GgaINT0143166 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1635483-1636292:-
Coord C1 exon
chr27:1636119-1636292
Coord A exon
chr27:1635606-1636118
Coord C2 exon
chr27:1635483-1635605
Length
513 bp
Sequences
Splice sites
5' ss Seq
GATGTAAGT
5' ss Score
9.11
3' ss Seq
CCTCGGGCTGCTCCTTCCAGGTC
3' ss Score
8.57
Exon sequences
Seq C1 exon
GCTTTTGAGGACATCTACATAGAGCAGCGGAAGGTGATCCGCACCATCCTGGAGTATGCTGATAAGGTCTTCTCCTACATCTTCGTCATTGAGATGCTGCTCAAGTGGGTGGCCTATGGCTTCAAGGTGTACTTCACCAACGCGTGGTGCTGGCTGGACTTCCTCATCGTCGAT
Seq A exon
GTAAGTGGTGCTAAATGAGAGCCTATGGTGTCATCCTTAGCGATTTAGGGGGCTGTCGTAAGTCATTGCTAACCAGCCCTTGCTTGTATGGGAATGAGGGCTTAAACAATGGTTTAAACTCATGGTGGTTGGGAGGAAGGGCCACCCCTTTTCCAGGCTGCAGGAACCCTTTCAAACCTCTTTTGGTGCTTTATGCGTGCACCAAGCACACCATGCTGTACTAGACCCCAGCAGAGGTGTGAAGGGACACGGGGGTCTCCCACAAAGCAAACATTTACCTGTCCAGTATTTCTGCATTCCACGTCACTTCTACCCTCCTACCCAAAAGGAAGGGACATCCTGGTGGCAGCCCAGTCACCAGAGACCCGAAGACTCAAAGCCAGTCCCTGTGTCCCAAGACAACACGATACCCACATGCTGGGAAAAGAGGAGGGCAGGAGATGCCAGGATATGGTTCACACTCTGTTTTTTTTCACCTGAGATGCTACTCATTCCTCGGGCTGCTCCTTCCAG
Seq C2 exon
GTCTCCCTCATCAGCCTGACAGCCAACTGGTTGGGATACTCCGAGCTGGGAGCCATCAAATCCCTGCGGACACTGAGAGCACTGAGACCTCTGCGTGCCCTGTCCAGATTTGAAGGCATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:22
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=PU(17.1=67.2)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=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:
TTTGAGGACATCTACATAGAGCAGC
R:
CCTCATGCCTTCAAATCTGGACA
Band lengths:
294-807
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]