GgaINT0143168 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1633711-1635282:-
Coord C1 exon
chr27:1635004-1635282
Coord A exon
chr27:1633765-1635003
Coord C2 exon
chr27:1633711-1633764
Length
1239 bp
Sequences
Splice sites
5' ss Seq
GTGGTACGT
5' ss Score
8.61
3' ss Seq
TTCTCTCCCAATCCCCACAGGCG
3' ss Score
10.82
Exon sequences
Seq C1 exon
GTGGTGGTAAATGCCTTGTTGGGTGCCATCCCCTCCATCATGAACGTCCTGCTGGTCTGCCTCATCTTCTGGCTGATATTCAGCATCATGGGGGTGAACCTCTTCGCAGGGAAGTACTACCGATGCGTCAACACCACCACGGGGGACCTCTTTGACATCAGCGTGGTGAACAATAAGAGCGACTGCATGGCTCTCCTCCACACCAACGAGGTCAGATGGGTCAACGTCAAAGTCAACTTCGACAACGTGGGCTTGGGATACCTGTCCTTGCTGCAGGTG
Seq A exon
GTACGTACCGATCACTGCGCATCGTCATAGCAGAGGGTCATCCATCATCATCGTCATAGCAGAGTCAGCAATTGCCATCGTCATAGCATGGGGTGAACAGCATCAAGGCTAAAGTGAAATGCATGTCTGAAGCCCACGCCAGGGTTCCTGGCTGCTGCTTAGCTCCAAGATTTAATTTAACCCAAAAACTGCAGGCTCGAGGAGGAAACAGGCAGGATAGAAGATGGGAGGGGAAAATTAAGTGTAGCAAGGGAACTGTTGGGGATGAGTACACAAAGCAGCAAGGTTGGAGCTGTGGGAAATCCTCCACAGCACGGCATGCAGGAGCAGGGAGGAGAAAGAGTTTTAAGCACCATTATTTGGAAAAGGAAGATGCTGTGACCCAGGGTCATAGAGCCACTTGAGCCTCTCACTTGCTCGACCTGTCTCTCAGTCTTCCCAAAATCGAGACTCCCATCCCCCCTTCGCAGCCTCCCTGCATGAAGATGTTCTTGCTAGAGTGAGGTCTGCGACAGTCATAGGCTGCAAGAGTTTTGGCTGGGGAAGATGACGACTGGAAAAAAGAGCATGTGAGCATTGGCCATGGGTGAATGCAGCCATGCTTCCATTGAACTCACCACAGCTGAGCAAGGCGAGCAGAAGGGGAACTGCTCACCACGACGTTAATAAAAGTACAGGTGTGGGCTCTGTTATTGGGTCACTCCCACTGGATCCAGGGGAACTAGTGGTTGCAGAACTAAAGCAGAACTCAAACTGATCAACCAGCTATAAACTCAGCTTCCTCTTCAAGGCTTGTTGTTTCCTCAGACTCAGGAAATAAGATGTTCTGGCTTTTTGCTTAACAAATCAACTGCAGAAGCCTATAAAAGATGCAAGACGCCCCCACCTCAGTGGGACAGAATCATAGAACCATAGAATGACTGGGTTGGGAGGGAGAATGGTTGGGCTTGGAAGGACCTCAAAGATCATCCAGTTCCAACCCCCCTGCCTTGAGCCAGGTTGCCAACCACCAGATCAGGTTGCCCAGGGCCGTATCCAACCTGGCCTTGAACACCTCCAGGGACATTCACAGACTCTCTGGGCAGCCTGTGCCAGCACCTCAACACCCTCTCCATGAAAAATTTTCCCCTGCCATCTGAACCCCAACCTAAACCCCAGAAGTGTCCCCATTGCCTTCCACTCCCTTCATAGCCCCATACACCTCCTGTTGAGCTTGCTCTTCTCTCCCAATCCCCACAG
Seq C2 exon
GCGACCTTCAAAGGTTGGATGGACATCATGTACGCTGCTGTGGACTCACGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:24
Average complexity
IR
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(40.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTGGTAAATGCCTTGTTGG
R:
GAGTCCACAGCAGCGTACATG
Band lengths:
326-1565
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]