HsaINT0145891 @ hg19
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium channel, voltage-gated, type V, alpha subunit [Source:HGNC Symbol;Acc:10593]
Coordinates
chr3:38620825-38622862:-
Coord C1 exon
chr3:38622422-38622862
Coord A exon
chr3:38620987-38622421
Coord C2 exon
chr3:38620825-38620986
Length
1435 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
ATAGGCTGGGGTCTTTTCAGCAG
3' ss Score
2.56
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTCCTGGCCTTGCTGCTCAGCTCCTTCAGTGCAGACAACCTCACAGCCCCTGATGAGGACAGAGAGATGAACAACCTCCAGCTGGCCCTGGCCCGCATCCAGAGGGGCCTGCGCTTTGTCAAGCGGACCACCTGGGATTTCTGCTGTGGTCTCCTGCGGCAGCGGCCTCAGAAGCCCGCAGCCCTTGCCGCCCAGGGCCAGCTGCCCAGCTGCATTGCCACCCCCTACTCCCCGCCACCCCCAGAGACGGAGAAGGTGCCTCCCACCCGCAAGGAAACACGGTTTGAGGAAGGCGAGCAACCAGGCCAGGGCACCCCCGGGGATCCAGAGCCCGTGTGTGTGCCCATCGCTGTGGCCGAGTCAGACACAGATGACCAAGAAGAAGATGAGGAGAACAGCCTGGGCACGGAGGAGGAGTCCAGCAAGCAG
Seq A exon
GTGGGCCCTCACCCCTGCATGTATAAGGCACCTACATATACAGGGCCCAGAGCTCTGCTGTCCGGGCCACCCAGCCTCTCTCAAAGCAGCTTCCCCTCCCAGACTGCCTTGGCAGTGGGTAGGGGTAGAAGGCAGGCCCTCCCCACAACAGCCAGCCTCTCAGAGGGGTGCTGAGACCAGCCCTCAACCCTCCCTTCCTAACTCAGTCCAGAAGCTGACCTGGGGAGGGGCTGCTATCCACCACTCATGCCCTGGCTGGGCATGGGGAGCTCATTGTACAGACAGGGAAACGGAGGCATGGCAAGAGAGACTTGCTGGGTGTTCCTCATGAGTTTAGAACAGAGCCTCTAGCCCCCAGTTCCCACACTGACCATTGTCCCCCCTCCAGGACTGGCAAGGTAGAGTGTCTTGGCGAAAGAGAAGTATGGTTTTCTGACCTCCAGACTGCCCCTTCCCCTCCTCCCACACCCAGGGCTCATTCTGAGATTTAAAAATAAGCATCCCTAAGACTGAGGTGTCAGGGACAGCACTATCTTATCTCGCAACCTGTTATTTTTAACACTTGGGACCAGAGTCTGCACAAAGCAGGCAGGGCCCACCCCTCCCCTCCCCTCCGTTCTCCCTTGGCCTGAGCCAGGCTCAGATGGCTTCTTCTCAGGGCTTTAGGTCAAGCCCCCAGGAGTGTTCTCCCTGTTGAGTCAGGCCCATCTTGGCTGCTTCCTCTGGGCCTGCACTGGCTGGGCCTGGCTGTGGAGAGCAGCTGCTCCCCATGTGTGGAACTTGATCTAAGGCTCTGGGCTTGGTTTCACATCCTCCTGCCTCCCTGTGGTCCCAGAGGCCACCCTTTCAAGTCAGGTTGCGGGGCAGTGGCAATGTCTGCTCAGGGAGAGGGAGTGTTGGTGTTGCCAGGACCACAGTTTCCAATGATCTCCAGCACAGGAGGGGAATTCCGGCTGTCTCTCATTTCCCTTCTCTGTTCCTTCTCTTGAGCCCATTGACTCTGGCTCCTGGGTGTGTGTGGTGTGTGTGGGGGTGTGTGTGTGTGTGTGCGCGCGCGTGCGCGCACGCAAGCCGGGAGTGCCACAGGGATTCATGAGGGAAGTCAGTGTGACCTTCCTAAGTACAGTGGCCAGCATTTGTGAGCTGGGCATCGTGGCCCAGCTGCACCCTTCCAGGGAGTCTGGGGAGGGGGAGTTATGCCAGGCCGGCCAGGGGCTTCCTGTCTCTAGGCCCTTTGCTTGGACCTACCAGGAGCCTCCCACCTGCCTGCTCAGGCCCCTTGAGGGAGGAGTCTTCAGTGAGATGGAGGCCCCATGAAGACAGCTGGAGGCAATGCCCCAGATGCATGGGCAGGGTCTGAAACCCCCAGGGTCAGGGCCCTGGAGACCCTCTGGCTGGGTGTGTGGACTCAGCTCATAGGCTGGGGTCTTTTCAG
Seq C2 exon
CAGGAATCCCAGCCTGTGTCCGGTGGCCCAGAGGCCCCTCCGGATTCCAGGACCTGGAGCCAGGTGTCAGCGACTGCCTCCTCTGAGGCCGAGGCCAGTGCATCTCAGGCCGACTGGCGGCAGCAGTGGAAAGCGGAACCCCAGGCCCCAGGGTGCGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873-SCN5A:NM_001099404:17
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.527 A=NA C2=1.000
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(20.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGCCACCCCCTACTCCC
R:
GGTTCCGCTTTCCACTGCTG
Band lengths:
356-1791
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)