HsaINT0145914 @ hg19
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium channel, voltage-gated, type V, alpha subunit [Source:HGNC Symbol;Acc:10593]
Coordinates
chr3:38651225-38655557:-
Coord C1 exon
chr3:38655466-38655557
Coord A exon
chr3:38651456-38655465
Coord C2 exon
chr3:38651225-38651455
Length
4010 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTTGTTCTTGCCTTCCCCAGGGC
3' ss Score
11.11
Exon sequences
Seq C1 exon
GTATGTATCAGAAAATATAAAACTAGGCAATTTGTCGGCTCTTCGAACTTTCAGAGTCCTGAGAGCTCTAAAAACTATTTCAGTTATCCCAG
Seq A exon
GTAAGATGCCCAGGTTTGCCTCTCAGATCTCAGCTACAAGTGACTCTCTCTCTGTCTTCCCCACCCCCTTTCCTCCTCTGACTGTGTGTCTCCTATTGGTGTGTTGTCATTGTCTCGTGTGTGAATTTCCCTTGTTACAGATACACAACTGAATTTGTGGACCTGGGCAATGTCTCAGCCTTACGCACCTTCCGAGTCCTCCGGGCCCTGAAAACTATATCAGTCATTTCAGGTGAAAATCAGGTTAAACACCAAGGCTAGAGGGATATGCCTGGGCCTTTCCAGCCACCTGGGAGCCAAGGCAACCCTCCAGAAGGCCCTTCGAATGTGCCTGTCACCAGAATACCTTTCCCAGGGCTCAGGTGCCAGGGGCTATTGGCAGTGGACATGCTTGTCCCCCTGGAGCCTCAGAATGGGCTTCAGGCTGCCCACCCCAGCAAAGCCCACTCTCATAGACACCAGGGGGCACAGAGCACCCCACGGTGGGGCCTACACTGAACCTAAATTTTTTCCAAGATAGTGGACTGCTTTTCCAAACCACACTCAGCTATTTGAATAGCTAAAAGTTTTACATGAATTGCTTCAGCCTGAAATGTCAGATTCTGATGAGGAAACCAAAAGAAGTGTGTTTGTGGGAACCCCCACACACACCCGGAGTGAAAGAGGAAAACTCCAGCACGGTCCTTCATGATTGAGTGCCTCGGCCCGCCTTGTGCCCCATCTGGTGATAGAAGTAGGGCCAGAGCCCCAGCCCCATTTTGTGAAACAAAGCATAATCTGTGGACAGGCATCATCGGGCCTTGGTGTCTAACAGCCCTCGCTGCATGGTGCGGTAGAGGTTTAGCAAACCATGCATGGTAGCCTCAGGAAGAAATTCTCCTTGACAGATGTTGGCAATTGCATCTGGGAAATCTAGGCCCAGATAACATCTCTAGAAACCATTCCATCCATCCATCTAGGAAAACTCTGAAAAGACTTGTGATTTCTGAGCCTGGTTGTGCGATGGGCCGGTGCTGAAGCTGAGTTCCACCCAGGAGACATTCCTATCCTAAGTTTGTATTCCCTCTCCCCAGACTCAAAGCTCCTCCTGTTTGGAGGAACTTGCTCTGGAGGGGCAGTGCCCAGAGGTTCCTTCCAGAAGTCTTTTCCGAAAGCAGCCACACTTAGAACTGGGTAAGGCACCTCTTTTAAAAAGACAGCCCAGCAGGGCACAGTGGCTCACATCTGTAATCCCAGCACTTTGGGAGGCCGAGACGGGTGGATCACTTGAGGTAAGGAGTTCAAGACTAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATATAAAAATTAGTTGGGCGTGGTGGTGCACGCATGTAATCCCAGCTACTTGGGAGACTGAGGCAGGAGAATTGCTTTAGCCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATCACGCTGCACTCCAGCGTGGGCAACCGAGTGAGACTCTGTCTCAAAATAAATAAATAAATAAATAAATAAGGCAGCTGGAGATAGGTTGCATGCCATCATTCTAGGGAGGTGTGAGAGCTGACGGAAGCATCGGTTGAACCAGATGGCTACATCCGCACCTGATGTGGAACCTGGTGGCTCCCAGGCCTGCATTGAGCTATTGTCGCCCCCAAGGAGTCAGAAGCCCTGCTCTAAGCTCCAATAAGGAATCTGGACTCCCCCTGGTAGGGCTAGTTATCTTGCCAGAGCAGCCCCCAGTTATGCTATGTTCACATTGAGCTTTCTGGCCTCTAAACCCACTATAGTATGTTCATAAGGGCCGCATCTCCCCCAGAGCTCCCACAAGTGGCCCAGACCCCTGCCAAGGGCCAGTAGCAAGGAGGCAGTCTGCTCCCGCTCAGTCCCATGGAGCCACCTGCATTGAGACAGACATCATGGGCCCTGGCACACATAGACTCAGAAACCACATGGTCTGTCCTCTAGGGCCCTGGGGAGAGCCTCACAGGCACACACCCCACCGAAGTAGACAAACACACTAACCACAGGACTTAAGGCATATTCCTGGTGTGTTTTATAAGAAAGATTTACAAAGGGAAATATTTCTCGGTCCTGGGGAAAAGGAGGAAGCCCACCAATCTCAGCCTAGCTCCATGGGACCTCTTCGCAGCTGCCAGCAACCTAGTGAGCCAGCAGGCTCTGAAAGTGGCCAATAGAAAAATGCCATGGTCGGCATTATGGAAGGCCCTCGGGAGGAGGTGTCCTCTGAGCTGAGTCTGAAATAGCCCTAGTCCTCTCTAGACTCAGTCGCTTTTCCATAAAATGAGAGTGAAATCAGAATTGGTGATTTCCAAGGGCTCTTCCACCCAGCCTGTTAATTCAGTGGCAGGAGGATTTCCCAGTTGATCTCCTGGGGCCAATCCCTTCCTGGGTCTTTTCAGAAAGAATCCTGCAGTTTCGTTGCAACCATTCTTGCCAGAAGTGAAATCTATCATCAGTATGAGAAATGTTCAAAGGGGTGAGTTACCCTTGGCCACTATGTCCACAGACCAGGTCAGGGGGTGCTTTGCTGGCCTTGAATGGGATACTTCAGGCCAAAGAGACTTTAGCCTAACAATTGAGGCAGAGACCAGTTTGGGTATTGGAGCTGCTGTCCATCAGTCTTCACTTTGTTCCCTTCGAGACATGCAGGTCTCCAGCCCAGTAAACCCACCAAAGGGTACAGGAAGCTCTGTTACAGATGAGGAGCTCTGGACCATGAAGAGCTTGTGAATCTCACCACCGCCACTACTCTGGACCCAGACCTGTGAGGTCCACCCACTGCCCAGGCAGTTGCCAACATCTGCCAGGAACGATTTCCACAAGGAAGGCTGAGTGCCTCTGAGCCCTGGGTGGGCAGCAATGTCAGTGGCACCATGGGGAGGTCATCCTCTCCCCATCTTGTGTTTGCTCATCATGGCCTCCCTGCCTGTGGGTCACAGGCCCAGCAGCAGCAGGCACAGAAGCCACAGGCGCTCCTAACACATTAACCGGCTGGACAGTGGATGGATGGAGCTTAATCTGAGATCTGGCCGCTTGGGACAGGGACATGAGGGGCAGGGCCCTGCCGCTGGCAGAGGAGCCTCCTCATTCCCCATGCTCTGCTTGCACTTGTCCTAGGACAGTCGCTAAGGGCCAGACTGGTGTCTACACATGCTTTTCTGTCATTCTGCTATGTGGTGCTGGCTTCTGCAGGGAGCTAGGCTGTGCAACTAACAGAACACAGCCTCTCAGCTATGGGAAATGGGATGGATGGGGGTGTGGGGAGGTTCTAGAGGGACAGGGCAAGTGAGAAGATGCAATGCAGGTCAGTCCTGTTCCTGAACCTTCCCTAAAGGTGGGCCTGAGCCAGCGCAGGCCCCTTAGACATCACCCGCCATGACCCCGCCAGACCGTCACCCACAGCCCCCAGCACACACCTGACCACAGCCCTCAGCCCCTACCCGACCAGACCCTGGGCCCCTAGTTTCCTCCAAACAATCCACACTCCCTGTACATCAAATAGAGCCAGCCCCAGCAGTGGGGCAGGAGGACCTCCAGCAGGAATGGCTCTATTTCTCCCCATCTCAAGATCAAGGCTGAGGCCCCTCAATTGCCTCCATCTCCTTTTCCATGGACTACATTAAAAGGGGTAGGCCTAGCACACCTTCAGACTAGCCAAAGGGGGTCATGCTCTGAGTATGTGTTGTCTCAAGAAAGCAGCACTTTCCACACCCATGCCATATATTTGGCTGGTGGAGAGCAAAGAGGAGCAGGCTCCCTCTGAAACTACAAAGCCAGCCTAGACTCCTGCCCAGGGAAATCAGGACAGAATCTCAGCTGTGAGGAAAGTGGGGCTTGGGTCTCAAAGCCCAGGAGAAGCCTCCCTTATTCTGTCCCCACCTCTGGTTGCCTACACTGGCCCCACCCCAGCTCAACTCAGGCCCAGCCCCCCACCAGTGGAGCACAGAGCTCGGTGCCCCTGGGTGACCCCGTGCTTGTTCTTGCCTTCCCCAG
Seq C2 exon
GGCTGAAGACCATCGTGGGGGCCCTGATCCAGTCTGTGAAGAAGCTGGCTGATGTGATGGTCCTCACAGTCTTCTGCCTCAGCGTCTTTGCCCTCATCGGCCTGCAGCTCTTCATGGGCAACCTAAGGCACAAGTGCGTGCGCAACTTCACAGCGCTCAACGGCACCAACGGCTCCGTGGAGGCCGACGGCTTGGTCTGGGAATCCCTGGACCTTTACCTCAGTGATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873-SCN5A:NM_001160161:6
Average complexity
IR-C
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(12.2=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.3=100)
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:
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
- Genotype-Tissue Expression Project (GTEx)
- 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)