HsaINT0145924 @ hg19
Intron Retention
Gene
ENSG00000136546 | SCN7A
Description
sodium channel, voltage-gated, type VII, alpha subunit [Source:HGNC Symbol;Acc:10594]
Coordinates
chr2:167285679-167289262:-
Coord C1 exon
chr2:167288828-167289262
Coord A exon
chr2:167285785-167288827
Coord C2 exon
chr2:167285679-167285784
Length
3043 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
GGTGGGACTTCACCTTTTAGAAA
3' ss Score
5.34
Exon sequences
Seq C1 exon
GTACTTTACCTGTTTCTGGCATTGGTGAGCTCATTTAGTTCATGCAAGGATGTAACAGCTGAAGAGAATAATGAAGCAAAAAATCTCCAGCTTGCAGTGGCAAGAATTAAAAAAGGAATAAACTATGTGCTTCTTAAAATACTATGCAAAACACAAAATGTCCCAAAGGACACAATGGACCATGTAAATGAGGTATATGTTAAAGAAGATATTTCTGACCATACCCTTTCTGAATTGAGCAACACCCAAGATTTTCTCAAAGATAAGGAAAAAAGCAGTGGCACAGAGAAAAACGCTACTGAAAATGAGAGCCAATCACTTATCCCCAGTCCTAGTGTCTCAGAAACTGTACCAATTGCTTCAGGAGAATCTGATATAGAAAATCTGGATAATAAGGAGATTCAGAGTAAGTCTGGTGATGGAGGCAGCAAAGAG
Seq A exon
GTAAGATGTTTAAATATCCTGATTGCTTAGTGGTGATTTATAGTATTGTTGATAAGGAAGTAAATCAGCGCCGAAGTTCCACAGCCAGATTATCCACTCAATTCTAACTCCATCACTCCTAGCTCCATCACTCTTAGCCTCTGACTTTATGCTTTTGATCAAATTACTTAAACTTTCCAAGCTTCAGTTTTCTCATATTTAAATGAGGCTAAAATGGTATTTAGTCCATGGAGGGGGGGAGGTAATAGTGCATAGAACAATACCTAGTAAAGAGTAAGCACTTAGGAAACATTAGATGATATAATTGTGACATTCTATAAATTAATAACCAGGCAGTTTGAGGGTGCTGAAAAGTATACTGAGGAAACCAAAGTTTTCTAAATCAAGGTGTATGATTTAACAAATCACTAAATTTCCATGGGCTTTATAATCTTAAAATGGGAGATTGAATTAGAAGAGTGCTACAATTCCTTCTTGCTTGCTAAAATTCTAAGATTTGAATCAGATCATTTCTGCCCATATTTGGACATTATAATTAAGTTGGACTAAAGGAATTTTTAAAACCTCCCAGTTTGAATTTTGAACAGTTGGTAGCTTTATAACGCACTGGCTTTAAAAAAAAATCAGAGTCGCATTCAAAGAAGGGTAGATACTGCTGTTCACTTAGCTTCTAAAATATACACCCTACTGGAAACAGTCTTATTGTCTCCATTTGCAAGCAGCTTGTGTTTTAGAAGGAGGTGTAACTTCATAGAAAGCTACACCTACAGAGATCACATCTGCACAAGGGCTTTTTACCTTGGACCCCACTAGGGAATCATTTCAGATCACTCAGGGGCACTGGAGGGTCGGGGAATGTGTCTTTACAGGTCCCCATCATCTGTGGCACCATCTTGTCTCCCAGACCTCTTCTGTTTTGGCAGATGCTCTCTACAATAACTTCACAAATTGTCTTCTAAGAGGAATTCAGTTTCAATTATCCAAGGTCCTTCCATCACCTACTAAAGCCATCTTTATTTTAGTTAGAGAGACATTTTTAATCCACATGCCCAATAGTCTAAGATTCATTTACCTTTTAAATTAATACCATTGCTATAAAACAGGCATAAATTCTTACTCAGCACACTTCTCAATCTTCGTTAAAGATTTGGATTACTATCCATTTCTGGGTGAAATTGCTATTTACCACAGCACAGCATGTTGGAGTGTCCCTGAAAACTTCATGCTAATCTCCTTAGAAATTCTGGAGTATGAAAATACATAGGAAAGCTGTAACTTAAAATAACTGTAAATATTGAAATTGCAGTTTTTATTTATGCTGCATAGTTATTTGGTCTTGCTGGTTGATTAACTACTCACAAAAGATGTATTCATTTATTTATATATTTAGTTACATATTTAGTTAGATGCTTTCTAGATTATGTAGCCCATGACTACTTAGGATATTGATATACCCACAGCCAAAAATAAAACACAAAAATATTATAAATGATCTGATAATTCAGAGATACACTGTCTTGTTTCTTTGCTATTTGTACTTCCAGCCTATTTTTATTAAAAATATGCATATATATTTACATATTATAAAAATAACATCAAAATTTACATCGTGTTTTGTAACTTGTATTTTTTGTAATGCAGAAGTATATCATGGTCACTTTATGCCATTAAATAATCTTTTATCAAAATAAATGATTTATAATTTGAGTCTTAATTGATTTATTTGTAAAATTAGAAAAATACCTACTCACCGGTATTTTGGAAAAATCACATCAAATAGGATATGTACAAGGCTTTTTACAACTCTTTAAAAATATAAATTTATGATGTATAATTTTAATTACTGTCAAATATTATGTTTAAATTACTTAATGCCTAGTCTCAAATAAATATATTGCTACAGATTTTATTTCATTAGAAATAAATAAAGAATATATAAAAGTAATGGAAATAAAAATATCTGTGTAAGAATAATATTCTGCTGGATACTTTACTTTTTTTATTTGAGCACTATAATGATTTACTGACAACTGACCACGTAAGAACTAAAGCAAAAAAAGCTTTCTAATTATATTTCCTTGACACTTACTGTGTATAAGTCTAAGAGGTAGGACAAAATATTGACAATTTCTCTGGTTTTTTGGCCGTCTACCTAGATTTTTTTCTTAATTTTTATGAAATAAGATTGGTTTCATTCCAAATGTTAAAATGCGCTTGCCTTAATTTTTGTTTTAATTAGAAAATATTACTTATATGCTATTAACCTTAGATCTTGGTGATTTTAAAGAATGATTTACGGTATCCTTATTTTAAAATAAGGTAAAATAAAGTATTGTGAGAAAATAATTTTAAATAAAGGCAAAGAGTATCATTAGCACTATTACCTATGTAAAGCAATGACCACCTTATTCTACCCAGCCTTGAACTTCAGTCAAAAGCAGAGTTAGAAAGAAGGTCAATTCTGCATCTGGGTGCTTTTCATAAGGCTGTGCCCCTTTCCCAGGCCTGTTCTTGTCCCTATTTCTTGTGCCTTTCCCTCATTTTACTTCATGATAAATCCCATCCTGTGATGACATACATAAGACCATCTGGACTGAATTTTACAATGAAACCTAGGTGCACTATTATCTACCCATCTTTAGCATCAAGGGATGATTTGTTCTGATTCTACTCATCTAATTGAAATAGCATATATGGGAAACTTGTGACTTACTCCAAGAAAACTTTGGAACCCCAATCCTTTTGTGAATTGGAGACAGCCTATACATCTTTAAGAAGCAAAGTGTTATAAACTAAACATGAATTTTAATCTAAATGTTATTTTAGCTTAAAGTAAGTATCATACAATATTTTTTTAAACTTCAACTCTTACCAATATGTACGCATTTTAATCTCAGTCATGAAATTGGCCTTAAGTCTTTTAAACCTAATAATATTATTTCTGTACAAAATTTTTCTTACTTCTGAAAATGAAATAAACTTTGGCCACCATGGGTAAATGAAACTTTAATCACAACTTTTTTGGTGGGACTTCACCTTTTAG
Seq C2 exon
AAAATAAAGCAATCTAGCTCATCTGAATGCAGTACTGTTGATATTGCTATCTCTGAAGAAGAAGAAATGTTCTATGGAGGTGAAAGATCAAAGCATCTGAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136546-SCN7A:NM_002976:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.5),PF065128=Na_trans_assoc=PU(60.1=84.1)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.2=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)