GgaINT0143144 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1652645-1653305:-
Coord C1 exon
chr27:1653042-1653305
Coord A exon
chr27:1652766-1653041
Coord C2 exon
chr27:1652645-1652765
Length
276 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CACCTCTCTTCTCTCTGCAGACA
3' ss Score
11.87
Exon sequences
Seq C1 exon
ATGGCCGGCCTGCCGTACATCCCGGGCCCCGAAAACCTGCGCCCTTTCACCCCTGCCTCGCTGGCTGCCATCGAGCAGCGCATCGCCGAGGCAGAGGCACTCAAGCTAAAGAAGCAGCAGGTGGAGATGCCCGAGGAAGAGGAGCTCAAGCCCAGCAGTGACCTGGAGGCTGGCAAGAACCTGCCCCTCATCTACGGGGATCCCCCCTTGGAGCTCATCGGGACCCCTCTGGAGGACCTGGACCCTTTCTACAAGGATAAGAAG
Seq A exon
GTGAGGGACAGTGCTTAGCCCGTGGGTGTTTGGTGAAAGACCCAAAAAACTCAGAGCATGGACCCCTCCTTCTTCCATCCATGCCTCTGGGTCCCATTTGAGCCCATCTTGGTGAGCCAAAGCTCCACGTTGCTTTGGTTCCTTCTCCTCTGAAGCAGAGCATCCCTTCCTTGTCCTGTTCTCCGGCCTTTGGAGATTCAAAATATGCGCTTCTAAAGGCATCACTTTATCCATGGAGTTGTGTCAATTTGTGTCCCACCTCTCTTCTCTCTGCAG
Seq C2 exon
ACATTCATAGTCCTCAACAAAGGGAAATCCATCTTCCGCTTCTCTGCAACTCCTGCGCTCTACCTGCTGGGGCCCTTCAACCCCATCCGGAGAGGAGCCATCAAAGTGCTCATCCATTCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.136 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:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAACCTGCGCCCTTTCACC
R:
CAGGTAGAGCGCAGGAGTTG
Band lengths:
300-576
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]