGAGGTATGGATCAGTTATATATTGTAATAGCAATGCTGTGTATCAAACCACCAAAAACCCTGGGCTCTAAGCTGCTTTTCTAGTTTTGACTCCTATTTCCTTCTGTGTAACTCACAGACTTTCTTGTCACTAAGTTTTACTTGTATCATTGTTTCTCTATTCTTACAGCTTCATTTTCTACATATGTCTCTTATATATCCTTCAAGATCTAGTCTCAAATCCATTTCCTCCATAAAGCTCAGAAATTAAAGTTTACCAGAAAACTCTCATAATACTTTGTTTTGTGATAATTGTTGCTTTCCATAACTATAGAATTGTAGACAAATTGCCCCAACTTAAAATGTACATTCTTTGAGGACAAGGCTATGTTTTACATGTTATAGTATTACAATTTGTTCTATGCAATTTTTTGACAATAGTAGATACTCAATAAGTATTTGTTGAAGAGCCTTTGATCTAGCAATCCAGAAATTATACAAAGGTGTTTATTGGATTGTTATTGATAATGGCCAGATTTAAAGCAAACGAAGTATTCAATAATGGTGGAATTGGGCTGGGCACAGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCGAGGCAGGCGGATCACTTGAGGTCAGGAGTTCAAGACCAGCCAGGCAAACATGGTAAGACCCCATCTCTACCGGGCGTAGTGGTATGTGCCTGTAATACCAGCTACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGACAGAGGCTGCAGTGCATGAGCCGAGGTCAGGCCACTGCACTCCAGCCCGGACAATAGAGTGAGACTCCCTCTCAAAAAAAAAAAAAAAAGGTGGAATAGTTATATTAATTATAGTAATCATATTTAGAGAAATATTATGAAATCTTTCACAAATTTATTTACTTATAATAAAGATGGGAAATAGTTATACCATTAAGTGAACTAATCAGAATTCAAATATGTAAAGTGTCCATATAGAGTGGAATTACACTCATAGGATAAGGACAGGATGGAAATACCAACTTTTGGTAAGTTTATTTTCTTTTTGGTTCTTCTATTTTTTATATATTGTGTTTTTGTAATGTAATCCATTATAGTAGTGCTATAAACATAAAAATAAATATTTATTAAACAAATGATTAAAAAGCCATATAGATGATTTTAAGATAGCTTTTGTAAGCGGAAGCTATCTTAAAAATTAATGTTATTTACAATGTATTATCAGGTAATAATGTAAATGAATCTCCCACCAACACAAATATACCTAATCAAAGAGTAATTTTTTGTCTTCATTTTTTTCCCACATATTTTAG
Seq C2 exon
ACTGTGTACGGAAGTTCAAGTGTTGTCAGATAAGCATAGAAGAAGGCAAAGGGAAACTCTGGTGGAATTTGAGGAAAACATGCTATAAGATAGTGGAGCACAATTGGTTCGAAACCTTCATTGTCTTCATGATTCTGCTGAGCAGTGGGGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531:ENST00000283256:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.799 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=84.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTAAATGCAACTAGTTCATCTGA
R:
TGCTCAGCAGAATCATGAAGACA
Band lengths:
264-2217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development