GgaINT0143147 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1651435-1651741:-
Coord C1 exon
chr27:1651613-1651741
Coord A exon
chr27:1651527-1651612
Coord C2 exon
chr27:1651435-1651526
Length
86 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
TTTCCTCTGCCATCCTGCAGCTA
3' ss Score
10.2
Exon sequences
Seq C1 exon
ATACACCTTCACTGGAATATACACCTTCGAGTCCCTCATCAAGATACTGTCAAGAGGTTTCTGCATCGATGACTTTACATTCCTGCGTGACCCGTGGAATTGGCTGGACTTCATGGTCATCTCCATGGC
Seq A exon
GTGAGTGCAGTGGGACCCTGGGGACCCTGGGGACTTTGGGGACAGTGTGGGGTGACATTCACACCCTTTCCTCTGCCATCCTGCAG
Seq C2 exon
CTACATCACTGAGTTTGTGGACCTGGGGAACATCTCTGCTCTCAGAACCTTCCGTGTCCTCCGGGCCTTGAAAACCATCACAGTGATACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:4
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(15.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.2=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:
ACACCTTCGAGTCCCTCATCA
R:
GACACGGAAGGTTCTGAGAGC
Band lengths:
167-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]