HsaINT0145820 @ hg38
Intron Retention
Gene
ENSG00000136531 | SCN2A
Description
sodium voltage-gated channel alpha subunit 2 [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr2:165310323-165312088:+
Coord C1 exon
chr2:165310323-165310595
Coord A exon
chr2:165310596-165312024
Coord C2 exon
chr2:165312025-165312088
Length
1429 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGA
5' ss Score
6.91
3' ss Seq
ATTCCTTTCTCTTTAAATAGGTC
3' ss Score
11.19
Exon sequences
Seq C1 exon
GCCTGAAGACCATTGTGGGGGCCCTGATCCAGTCAGTGAAGAAGCTTTCTGATGTCATGATCTTGACTGTGTTCTGTCTAAGCGTGTTTGCGCTAATAGGATTGCAGTTGTTCATGGGCAACCTACGAAATAAATGTTTGCAATGGCCTCCAGATAATTCTTCCTTTGAAATAAATATCACTTCCTTCTTTAACAATTCATTGGATGGGAATGGTACTACTTTCAATAGGACAGTGAGCATATTTAACTGGGATGAATATATTGAGGATAAAA
Seq A exon
GTAAGATATACTCTATAAACCATTAAGTTGTTTAGTTCTCTAAATATTAAATATTATATATAATGGAAATTATCTCAATTTAGATGTGAATCAAGTGACTTAGACTAATTTAAGATGATTTAATACATATAAAAGAGATATCAAATGATACCTTATTCTATTTTTCTTATCTGTCCATTGATATAGTAAAAGTTCTCATTTGAAAATGTGTTGTCTTATACTCATGTTGAAAGTAATTTCATATTATGCCATATTAAAAAATGTTTATTTGGTAGACATTAATCAGGTTTTTCAGTCATTTTAATAAATAAGTCAGTAGTTTGAACTATTCAGTGTATTCCACTGAAATGTGTTAAGAAGACTGAGGGGAAATAATTTGGCCCTATTTGGTTGATGCAACATATGTATTGAGTACATATGCTATATCTGAAAATAGAGAAACCATTTATCAAGATGAAATAAGAATTTGTGTGCTCCTCAGAAGGTTAAGTAACCCTGATTTAGCCATTCACTTATTCATATTCTAATTAGTCCCTTTAGTGTCATCATTGTATTGTAGTTACCAGTTTAGTTTGATTATATTTAAGGTATGAACATCAGAATAAGCTTATGCCATATACTTCAGCATGATTTCTTAACATTGAGCCCAGCCCCTCTGTCATTTTTCATATGTGTGTGCATGTTTGTATGTGAATATAAAAATACGTATGTTTGCATGTGTGTGCATGTTTTCTGAGATCATCTTTGCAACTTACTGAAGTTATATGTCATGCCTTAAAAATAAAAACTAGATAGCTCTCCATAGCTTAAAAATAAAAACTAGATATACTCAGACAACATATCTCTCCAAAGAAACAAGTTTATTTTCTTCATTTGAAAGGCAGAAATCAAGCAAAAATTTCAAACAAAACACTTATTTACAGTATCATAAGAGGGAATAAATACCTAATCCCACTTCTCACAGGAAATTAAGTTAAAATTGGCGGGAAAAAATGTCTGAATCTATTTTGAGCCTGGGGAGAAAAGTATATGTAAGGTAAAATTTATTTGCATGAAAACACCTAGAAACAACAAGGCTTTCTTCTTTCTTACTTTTTGTGCCCAGCAATAGACTGGCAGCTCTTTCTTAATGTATCCCATGCAATTTGAGCTTATATTTGCAATGAATGCTGATATAAGAATGTTATCATAGTAATTCCTTCTGAACATTTTTCTTTTTAACATAGATTTGCTAACCATTTGTATAATCAAAAATGTTATATATTGATATTTGTTCAATATTGTGAAAAATCTCTTTAGCCATATATATTTATTAGTTTATCCATCTCATTATGATTGAAAACATTTGTGAGCTTTGCCACCTAAACAGGGTGGCTGAAGTGTTTTACAGGATTTTAATGATTCTTTCTATTCCTTTCTCTTTAAATAG
Seq C2 exon
GTCACTTTTATTTTTTAGAGGGGCAAAATGATGCTCTGCTTTGTGGCAACAGCTCAGATGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136531:ENST00000283256:7
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:
PF0052026=Ion_trans=PD(53.6=89.0)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.8=100)
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:
GCCTGAAGACCATTGTGGGG
R:
GCATCTGAGCTGTTGCCACAA
Band lengths:
334-1763
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