HsaINT0145851 @ hg19
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium channel, voltage-gated, type III, alpha subunit [Source:HGNC Symbol;Acc:10590]
Coordinates
chr2:166025246-166027058:-
Coord C1 exon
chr2:166026940-166027058
Coord A exon
chr2:166025336-166026939
Coord C2 exon
chr2:166025246-166025335
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-SCN3A:NM_006922:4
Average complexity
IR-S
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:
PF0008319=Sugar_tr=PU(38.9=70.0)
A:
NA
C2:
PF0008319=Sugar_tr=FE(41.7=100),PF0052026=Ion_trans=PU(4.4=6.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)