HsaINT0145882 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62043841-62045715:-
Coord C1 exon
chr17:62045383-62045715
Coord A exon
chr17:62043905-62045382
Coord C2 exon
chr17:62043841-62043904
Length
1478 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTGGCCTCTGACTCCCAAAGGGA
3' ss Score
4.66
Exon sequences
Seq C1 exon
GGCTGAAGACGATCGTGGGGGCCCTGATCCAGTCGGTGAAAAAGCTGTCGGATGTGATGATCCTCACTGTCTTCTGCCTGAGCGTCTTTGCGCTGGTAGGACTGCAGCTCTTCATGGGAAACCTGAGGCAGAAGTGTGTGCGCTGGCCCCCGCCGTTCAACGACACCAACACCACGTGGTACAGCAATGACACGTGGTACGGCAATGACACATGGTATGGCAATGAGATGTGGTACGGCAATGACTCATGGTATGCCAACGACACGTGGAACAGCCATGCAAGCTGGGCCACCAACGATACCTTTGATTGGGACGCCTACATCAGTGATGAAG
Seq A exon
GTAAGAATGGGGAGGGTGACGGGCAAGGGGGATCCTGTCCCAGTCCCTAGGGTAGCCTCTGACTCCACATTTTCTTTTTTTTTTTTTTTGAGATGGAGTCTCACTCTTGTCACCCAGGCTGGAGTGCAAAGGTGCCATCTCAGCTCACTACAACCTCCGCCTCCCGGCTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTAGGATTACAGGCATGTGCCACCAGGCCCAATTAATTTTTGTATTTTTAGTAAAGATAGGGTTACATCATGTTGGCCAGGCTGGTCTCGAACTCCTGACCTCATGTGATCTTCCCACCTCGGCCTCCTAAAGTGCTGGGATTACAGGCGTGAGCCACCGCTCCCCGCCCTGTCTCCACTTCTTATGAGACAAATAGTATGGCGAGGACCTGAGCTTAAAGCTAGCACTTGGCAGCCTGTGTCACCTCTGACTAGTCACTTGATCTCCCCAGCCCTCCGAATCCTCACCTATAAAATCAAGATAACAATACCTTCCTCAAAGGGTTACTGCAGCAACAAATGGCAAACTGTTTTAAAAACCCTAAAGTGCCAGGCACGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGGCGAGGCAGGCAGATCACCTGAGGTCAGGAGTTCCAGACCAGCCTGACCAACGTGGTGAAACCCCGTCTCTACCAAAAATACAAAAATTAGCCGGGCGTGGTGACGCATGCCTGTAATCCCAGCTACTCCAGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGCAGACAGAGGTTGCAGTGAACCGAGATCATGCCATTACACTCTAGCCTGGGCAACAAGAGTGAAACTCAGTCTAAAAAAAAAAAAATCCTAAAGCTCTCACTATGCAAAGCAAGAGTCTATAGTTCCTACTCCCTAACCTGTGCACCCCCTGTCCTCCTTCATCACACCACATTTTCACATGCTCACATCCTGGCAGGGTCACCATCACCCACCCACACACCCACATCCTATTCACATATGCATCTTCACAGGCACACATGCCAGAAACACACACATTCTCACACAGCCACTGTTAGTCTACATAGCGCCTTCTTGCAAATTAGGAAAAGGTAACCCTTCTCACCCTGGCACCTGGATTCCAGCCCCCACTCACCCTTCACTCAGGGGCCCTACATAGGTACACAATAACCCCATGCACACACGTACACGTTCCGTCTCTGTGCCACTGCTGCGTCATGACTTTTCGTCCACACTGGGCACTGGGCTGACAGGGCTCAAGCTGAGCTCCCTGCCGAGTCCCTACCCAGAGACCTTGGAACTTGGAGCTGTCCTTAAAGGACGGGGAAGAGGCAGCCAGGGAACATCCGTTTGGTTTATGTGGTACGCGCAGACCTGTCCACAGGTGTGCAATGGGCGCAGGTGCTCACACTGTGTCCATGTGGGTGACTTGCCTCCTTTGTGGCCTCTGACTCCCAAAG
Seq C2 exon
GGAACTTCTACTTCCTGGAGGGCTCCAACGATGCCCTGCTCTGTGGGAACAGCAGTGATGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:6
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:
PF0052026=Ion_trans=FE(38.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.3=100)
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:
GTCGGTGAAAAAGCTGTCGGA
R:
CACAGAGCAGGGCATCGTTG
Band lengths:
347-1825
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)