HsaINT0145901 @ hg19
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium channel, voltage-gated, type V, alpha subunit [Source:HGNC Symbol;Acc:10593]
Coordinates
chr3:38618152-38622862:-
Coord C1 exon
chr3:38622422-38622862
Coord A exon
chr3:38618273-38622421
Coord C2 exon
chr3:38618152-38618272
Length
4149 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
TCCCACACCCCTGTCCATAGACC
3' ss Score
7.79
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTCCTGGCCTTGCTGCTCAGCTCCTTCAGTGCAGACAACCTCACAGCCCCTGATGAGGACAGAGAGATGAACAACCTCCAGCTGGCCCTGGCCCGCATCCAGAGGGGCCTGCGCTTTGTCAAGCGGACCACCTGGGATTTCTGCTGTGGTCTCCTGCGGCAGCGGCCTCAGAAGCCCGCAGCCCTTGCCGCCCAGGGCCAGCTGCCCAGCTGCATTGCCACCCCCTACTCCCCGCCACCCCCAGAGACGGAGAAGGTGCCTCCCACCCGCAAGGAAACACGGTTTGAGGAAGGCGAGCAACCAGGCCAGGGCACCCCCGGGGATCCAGAGCCCGTGTGTGTGCCCATCGCTGTGGCCGAGTCAGACACAGATGACCAAGAAGAAGATGAGGAGAACAGCCTGGGCACGGAGGAGGAGTCCAGCAAGCAG
Seq A exon
GTGGGCCCTCACCCCTGCATGTATAAGGCACCTACATATACAGGGCCCAGAGCTCTGCTGTCCGGGCCACCCAGCCTCTCTCAAAGCAGCTTCCCCTCCCAGACTGCCTTGGCAGTGGGTAGGGGTAGAAGGCAGGCCCTCCCCACAACAGCCAGCCTCTCAGAGGGGTGCTGAGACCAGCCCTCAACCCTCCCTTCCTAACTCAGTCCAGAAGCTGACCTGGGGAGGGGCTGCTATCCACCACTCATGCCCTGGCTGGGCATGGGGAGCTCATTGTACAGACAGGGAAACGGAGGCATGGCAAGAGAGACTTGCTGGGTGTTCCTCATGAGTTTAGAACAGAGCCTCTAGCCCCCAGTTCCCACACTGACCATTGTCCCCCCTCCAGGACTGGCAAGGTAGAGTGTCTTGGCGAAAGAGAAGTATGGTTTTCTGACCTCCAGACTGCCCCTTCCCCTCCTCCCACACCCAGGGCTCATTCTGAGATTTAAAAATAAGCATCCCTAAGACTGAGGTGTCAGGGACAGCACTATCTTATCTCGCAACCTGTTATTTTTAACACTTGGGACCAGAGTCTGCACAAAGCAGGCAGGGCCCACCCCTCCCCTCCCCTCCGTTCTCCCTTGGCCTGAGCCAGGCTCAGATGGCTTCTTCTCAGGGCTTTAGGTCAAGCCCCCAGGAGTGTTCTCCCTGTTGAGTCAGGCCCATCTTGGCTGCTTCCTCTGGGCCTGCACTGGCTGGGCCTGGCTGTGGAGAGCAGCTGCTCCCCATGTGTGGAACTTGATCTAAGGCTCTGGGCTTGGTTTCACATCCTCCTGCCTCCCTGTGGTCCCAGAGGCCACCCTTTCAAGTCAGGTTGCGGGGCAGTGGCAATGTCTGCTCAGGGAGAGGGAGTGTTGGTGTTGCCAGGACCACAGTTTCCAATGATCTCCAGCACAGGAGGGGAATTCCGGCTGTCTCTCATTTCCCTTCTCTGTTCCTTCTCTTGAGCCCATTGACTCTGGCTCCTGGGTGTGTGTGGTGTGTGTGGGGGTGTGTGTGTGTGTGTGCGCGCGCGTGCGCGCACGCAAGCCGGGAGTGCCACAGGGATTCATGAGGGAAGTCAGTGTGACCTTCCTAAGTACAGTGGCCAGCATTTGTGAGCTGGGCATCGTGGCCCAGCTGCACCCTTCCAGGGAGTCTGGGGAGGGGGAGTTATGCCAGGCCGGCCAGGGGCTTCCTGTCTCTAGGCCCTTTGCTTGGACCTACCAGGAGCCTCCCACCTGCCTGCTCAGGCCCCTTGAGGGAGGAGTCTTCAGTGAGATGGAGGCCCCATGAAGACAGCTGGAGGCAATGCCCCAGATGCATGGGCAGGGTCTGAAACCCCCAGGGTCAGGGCCCTGGAGACCCTCTGGCTGGGTGTGTGGACTCAGCTCATAGGCTGGGGTCTTTTCAGCAGGAATCCCAGCCTGTGTCCGGTGGCCCAGAGGCCCCTCCGGATTCCAGGACCTGGAGCCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTGCATCTCAGGCCGACTGGCGGCAGCAGTGGAAAGCGGAACCCCAGGCCCCAGGGTGCGGTGAGGTAATGCATGCCTTTGTCCCTGAAGCCAGCTGGGCGCCGCTGCTTGGGTCAGAGCCAGGCTGTGAGAGGTGCATGCCTGCATTTGCTGTTGGGAGCCACAGCCACTGTCACAGGCAGCGTGGAAGACCAGTCTGCAGAGGGGAGGGTGGGCATCCCTGTCCTGACAGGGGAGAGACGGTACAGGGCCCAGGGCCAATGGGAAATTCTGGAAATTCTGGTCCCAAACTCTGATGCAGGACTAACCCACTACCTCCATGTGTTCACCCTCTCCACATACTCCATCCCTGTGTTTTGGTCCTGTTTGGCAAATGTTTGTCCTGTGAATCTCCCCATCCAAAGAAGACTTCAGGAGGCTGGGCACGGTGGCTCACGCCTGTAATTTTAATACTTTGGGAGGCCGAGGCAGGTGGATCACTTGAGGTCAGGAGTTCGAGATCAGCCTGGCCAACATGGTGAACAGGTTACCCGCCTGATTCTGTAAGCATTGGAGTTCGCAACCCCTGAGCAAAAGGCTTGTGGCATTGCTGACTAAGCCGCCCAGCCTCACTCACATCTAGCCCACGGAAGGTGGAGGGCACGTGTTCAGAGTGCTTGGTGGCCACTGTCCTGCAGCTTGACCTCACTCCGTCCAGCACTTGTGCCTTCTCCTCTTTTGTGAGATGGGCCCATGTGAGCTTTGCAAGCATGGTCAGTTTTTGGAGCACAAGGGCCTACTGGAGTCATCTTCCTGACTGTGCAGATCACGGTTCTTCCCCTGATGGTCTGAGCTGTGAAGGCATGTGGGGACAGGAAGACACAGGAGAGAGGCAAAATGCCATGGGAGAGAAGTGGCTCTCTCACACGGATGCTAACCTTTGAATGAATTTTATAAGTCTTCCTTTCTTCAAATCAGTTCATGGGGGAGCCTATATAAGGAGAAACAGGCTGGAGTTTTCCCGGGAAAGGGACTCCCTCGTCTCACCTGCAGTAGGACCTGAGAACGTGTCCTCTCACATGACAGCCCCATGGACTTCAGACGGCTCCAGTGTTTGGAAAGAAAAAATAAGCATGCTGCTCTCCTCTGGCCTGCCCCTTTCATCACCCAACTCCTTTCATCCCCCAGCTGAGCTAGGAGGAGAGGGGAAGGAACCCTCAATGCCATGGGGGACCACAAAAGACTGAGCCTCACCTCTCTGGCCAAGGATCCACCTTCTCTGAGCAGTAGGCTCTGTTTTCCCTCCAGAATCCACCCCTTTCCCATCACAGATCTCAAAAATGGAAAAGAAGCCCCTGAGACATCAGCAGATTGATTCATCAAAGGAAAAGAGAAGAGAGAAGGCAGCTGTAGGAGCATAGCCATGCCCAAGAATTCAGACAAGCCCCTCTCTAAATGGAGCCTGAGCCTGAGATGATGTGAGGCGGGGGCAGCGGAGATGGGGTCTTTGGACCTGACCTGATGCAAACGATGGATTTTCTTCCTTCACTGACACTCCTCCCCTGACGTACCGTTCCCTAGAAGCAGAGGGATTCCTATGCAAATGACTTGTTGAGGGGTGTTCTCAGGAGAAAGTAAGAGAAACAGGATGAAGCAAAGAAGGAAGCTACGGAAAGGCTTTCCAGCTGGAGTCAGCCTCATCCTGTCCCAAGTAGAGCTCTGGGGCATGAATTGCACCACAGCATTGCCCCAACTCAAGGCTAGGGGCTGGCCTTCTGTATTCTTGTATCAGTGGCTGCTGGGCACCGGCCACCCCTTGGGACGGCAGTCCCCCAGCTGAAGATGATTTTCTGGAGGAGGGCCAGCTAAGCAGCTAGCATTCAAGTGGCTGGGAATGGGTGCAGTGGTCTTATGTAGTGGAATTGGGCAGGGTACCCACAGTGGCCCCTGTAACACCCCTTTACACCCACACCCACAAGTGACACACACAGACACTCACAAGGGCACACCTGCATGCACATGCCTCTCTGTAGCCTCCCTATAATCAAGTTATTGAGGTCAGGGCAGCAGACTTGCAAGGACAGGAAGTGGAGGGCTCCATCACCTTCTCAGTCTCCGGGCTCTGTCCAGCACACCAGAACCCACGGGAACTGCGCAAAATGTGTGGGTGGGGTTGCTGGCCTGTTCTCTGCGGTCTGACCTTGCTGCCTGTGTGTTGCCCGGGATCCTGGTTCTGACTCTGTTCTGGATGTGACATGCCTGTTTCCACTGTGTGTGCCACACCACCACGATGTGTCCATGTCCCACTGTGTGTCCAGGTTGCTACCCCATGTCCGTTTTGCTCCCAGCTAGATGCAGTCCCCATCCCCAGTGGCTTCCCAGAGCTCTTTCACAGCCCCCACACCCCAGCCTTAGACTCCAGCAGACCAGAATCACAGACCCGGGAACCCCGAGGTCCAGCCTTGGCCCAGCCCTGACAGGCAAAAGTGGCTCTGTGCAGGTCCCAGGGTGCGTCATGAAGATGCTGCCTCCCTTCAGGGAGCCCTAAGCTCCTGCAGACTCTGGGCTCGAGGCCAAAGGCTGCTACTCAGCCCACACTCACACCCTTTCCCACCCTGTCCCACACCCCTGTCCATAG
Seq C2 exon
ACCCCAGAGGACAGTTGCTCCGAGGGCAGCACAGCAGACATGACCAACACCGCTGAGCTCCTGGAGCAGATCCCTGACCTCGGCCAGGATGTCAAGGACCCAGAGGACTGCTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873-SCN5A:NM_001160161:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.527 A=NA C2=0.663
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.3=5.4),PF065128=Na_trans_assoc=PU(46.8=83.7)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(15.2=100)
Main Inclusion Isoform:
NA
Other Inclusion 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)