GgaINT0143164 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1636573-1637019:-
Coord C1 exon
chr27:1636890-1637019
Coord A exon
chr27:1636728-1636889
Coord C2 exon
chr27:1636573-1636727
Length
162 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GGCTCTGTGTCCACCCCCAGGCT
3' ss Score
8.47
Exon sequences
Seq C1 exon
AACCCCCTTTCCAGTGACAACGCCTCATCCCTGTGCAGCACTGTGGACTACAAACCACCGCTGCCCGAGGAGGAGGAGGTGGCCGAAGAGGCTGAAGAGAGCAATGAGCCCGAGGAGTGCTTCACTGAAG
Seq A exon
GTGAGAGCTATGAGCACCTTGGAGAGGGGTGTTCCAAAACTCCAAATTCTCCCATTTCCATGGAGATGTTTCCCAGGAGCGGACATCTCCAAATGGGGTTAAAATGCTATCACGGCGCAAATAGCAGTGGGGAGGTGACCCAGGCTCTGTGTCCACCCCCAG
Seq C2 exon
GCTGCGTCAAGAGGTTTCCCTGTCTCCACGTGGACATCACCAGTGACAGAGGGAAGATCTGGTGGAACATTCGTAAAACCTGCTTCCTCATCGTGGAGCACGACTGGTTTGAGACCTTCATCGTCTTCATGATCCTCCTCAGCAGCGGGGCGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.591 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(20.7=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(21.2=84.6)
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:
AACCCCCTTTCCAGTGACAAC
R:
GTCTCAAACCAGTCGTGCTCC
Band lengths:
245-407
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]