HsaINT0145872 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63945360-63947167:-
Coord C1 exon
chr17:63947045-63947167
Coord A exon
chr17:63945639-63947044
Coord C2 exon
chr17:63945360-63945638
Length
1406 bp
Sequences
Splice sites
5' ss Seq
AGGGTGGGT
5' ss Score
5.37
3' ss Seq
ATGGACCCCCTGGCCCCCAGGTG
3' ss Score
6.98
Exon sequences
Seq C1 exon
GTCTCCATCATCAGCTTGGTGGCCAACTGGCTGGGCTACTCGGAGCTGGGACCCATCAAATCCCTGCGGACACTGCGGGCCCTGCGTCCCCTGAGGGCACTGTCCCGATTCGAGGGCATGAGG
Seq A exon
GTGGGTGCTGAAGGGGCCTCTGGGGTGGGCTGGGGATGGGGGACCGGCCACCTTCACTGCAGGGTGGAGGGTGCATGTCTATACTCCAACCACCACCAGAGGGAAGCAGAGAGCTTGGACCCACGGCCCTGCCTGAGGCCAGGTCTGGCCCCCACCTCCCCTAGCTGTCCTCCCCGCAGGCCATCTTCTGCCTGCCCCATTCCCACTCTCAGCCCCCGATCCAGCCCGCCCTTAGCTTACCTCTGCCACTACTTGAGGGGAGCAGAGACTGCAGAAGCACCCAGGAGGGCCCCACGGCCAGGGAAGAGGAGGAAGGAAGGCAGGTTTATGTGGTGTTTATGGGTGGTTTATGAGTGGGTTTATGGGTGGCCCTCCCCAGCCTCAGACTGAGCCACCCAGGGCTTTGAAACAAGGTGCCTGCACCCTGGCTCTGAGCCTTCCCCTCACCCCCCACTGATGAGCTTGGCGTCACGGTTGGGGCCATGCCCTTGAGCTTGGGGTCAGTTTGGGGAAGATCCACTCAGGCCCTGGAGAGCGGAAGTGGCAGGTAAACACAGGGTTGCGGCGGGGTGGGGGGGGGGGCAAGAAAAATGGGACTTCCCCAGGAAGAGAGATCTGCTGGGAGCAAGACCTGCTCCAGCGGGACAAATTTCTGCAAATCTAGAGGCCATGGCGAGCCCCCCCAAGCGGCCCCTTCCTGTCCCTGCAAGAGGCCAGCCGAATGCTGGGCCCTCTGACCCCCCAGAGCCAGGGAGCCCTCCCGTTGAGGGGAAACAAGCTGCCTGTGGCCATGCAGCTGGTCAGTGCCCCAACCAGGAACAGAGCTCCCCTGGGCACACCAGGCTTGTGCCACCCACTCTAGAGGTCATGAAATGGCTCCTCCTTAAAAAGAGAGGGGTGTCAGATCCAGCCCAGTCTGCAGTGGTCAGGTGGGCTGTGTGACTAGGGCTGGTGGGGATGGGGCTTCTGTCCCAGAGCTCCTGCTGCTTCAAAGACCCTGGTGCCCTCTTTTCTGTGCCTGTGTCTGGGGCTCTGGGGCTGAAAACCCATGAGCAGGGGCTGGGTCACGTGAGCTGAGTTTCCTATGGGGGCTGAGCAAAGAGTGTTTGTCTCCTGCCTGGTGACCTGTGACCAGGCTGCTTCCAGAGAAACCCAGCACCCCTACTCTGGGCTGATGGCTCCAGTCAAGCAGAGAGCCCTCTTGACCACCAGGCCTGCAGCTCCCTCCCCCTCCCCCTTACCACCCCCAACCTGCACACACACAGCCCAGCAGGTCGGCCCTCCTCTAGGAAGCCCTCCCTAATTGACAATGCCCAGCTCTGCCTGGTCCCCTGGGTGGCGTAGAGATGTGGAGCCCTCTCTCAGAGGCTGGGAGAGGCACTGGCAATGGACCCCCTGGCCCCCAG
Seq C2 exon
GTGGTGGTGAACGCCCTCCTAGGCGCCATCCCCTCCATCATGAATGTGCTGCTTGTCTGCCTCATCTTCTGGCTGATCTTCAGCATCATGGGTGTCAACCTGTTTGCCGGCAAGTTCTACTACTGCATCAACACCACCACCTCTGAGAGGTTCGACATCTCCGAGGTCAACAACAAGTCTGAGTGCGAGAGCCTCATGCACACAGGCCAGGTCCGCTGGCTCAATGTCAAGGTCAACTACGACAACGTGGGTCTGGGCTACCTCTCCCTCCTGCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314:ENST00000435607:18
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=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATCATCAGCTTGGTGGCCAA
R:
TGACCTTGACATTGAGCCAGC
Band lengths:
353-1759
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