GgaINT0143165 @ galGal4
Intron Retention
Gene
ENSGALG00000000252 | SCN4A
Description
sodium channel, voltage gated, type IV alpha subunit [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr27:1636119-1636727:-
Coord C1 exon
chr27:1636573-1636727
Coord A exon
chr27:1636293-1636572
Coord C2 exon
chr27:1636119-1636292
Length
280 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
TAGCTCCACATCTCTTCCAGGCT
3' ss Score
5.65
Exon sequences
Seq C1 exon
GCTGCGTCAAGAGGTTTCCCTGTCTCCACGTGGACATCACCAGTGACAGAGGGAAGATCTGGTGGAACATTCGTAAAACCTGCTTCCTCATCGTGGAGCACGACTGGTTTGAGACCTTCATCGTCTTCATGATCCTCCTCAGCAGCGGGGCGCTG
Seq A exon
GTAGGTCCCATCCCTCCTTTTTCCCCTTCCCCTTCGCTCTTCAGCAGCTGCAGGCCAGATGTTTTAGTTAAAACTCCTTTTGGGCCATGCCTGCTCGGTGCAAGGGGATCTAAGCATCCTCCAGGTGCCCTGCATTGGTAGACCATGATACAATCCTCCTCAGCCTTCACTTTTCAAGCTGTCCCAGGAAAGTAGGGATGATGCAGCCACGGTCCTGCACCAAGCCATGCAGTGGGTCTAATGGCAGAATGACTGTCATGTAGCTCCACATCTCTTCCAG
Seq C2 exon
GCTTTTGAGGACATCTACATAGAGCAGCGGAAGGTGATCCGCACCATCCTGGAGTATGCTGATAAGGTCTTCTCCTACATCTTCGTCATTGAGATGCTGCTCAAGTGGGTGGCCTATGGCTTCAAGGTGTACTTCACCAACGCGTGGTGCTGGCTGGACTTCCTCATCGTCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000000252:ENSGALT00000040680:21
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:
PF065128=Na_trans_assoc=PD(21.2=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.1=67.2)
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:
CGTGGACATCACCAGTGACAG
R:
GACGATGAGGAAGTCCAGCCA
Band lengths:
298-578
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]