GgaINT1024552 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:92358-93324:-
Coord C1 exon
chrLGE22C19W28_E50C23:93086-93324
Coord A exon
chrLGE22C19W28_E50C23:92532-93085
Coord C2 exon
chrLGE22C19W28_E50C23:92358-92531
Length
554 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
TCTCTCTCCCAACACTCCAGGTT
3' ss Score
7.65
Exon sequences
Seq C1 exon
AGCTGGAGGAGTCCCAGAGGAAGTGTCCCCCATGCTGGTACAAATTTGCCAACACATTCTTGATCTGGGAATGCCACCCCTACTGGATCAAGCTGAAGGAGATAGTGAACTTAATCGTCATGGATCCCTTTGTTGACCTGGCCATCACCATCTGCATTGTGCTCAACACTCTGTTCATGGCAATGGAGCACCATCCTATGACCCCAGAGTTTGAACACGTGCTCTCCGTAGGAAATCTG
Seq A exon
GTAAGATAGTGTTGGTAAATATTCACTGAATCATTGAGGTTGGGAAAAGGCCACTAAGGTCACCAAGACCAGCCCCAGCCCATCCCACTGTGCCCATCACCAAGATCAGCCCATCCCATGTGTGCCCACATCCCTCAGTGCCACATCTCCACAGTTCTTGAGCTCCTCCTGGGATGGTGACCCCACCACTCCCTGGGCAGCTGTGCCAATGCATCACCACTCTTTTGGAGAAGAAATGTTTCCTAATACCCAACCTGAACCTCCCCTCTTCAACCTGAAGCTGCAGTCTGTGGCAGCTTGGAGATGTTGGGTGCACCTTTCTGGACAAAATGCAGTACTCCGTAAAAACCCATCCATTAATCTCTGGTATGCCTGAGTAGGTCAGTGAGATTTGTGCTAGTGAAGCTGAGAACTGGGGACAATTACACAGCATTGAATAGACCGTGTTTGAACTGTCATGATGAATTGAAGGTTCATCATGAAGACTGAAGATCACAGCATGGACAGATGTGAATCTGTGTCCATTCTTTTCTGTCTCTCTCCCAACACTCCAG
Seq C2 exon
GTTTTCACGGGAATTTTCACAGCAGAAATGTTCCTGAAGCTCATCGCCATGGATCCCTACTATTATTTCCAGGAAGGCTGGAACATCTTTGATGGATTCATCGTCTCCCTCAGTTTAATGGAGCTGAGTCTGGCGAATGTGGAGGGGCTCTCTGTGCTGCGATCTTTCCGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:13
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(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGATCTGGGAATGCCACCC
R:
AAAGATCGCAGCACAGAGAGC
Band lengths:
348-902
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]