GgaINT1024565 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:76656-78369:-
Coord C1 exon
chrLGE22C19W28_E50C23:78099-78369
Coord A exon
chrLGE22C19W28_E50C23:77602-78098
Coord C2 exon
chrLGE22C19W28_E50C23:76656-77601
Length
497 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
ATCCTTTTCTTCTCCTTCAGGAA
3' ss Score
11.75
Exon sequences
Seq C1 exon
AACCGCATTCAGGGAGCTGTCTTTGACTTTGTCACTCAGCAAGCATTCGACATCGTCATCATGATGCTCATCTGCCTCAACATGGTGACCATGATGGTGGAGACGGACACACAGAGCAAGCAGATGGAGGACATCCTCTACTGGATCAACCTGGTGTTCGTCATCTTCTTCACCTGCGAGTGTGTGCTGAAGATGTTCGCCTTGCGGCACTACTACTTCACCATTGGGTGGAACATCTTTGACTTCGTTGTTGTGATTCTGTCCATTGTGG
Seq A exon
GTAAGTGCAACACCCATTTTTCTTTCTTGGTGTTTGCAGAGAAGGTGCATTCAAAGAGGATGTGTAGGTACCCGGACTTCTGGCTTCTCTTTTCACCCATGGCAGAGTTTGGCAGCTCAAAGGCCCAACTTGCCTGCCTTCCTCCCTCTGTCCTGGCGTTCATTTCCAGTTGTATGGAGTAAAACACTTGACAATTACTCCCCGTATCTTTAAAAGCAGACTTTTTACTCACCTCCTTGGAATGTTATAATGCTTACCAACCACTGAAAATAGCATTGCAGCACTTCCTACATCAGCATGTGATTTGCACTCCTGCTTTCTGTTTGGTTGGATGTTGAATCGAGTGGTTTCCTCCAATAAATTTTTCTTTTTAGTGGCTAATCTGTGAGATGCCTGTAACTTCACAAATACAAGTTATACAAACACAACTTAAGGGTCATTTAAGCCTGGCTGACCAAGGCATGCTGACAAAAGCCAATCCTTTTCTTCTCCTTCAG
Seq C2 exon
GAATGTTCCTGGCTGAAATCATCGAGAAGTATTTTGTATCCCCCACTCTCTTCCGAGTCATCCGCCTGGCTCGTATTGGACGTATCCTGCGTTTGATCAAAGGAGCCAAAGGGATCCGCACCTTGCTTTTTGCCTTAATGATGTCTTTGCCTGCCTTGTTCAACATCGGCCTCTTGCTGTTCCTGGTCATGTTCATCTTCTCCATCTTCGGCATGTCCAACTTTGCCTACGTCAAGCATGAGGCTGGCATCGATGACATGTTCAACTTTGAGACCTTTGGCAACAGCATGATCTGCTTGTTCCAGATCACGACGTCGGCCGGCTGGGATGGCCTCCTGCTGCCCATCCTAAACCGGCCTCCAGACTGCGACCTGGACAAGGAGCATCCCGGGAGCGGCTTTAAGGGGGACTGCGGGAACCCCTCAGTGGGGATATTTTTCTTTGTGAGCTACATCATCATCTCCTTCCTGATCGTGGTCAACATGTACATCGCCATCATCCTGGAGAACTTCAGCGTGGCGACGGAAGAGAGCGCAGACCCGTTGAGCGAGGACGACTTCGAGACCTTCTATGAGATCTGGGAGAAGTTCGACCCCGACGCCACGCAGTTCATAGAGTACAGCAAGCTGGCGGACTTTGCAGATGCTTTGGAACATCCTCTGCGCGTCCCAAAGCCCAACACCATCGAACTCATCGCCATGGACCTCCCTATGGTAAGTGGAGACAGGATCCACTGTTTAGACATCCTGTTTGCCTTCACCAAACGCGTCCTGGGGGACAGCGGAGAGCTGGATATACTGAGACAACAGATGGAGGAAAGGTTTGTGGCTTCCAACCCTTCCAAAGTGTCTTACGAGCCCATCACCACCACGCTGCGGCGCAAGCAGGAGGAGGTCTCGGCCGTGGTGTTGCAGAGGGCTTACAGGTCGCGGTTGGCGAGGCGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:25
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=0.006
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(20.5=47.3)
A:
NA
C2:
PF0052026=Ion_trans=PD(79.0=52.5)
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:
CACAGAGCAAGCAGATGGAGG
R:
GAACAGCAAGAGGCCGATGTT
Band lengths:
344-841
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]