HsaINT0145904 @ hg38
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium voltage-gated channel alpha subunit 5 [Source:HGNC Symbol;Acc:HGNC:10593]
Coordinates
chr3:38630311-38633359:-
Coord C1 exon
chr3:38633035-38633359
Coord A exon
chr3:38630430-38633034
Coord C2 exon
chr3:38630311-38630429
Length
2605 bp
Sequences
Splice sites
5' ss Seq
AAGGTGACT
5' ss Score
6.64
3' ss Seq
ATGCTACTGTCTGTCCCCAGACT
3' ss Score
10.48
Exon sequences
Seq C1 exon
CTTCCCCACAGGCAACGTGAGGAGAGCCTGTGCCCAGAAGCAGGATGAGAAGATGGCAAACTTCCTATTACCTCGGGGCACCAGCAGCTTCCGCAGGTTCACACGGGAGTCCCTGGCAGCCATCGAGAAGCGCATGGCAGAGAAGCAAGCCCGCGGCTCAACCACCTTGCAGGAGAGCCGAGAGGGGCTGCCCGAGGAGGAGGCTCCCCGGCCCCAGCTGGACCTGCAGGCCTCCAAAAAGCTGCCAGATCTCTATGGCAATCCACCCCAAGAGCTCATCGGAGAGCCCCTGGAGGACCTGGACCCCTTCTATAGCACCCAAAAG
Seq A exon
GTGACTACCACCCACCTCCAGCCCTGCCTACCCTTCTGTGCAACTCCCTTGTCAATGGAGCAGAGGGGGAAGAGGGCCTGGCCTCCATATGGGGCTCTATTTAGGGTGGCTCATGAGGCTCTGGGGAAATGAGTCACTGGTGATCTATATTCCAATCACCTTAATTTTGGAATTCTGGAATAAAAACAGGAATTATGCAGCCTGAGATGCTGGTTTGGTGTAATGAAGAAGAGAGGGTAGCCTCAGGGAAAACACGCCTCCTGTGATGTCCTTCTTTGGGAATTACGTGTGGTTAGATTTTTACCCCTGAAGGACTCCTCCCCGTTGTGTGGTGTGTGTGTGAATTGGAGTCAAGCCCCAAGTTCTGGCCTGCGTTTGGGCCCTGCCTGAGTTTGGGCCACAGAGCATAGCCTGTGGTCCTTTCTCCTTAATGGGGACAGCATGTAGTCCCCACACCCACGAACTATGCATGGCTATGCTGGCTGGCTCAGGCCACGGCCACAGCAGCAGTTCCCTGAGCTTTGAGGGCTGGCAATGGGACCAAGAAGGCCAGTGGAAAGTCTGAAAGGGATGGAGAGGGCAGTGATCACTGGGGGATTTTTGGGGGAGGGTGGCGTGTGATGTTCTGCCATTGTCCCTTCTGATCATAGGGAAGGGAAGTGGCTTTTGTCTGCTAGGGCAGGGAGACTTGGGCTTCCTCCTAGCATGGCTCCGACCCAAGAGGTAACTGCCCCTGTCCAAATTCCCTGCCCTGGCCTCCCTCCTCCAGATCTCAGGCCCATTTGTGCCCCATCCCCACCACACACAGAGCTCCTGCAGAGGCTTGGTCTCCAAGCTACCCACACTTCTGGGCCTTACTTCCAGAGGAAGGTGGATTTGAATTTGGGGGAGGTATTTTTCCCAGAAGGCTGAGTATGAGGAAGACAGTGGCCAGGCACAGTACTGCAGTCAGCACCAGGCTGAGGAAGCTCATGGGGGTCAGACAGGGCTGGTGTGGCCAGTGAGAAAATGTGACTACAAGAGTGTGTGACTGTGGTTTAAGACCAAGAGCCTGGGGATGAGCCTGGGCCGTGTCTTTGGGTGTGCATGCATGCATTGGATACGTGAGTGGTTGTGCATGTGAAGTAAAAGCCCACCCAGTCCACATAAACAGGTGGGGGAGGAGGCCTTGAACTTGGTCCTGCTCCCAAGCCCCCAGCTGAACTTTCCCTTGGTTCAAGTGACTCCAGTGGAGTGCAGGCCAGGTTGGGGCCATAGCTGGAGTCAGAATGAGGCTGGAAGGTGGGCTTAGTCAAGGTGGGCGGGCCTAGGTCATGGTTGGTCGGAGATGGAAGTAGGAATTGGGGTTAGGGTTAAGGCCACAGCTGGTAGTGTGAGTCAAGCTTATGGGGAGAGGATGAGTGGCGATTAGGCTGAAGTTAGCTGGGACAGGCAGGCTCCACGGCAGGTGGACCTGACTGAGGTTGAGGTCAAGACTGGACTGGGCTTTTGGGGGCTGGTGGCAGCTGAGCCTGTGAGAGATCAGGGACACCATCTCTTCTGTCCTTGGGTCTGGGAATGCTTGAACAGCAGCTCCAGGGATGATTCCGGCCTCTCACTTTCTGTTTCCACTTGTTGATCCCTGGCCACGCTGCCTGCAGCCCCACAAGGCAATGGAGGCACCACAACAGAACTTTTGGTCCTAATCTATCTGGTCAGCTTGTCTCCCCAGACCAGATTGGGTAGAACCTTGTCCCACCAGCTCATTCGGCAGAATAGTGGACTCACTGCCTTGCCCATGGGTGGAGGTGAGGGAGGTCTCAGGGGAATGTCAGGTTGTGACATTCCCCTAGACCTCCGTGAGGCCACAGAGCTGTGACCACCACACACCGGGGCAGGTGGGGAGGCACTGCTGTCCTCAAGGGCTGCTTGGGCACCTGATGTGCATGTGTCTCAGCATTTGGCTCTCATTGTCCGCTCCTGTGCCCCATTGTGCTGTGTAGAAAGGATCTTCCAGAAGCTCAGGGAGGGGTTGCATTGCACTGTTCATGATCCTCTGGAGGGAGGCAGTAGGCTGTGTCCTGTGGGATGGGGCTGACATTTGTCCTGGACTCCAGGAGACAGGGTCCCAAGAAAAGCTCTCTCAGGGGACTGCTTCTGCATTTTCGTTTTCCCTTCTCCTCACCCGTAAGTCCTTCCTGCTGACGCAGCTTCCCTATCACGCCCTCCCTCCCAGTGGGCCTGGCAGGGACCCCATGCAGGGTGAGGAGGGGTCAGCTAAGGGAGAAGGGGAGGGAGGAGGCATTCCCAGGTCTGCTGAGCCTCTGCTGTGACAACAGCTGGGCAAGGACTGTAAAAGCTCCCTTCTTTTTGTGACTATAATTTTGAAACTAAATCTCAACCAACCGGACATTCCCCTGAGATCTCCCTCACCTCCACCCATGGGCAAGGCAGTGAGTCTACTGACCTGCCAAATGTGCTGGCAGCCTCCCTTCCCCCTCTCCTCCCTCAGCCCCTCTCCTCCTCCTCCCACCTCACCGCTCAGCCACAGTCCAAGGGCTCTGAGCCAAAAGCTGCCCCCAAAAGCCTTTCTACACAAGGGCCTAATGCTACTGTCTGTCCCCAG
Seq C2 exon
ACTTTCATCGTACTGAATAAAGGCAAGACCATCTTCCGGTTCAGTGCCACCAACGCCTTGTATGTCCTCAGTCCCTTCCACCCCATCCGGAGAGCGGCTGTGAAGATTCTGGTTCACTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873:ENST00000413689:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.352 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
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