GgaINT1024554 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:90236-91775:-
Coord C1 exon
chrLGE22C19W28_E50C23:91419-91775
Coord A exon
chrLGE22C19W28_E50C23:90707-91418
Coord C2 exon
chrLGE22C19W28_E50C23:90236-90706
Length
712 bp
Sequences
Splice sites
5' ss Seq
GTGGTCAGT
5' ss Score
4.85
3' ss Seq
TGTGACCTCTTCTCCCTCAGGTG
3' ss Score
11.66
Exon sequences
Seq C1 exon
CTGAGAGTCTTCAAACTGGCCAAGTCCTGGCCCACTCTGAACATGCTGATAAAAATCATCGGTAACTCAGTGGGTGCTTTGGGCAACCTGACCTTGGTGTTGGCCATCATCGTCTTCATCTTTGCGGTGGTGGGCATGCAGCTCTTTGGCAAAAACTACAAGGAGTGTGTCTGCAAGATCAATCCGGAGTGTGAGCTACCCCGCTGGCACATGCACGATTTCTTCCACTCCTTCCTTATTGTCTTCCGTGTGTTGTGTGGGGAATGGATTGAGACCATGTGGGATTGCATGGAGGTGGCAGGACAGGCCATGTGCTTGATTGTCTTCATGATGGTCATGGTCATCGGAAATTTAGTG
Seq A exon
GTCAGTAAATGGTTACTGATGGTCTTTATCATTTTTTTTTTTTCTGGGTGGGGTAGAGCATGGGGAGACCACAGGACTGGGGCGGAACATGGGGAGACCACAAGTCTAGGCAGCCTCTTCCAGTTTGGTTGGGGTCCTTCATGGCCTGTGATGGATGAACAGTCCTGTTGACTTTGGTAGTACAGTATTAAGGCCTTAGCCAGTTGCCCACAAAAACAGCATCCAAGAAGCATGCAGTAAAAGCTTTTCAAATTCCAGGAGAGGAAAGTCCTGAAGTGCTAAAATAAGGTTGGAGGTTTCTTCTAAAATCTGCTAGTTCAATCCTGCAGCGTTATTGTATGCAAGAAGGGGCTGTTGAAATGGCACAGGCTGTCATGTGGGAGCTCAGACTGGATCAGAATGTTTCTCTCTAGACTTGTATTTTGTGAAGAAAAGTCTGTGGAGGAAAACATAAACAAGAATGAAGCAGAGTGACCGGTTGCATATCTTACAAGTAGAGTTTGAGCCTTATCTGGAAGGACTTGTTTCTCACTAAAGGGATTTAAACAAAACGAGCACTGGGACTACCAGTAGATGTGGGCAAGGAAATAAATCTGGGAGTGATCCCTCAAAATGCCCCTGTGTGGCACATTTCCTTCGAGCTTTAGATGGGCCCAAGGTGGAAATATTGTCCTCGTGTAGGCTCTGCCAAGTGTGACCTCTTCTCCCTCAG
Seq C2 exon
GTGCTGAACCTGTTCCTGGCTTTGCTGCTGAGCTCCTTCAGTGCAGACAACCTGGCAGCAACGGATGACGATGGGGAGATGAACAACCTGCAGATCTCTGTCATTCGCATCAAGAAGGGCATTGCCTGGACCAAGGCGAAAGTGCGTGAATTCATGCAGGCTCACTTCAAGCAGAGAGAGGCAGATGAGGTCAAACCCTTGGACGAGCTGTATGACAAGAAGGTGAACTGCATTGCCAACCACACGGGGGCTGATATCCACAGAGACATCGATTATCAGAAGAACGGCAATGGCACAACCAGTGGAATTGGGAGCAGCGTGGAGAAATACATCATCGATGAAGACCACATGTCCTTCATCAACAACCCCAACCTCACCGTCCGGGTGCCTATTGCTGTCGGGGAGTCAGACTTTGAAAATCTCAACACAGAAGATTTCAGCAGCGATACAGACCCTGATGGCAGCAAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:15
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=0.197
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(4.2=5.1),PF065128=Na_trans_assoc=PU(61.0=84.7)
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:
GGTGTTGGCCATCATCGTCTT
R:
ATCTCCCCATCGTCATCCGTT
Band lengths:
342-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]