HsaINT0145911 @ hg19
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium channel, voltage-gated, type V, alpha subunit [Source:HGNC Symbol;Acc:10593]
Coordinates
chr3:38663891-38671920:-
Coord C1 exon
chr3:38671802-38671920
Coord A exon
chr3:38663981-38671801
Coord C2 exon
chr3:38663891-38663980
Length
7821 bp
Sequences
Splice sites
5' ss Seq
CTCATATCC
5' ss Score
-13.36
3' ss Seq
CTTTCCTTGACCCCACGCACGCT
3' ss Score
-1.2
Exon sequences
Seq C1 exon
ACTTTCATCGTACTGAATAAAGGCAAGACCATCTTCCGGTTCAGTGCCACCAACGCCTTGTATGTCCTCAGTCCCTTCCACCCCATCCGGAGAGCGGCTGTGAAGATTCTGGTTCACTC
Seq A exon
ATATCCTTTGCAGTTAATACCTGCTGAGTACCCCCTGGGGGCCCACGCTGGGGATGTGCACGTGCTGCCCCCACCCCACCTCCATTCTAGTTTAGGAGTGAGAGTAGCGCTGATTCCCTGCTGGTCCTAAGACAAATGCATGGTCATGACCTGGGAGCTGGTTGGAAATGAAGAACCTCTGACCCTCCTCCAGACCTGCCAAGTCAGCACCTGCATTTTCATTTGATCCCCAGGGGATTCTTGGGCACATGAAAGTTTGAGAAACCCTCTTCTGATTCTTCAGAACATTCTAGAAGCTAAGCTACTGAGGATCCCAGAAGAAATGACGTCTGTCGGGCTCTGATATTGGCTCCAAATATCCCTCCCCACCACACCCCCTTGGTCCGTCCTCCTCCCCACCCACTTGCAGGGACCTTCAAGCAGGTCACCAGAACTTAGCCAAGGAAAAACCATTTCCCAATAAAGAGGCCTCTAGTTTATTCACATGTGGGCATCTTTTGAGGGAGGCAGCACTTGCTTTTTGATTAGGCGTTGACAAAATGTTTGCAGTTTCAGAGTATCTCAAAGAACTCTGGTTAGCATTAAATTATATAAACCACAGCTGAAAAAAGCTCCAGCCTGCAGAGGAGAGCCATTGGAGTGATGCAGCGTAATGAGGGACTTACCGGGCTTGGGCCTGAGAGGGGCATCATTTGGGCAGCACACTGCATGGGGCGCCAGCACCTAATCACTCTGTTCTCTGGACTTCAGAGAAGGGGCCCCATAGATGGAGCCTTCCGGGAGGGTGGTGCCAGCTGCAGTCAGAGGCATGAGTATTTCACTGCGAGGGCCTGGGCAGGCCTCCCTTTGGCCAGTGGCAACCAGGGTGAGTGCACACACGCAGGTGGCTCTGCTGATCATCTAAGCGACACTGCTGGGCTCAGCAGTGCGACCGATTGTGGGTCTAGCGGGCTGGCCCCACAGAGCTCTCCAAGGTCCCCTTCAGCCCCTTCTCTGAATGGACTTTTTTGAGGCCAAGACAAAGACTTCACTCACTAACCTCTGGCCAAGGCAGGAGGCATCAGGATTACAGATACCTAGTGAGGGACTAAATAACCAGGACTGAGGCTGGCAGGTCAGGAGCTTTTCCTGCCCGGGCAGGGATGGGGGATGCTCCTCCTATGGCTCCACTTTCTTCCCACCTGTGCCCAGTGCCTGATCCTGACCCCAGGGGTTCATTGGAGGGGCATGCATGGCAAGTGGTGTCTGCATGCACATGTGCAGTAAAATGCATGCGTCCAACCACGTGTCTGCTCTCCAGCCTACCCCTGCCTTTCTGGTGGGGTTCATGAGACAACCCCACATGCAAACCATGGCTGTGGCGTGAGCAAAGTGGGAGGCAGACACTGTGGAGAGGGACCATATGTAGCGAGCAGCCTGCCATTCACAGCTGCATCTTATTTTGTGGGGCAAGTGTGGGTCTAGATTTCATCTTGAGCCATCCTGAGTTCCCTGTAGGTGTCAGGCTCTTTGCTAGGCACGCTGGGGTATCGAGCCGAATAAGACCCCGTCTGGGCCCCTTGGGAATTTTATAGTTCCCCTAAAAGTGATAAGGCAGCTTCGCAAATAGTTATGCTTTCTGCCAGAGTGTGGTCACAGCCTGGTAAGAAGAACAGAGCAGCAGGAGGAGGAAAGGCCAGCTTTTCTTGCTCTGAGCCCGTCTCTGGCCTCACTCCGGGGGTGTGGCCTCTCTAACAGCATCCTCCAGCTCTCACCTGGGGCTTCTCCTCCAGGTATCTAACCAACCCAGCACTGTTTGGCAGCCACAGAAGCCCTCAGGGATGTAGCAGAAGCTCCAGAGCTCCTGCAAGGTGCTGAGCTGGGTCGTGGGGCAAATGAAAGGTCAGGGAGGCAGGTGGGCAAGGGAGGCAGTGGGGGGCCCTCGAGTGCCCAGCCTGGCCAGACTGTCCATTGAGCAATGGCTCTGAGGCTGTGAGGTGCTGCTTCCACCTGGAAAAACTGGCCCTGAGGGCTCGGAGCCAGCCTCTATCCCCCAGGACAGCTGCCCCAGGGAATTGTCAAGCATCAGTGAGGACCTGTACTGGGTTCCCAGTGGCTGCCTTGACACTGCTGCTGCCTGGGGATGGGAGCACATTGCTGGACCTCGACAGCGCCACTTAGTGGGCTCAGTGGGCACTGGGGGGAAGAAGAGGCCTAGATTTGTGGGGTTTGGGAGCAGCCCCTCAGCAACACTGTTGAGCCTTGACATTGAGTGTGGTGTGTGGACCAGTAGCATCAGCTTCACCAGGATGTTGTAGGAGTGGCCGAATCTTGGGCCTCACCCCAGAACCTATGTGTAGCAAGGTCCCATGTGCATGCCACCCTAGGGCAGTTGCTTCCAAATGCTAATCTGAGGGCCATCTCAGTCTCACCTGGGAAGTTTGTAAAAATGCAAAATTCTTAGCTCTTTCCAGACCAGAATCACCAGTGTGAGGCCTAGAAATCTGTAAGTGCTCCATGATTTTTTTTTAACTTGAGGTATACTACTTCATATACCATAAAATTTATCTTTTTCTTTTTCTTTTTTTTTTTTTGAGATGGAGTCTCACTCTGCCGCCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAACCTCCGCCTCCTGGGTTCAAGCGATTCTCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGCGTCCGCCACCACGCCGGGCTAATTTTTGTATTTTTAGTAAAGGTGGGGTTTCACCATCTTGGCCATGCTGGTCTTGAACTCCTGACCTCGTGATCCACCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCAGGAGCCACCGCACCCAGCCAAAATTTACCATTTTTAAGTGCACAGTTCAGTGGTTTTTAGTATATTCATAAGGTTATGCAACCATCACCACTATCTATTTCCAGAACATTTGCACCACCCCAAAAGAAATCCTGTGCCCATTATCAGTCACTATGCATTTCTAAAGAACATCAGGTCTCATGTTTTGAATGGTGAACTTTTGCTGTGCTTAAATTTTTATGCTCATTCAAACATCTAAGTTCCACATGTGCAAAGTTCTGTGCAACGCCCTTTGGGAATGGTAAGTGGGGCAAAGACAAACTTAAAAGTGGGCAGGAATGCAGCCTGGTGAGAAAACCTGCTCAGTCGTGACAATCCAGGAGCTCACAGACCGTAGCAAGTGCGCAGTGATTCCGCTTGGCCTTGTTCTTGGCTCCATGCTTGCAGTGTATCTCTGGGAAGTTACCAAAAAGTAAATATGGGCATGTGGAATGATTTTTTTATATGTATTTTTGTTATAATCCTGCAGAATGTGTTCCTGCTGGGATTAAATAAAAGAAACCAACTGAACTCCATATCCTACCGCAGTCACATTCAGAGAGGCCTCACACACACACTGAGAAGTATTTTGCCTTCTTGGTTGTATAGGATCTGTGCACAAAATCCTCCCACGTTCCTCTACCAGATTCAAATGGGCAATCAAACCACATGTCTGTGGTGTATGTGTGTGTGCCTGTTGATTTAATAGCACAAACACATGAAAATACCCCTCCAGAGTTAATTACCTTTTCTTTGGGTGGTTTTTTTTTTTAAACTCCCTGGGATCTGAAGACTTAGGCAGCCCAAGTGTCAGGCATTCCCCACAACTCAGGCACTCCTTGCTGGCATTTTTATCATGAGGCTAGGAGTGGGTGTTTAGGGACAATGACATGACAAGATTGAAGATGTTCAGCTGAGCATAGACCTGGAGAGCTGGCCTTTGCCTCAGCCCACACAAGGGACCAGCTCAATCATCAGCCTGAAATTACAAGGCAGTGCAAACAGGTGTGCCCTGGCCAGGAGTTCAGTTGACTCGTCTCTATGGTATTGGCTACGTGCTGGGCGCCATGGGGGACCTGGGTATGCTTTAGGCAGAGTCATATGGACTGGGTGCTCAGTCTAGGAAGGAAGAGATCTCATACGTGCAGAAGAAGGATTGACAATTGTGCAAGTGCTGTCCTCAAGGCCATGGGAACCAGGCAAGGATTTTGAGCAGTGAAGTGGCAGAGAGACAAGAGCTTGCTACACGTCACCCTAAGCCATTGCTGTGTCTGGAAAAGGTAAAACCCAGATAGACAGCTCCTGTCATTGCCCACCATGGGACCCAGGTCCTGACTGGTGGGATCCAGAGGGCTGTGTGCCCTGGCTCTTCCCTGAGTCTGGGTGTTCAAGTCTCACTCACCTCTGCCTGGGTCCAGCCAAGGCCTGTAGTACAAGGCAGCCTGTTCACACCACTGCTCCCTGCAATGGGGCCTGTTCCCCCACTCTAAGGAGAGCTGTGAGTGGTCCCCCTAGAGCTGGAAGGGACTTGGCTCCACCGAGAGGAGTCCACCACCCAGCCTTCAGCACATGCTGCTTCACCATGACCAGCTGGGCTGACTGGTTGCTGGAGCAACCCTGGCCAGCCTTGGTGCTTATCTAAATGCCTCTTCCAGGAAGCCTTCCTGCCCAGCCCAGCCAGAGGCATGTTTGGTTTTTTCATAATATCCCATGTCAGAGCGTTTTGGGGACATGGCTCCATTGCCCCCCTGGCTCCCACTCAGGGCCAGACACACATGCTCAAGTGGGATTTCCTCTTACAAATAACAAATAATTCCCTCCCTCCTGTACGGTAGTCTCCCCACATTCGACGGTGCTCTCTACCTCGTTTGGTTTTCACACCGCCCCATGGGTGGCAGAGGCCAGGCGTGGAATAGCTTACCTGCTTGGCATGTGAGAGCCAGAAGCAGCATGACTCATGCAGACCCTCCAGTCTGGAGGCAGGAGAGTGGACCGGGTGGCCTTGAATGTCATCTTGCAGAGGTGGTGCAGCATGGGGCCTCAGAGTGGGGCCCAGATCAGGAGAACCAGGGTGCATGCTGGCTCAGCCATTGATCAGCTTGGTACCAGGAGTACTTTCCCAGGAATGCTGTAACAAATTACCACCAATGCAGTGGCTTAAAGCAAAGCAGATTTATCACCTTACAGCTTTGGAGGTCAGAGGTCCAAAATGGTTCTTGCTGGACTAAACTCAGGGTGTCAGCAGGGCTACACACCTTTTGGAGGCTCTAGGGGAGAATGTGTTTCCGAGGCATTTCCAGCTTCTGGAGGCTGCACTGGATTCTTAGTCTGTGGTTCCCTGTCATCATCAAGCCAGGAATGACCGGTTGAATTTCATGTCACAACACTCTGCCTCTCTTTTGCTTAAAAGGACCCCTGTGATTATACTGAGTCTACCTGGATAATCTAGAATGATCTCCCCACCTCAAGATCCTTAATTTAGGGCCAGGAGCAGTGGCTGATACTTGTAATCTCAGCACTTTTGGTGGCTGAGGTGGGAGGATTGCTTGAGCCCAGGAGTTCAAGACCAGCTAAGCAACATGGTAAGACGTTGTGTCTACAAAAAAAAATTAAAAATTAGCTGGCTATGGTAGTGTGCACCTGTAGTCCTAGTTACTCAGGAGGCTGAGGCAGGAGGATCTCTTGAGCCCAAGATTTCAAGACTGCGGTAAGCTGTGGTAATACCATTGCACTCCAGCCCCAGTGACAGAGCTAGACCCTGTCTCGCGGAGGCCAGGGGAGATCCTTAATTTAATCACATCTGCACGGTCTCATTTTGTCATACAAATTAGCATATTCACAGTTTCCGGGGATTCCTCCATGGCCACCTTGGGGGTGGTGGGGGCATTATTCTGCCTACCACAGTGACCTTCAACTTAACCTCTTTGTGCCTCAGTCTTCTCATCACCTAAAATGGAAACAAAGTCCCCATCACATATGGTTGTTGGGAAAACTGAATTCGCTGATGGACACGGAGAGCAAATTCTGGTACCTAGGAAGGGCTCAATGAATATTCACTCTTAGCATCATTGCTTGCATATTTTAGGAGTCACCTGGGCTCCCCAGTAGATGCTTAGCAGCAGATCCGTGGGGATGAATAAAGACTGGTTGGGGGGCTTGTTAACCATCTGCCTAGTGAGGAAAGCCTTGGCACATACCCCGCATGTGGGCAGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGTGTGTGTGTAAGGGAGAAGGGGTACTGATACTGAGATGATTATCTGATCCTGCCTTGAAAGCTGGAGAGGGATATAAGCCTGGCCCTGGACACCCTCACACGGGCAGAGGGCTGGGCAGATACCAAACTGACGGAGGGACCCCAGGGCCTGAAGTGATGCCTTCTGGTCACGGAGAAATCAAGGCTTCCTGGAGCCATGGCATCAGAGCCGAGCAGTCCTGTTGGCTCAGTCCTTGTTTGACTAAGGGAGAGTCCCAAAGCCTAATTTCCTCTCGTCCCAGATGAGAAACTAAATAATTATAAACTGGAGGCTGGTTTGAGATGCTGATTTCCTGATTGCCTGACTCCCTAGAAGAGGAGCAGCACGGAGGGCATCTACCTGGTTAGATTCCCGAGAGGCATCCCCACTGTCCCCAGCAGGGGCAGTCGGCACCGCAGCCAGGCCTGGTCTGTGCTCGGACTGCACTGGCCTTCCCATCAGGTGAGGTGGAGCTATGCTAGGGAGGCAAGAGGCAGCCCCTGGAGCTCAATTACCGCAGCTCCTGGGCGGCCTGTGGGAATCACCAGTTTGGCAGCTGTGCATACGGGGCTGAGGCCGGGCATGGTGTTGAGCGCTTGGGGGCAGCCACAGGGAGTGGAAGGCCTAGCCACTCCTCTGGGGCTGGGTAGGGATTTGTGAGAGAAGCACAGTGTCCCTGCTCTAGGCCAGGCCTCCAGGGGTGCCCCAGCCTACAGGAGGCCCAGAGTCTGCCCCCTTGTTCCTCTGCAGGCCTTGCAGAGGTGGAGGAGGGCGATTGGAGCTTTGTCTAGCCTGAAGCAGCAGCTAGGAATTGTAGCCAGAGTCAGGCTCAGAGAAGTCCTGGGCAGTTCAGTTCAAGGCCAAGAGCCCACAAGTAGACCTGAAGCACAGCTCTGGTACTTGAAGCGCTGCCTTGTGATGGGAGACAGATGGACATTGCCGTTCAGTGAGCCACCAGGGCTAAAAGAGGGGTGCCCGAAGCCCGCAGGGCACAGAGGCAGCACCGTGTTACCAGAAAGGCAGGACAGGCTGCTAGGGAGTTGGGTGGGGTCCTACTGACGGGCTCCTGCAGGGTGAGAAGGAGATTCCCAGGTGGAGCAGAGGGCTAGCTTGAAGACTAGGTGCACAGGCAGGAAGCAGCCAGAGGAGTGGTCCCCTGCCTCCCCAGGGGTAGCAGGCCCTGGCCAGGTGTGCAGTTGTTTGGCAGCAGGGCATTCTGCAGAGAACTTCTAGACAACGCCTGGCCTGGGCTGCTCCCCTAGAAGTGGAGGAGGGAACTCAGAGCCCTGCCACTCTGGCCTTGCCCTCCCCCTGAGGAGCAATTTATAAATGCCCATTTCTCTCCTATGTGACTGAGGACAGGGCCCCTCGCCTGACTGCGGTTAAAAGGCTTTGAGGTCTGGGGCCCACCTCTCCTGCCTTCCCTCCACACGAGACCCTACCAGCAGTGTGGTTTCAAGTCTCTGGTGCCTATTAGGTGTCATGGAGCAGGCCAGGGGGCCAGCTGCAAGTGCCGGGGAAGGGAAAGAGACCAGCCTGGGTGGAGGGGGATTGGCATGGACTGGTCACAGCCCCAGTGTGTCTCCTTGGAGACCCTGTTTATTGTCTGGTAGCACTGGCCTGGCAGTGATGACCCCCAGGGGCAGGACCCCCCCAGCGGTGGTGGCGTGGCCGGCCCATGCTGCTCAGCTTTCCTTGACCCCACGCAC
Seq C2 exon
GCTCTTCAACATGCTCATCATGTGCACCATCCTCACCAACTGCGTGTTCATGGCCCAGCACGACCCTCCACCCTGGACCAAGTATGTCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873-SCN5A:NM_001160161:3
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=0.001
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.8=6.5)
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
- 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)