HsaINT0145851 @ hg38
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium voltage-gated channel alpha subunit 3 [Source:HGNC Symbol;Acc:HGNC:10590]
Coordinates
chr2:165168736-165170548:-
Coord C1 exon
chr2:165170430-165170548
Coord A exon
chr2:165168826-165170429
Coord C2 exon
chr2:165168736-165168825
Length
1604 bp
Sequences
Splice sites
5' ss Seq
TTCATATCC
5' ss Score
-14.87
3' ss Seq
ATTCCTTAACTATAATCTACTTT
3' ss Score
-4.37
Exon sequences
Seq C1 exon
ACTTTTATAGTAATGAATAAAGGAAAGGCAATTTTCCGATTCAGTGCCACCTCTGCCTTGTATATTTTAACTCCACTAAACCCTGTTAGGAAAATTGCTATCAAGATTTTGGTACATTC
Seq A exon
ATATCCTTTTAATGTGAATTGCCTAAATGCTATTTCTAACAGTTGATTTTAAAGAAAATGTCAGTTATATTTTCAAGTATCTGTAAAATTTCTTTGAGATTAATGGTAACATTGTTAGTTTAATTCATTTATTTGCATTGGTTTTCCACTATTTATAATGAGAGTATTATAGAATGACTACAGCATTATAGAAGAAAATATGTAACCAACCATGATAGTGAATGTGCAAAGGAAACACATAGTAGGAAAAAGAGCAAATCTCCTTACACCTTTATCAGCTTCAATGAGGTCATATATAACCATTGCTAAAGATTAGATTATGGTTAGTATTACTATTTGCATTACCAAGTGTTCAAACTTTTACGCCTTAATTGTTTCTGTATCTTCAGCGCCTGGATTTATCCTTCTTTGTGTCCTTCCTTCCTTCTTTCTGTCCTTCCTGTCTTCTTCCCTTCCTTCATTCTTCCCTTTTCCCTTCCGTCTTATTCCCTTCTTTTTTTCAGTAAATATTTATCAGACTCTTACTATGTGCTCATGTACCTGGTTGAGAATATGTATCAAAAAGTCGAACTTGAAATTATTTACAATGTTAGTCAAAAAGCATATGTAAAAGGGCAGAATATGTTTGGATTTCAAGAAAATTCTCAAGTAATGATAAAATAGAATGGTGATTTTCTGAGGCAGTGTTCAAGAATGGGAATTTTGTATAGGCAGATTCAAAGCAGGCTTCTATATAAACTTAAAGACTGATTCACCTAGAGACAGGGCAAATGAAACTGATAACCTTTTGAGGTATGAATTCTCTCATTCTATGGCTTGATGTTGGAAAGTATTTATATTCTAAAATAAAATATTTATCTCAAAATAATCATAAACTTTCTTACAGGGAAGTCTGGACTTAGATCCCAAGAGAACGTACTACAGCTAATTCTCAGAAGAGCATCAGAATAGTGCTATCTGTTTAGGTATAATGTGGACTAGATACAAGAGTATAGCCAGATGGTCTGTTGGGGTCCGCCACAATCTAAAGTGTAAATAAAAAGCTAGAAAATAACATTACCTTATCAGCACAAAATTGGATCTCCCTCTTTTATGCTATAAATTGTAAAGGAGTAAGTTACATCACTACAAACCTACTATTTATGATAGAATTCTCAATCAATGTAATCTTTGATTATACTGGGCTCTACATTCTCACACTTTTTACATTGCATTCGTTAACGTTTTATAAGTCAGTGAGGATGAATATATCTGAAGTACACCTTTTACACTTATGGCATACTATAAACTTACTAAGGGATGGTGAGTTCTTCTTCCAGGGCAATTTCACACAACTGATTGGAATGCAAAATAACTTGCATTTGCTTCAAATAGAGATCATTTTTCTATTAAATTCAGTTTTGTGAGTATATGGTATAAAATGAAAAAAAGAGTGCACCAAGGCCATATCACAGGCTTTGAAGTTTCTTATTATTTTATCATTGTTTTAAAACAAATAATATTAATTTCACAGTTTTTGCATCGATAAACTTTTTTGTGTGTTTTGGATCATTTATAAATGGCCATGGTAACCTACTAACATTTATTCCTTAACTATAATCTAC
Seq C2 exon
TTTATTCAGCATGCTTATCATGTGCACTATTTTGACCAACTGTGTATTTATGACCTTGAGCAACCCTCCTGACTGGACAAAGAATGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253:ENST00000283254:4
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCAATTTTCCGATTCAGTGCC
R:
TCTACATTCTTTGTCCAGTCAGGA
Band lengths:
183-1787
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