GgaINT1024550 @ galGal4
Intron Retention
Gene
ENSGALG00000006060 | SCN8A
Description
sodium channel, voltage gated, type VIII alpha subunit [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chrLGE22C19W28_E50C23:94998-97327:-
Coord C1 exon
chrLGE22C19W28_E50C23:96968-97327
Coord A exon
chrLGE22C19W28_E50C23:95134-96967
Coord C2 exon
chrLGE22C19W28_E50C23:94998-95133
Length
1834 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAAA
5' ss Score
2.91
3' ss Seq
TCTGCATATGAATGTTGCAGGGT
3' ss Score
5.24
Exon sequences
Seq C1 exon
TCTCTCCTCAGCATCCCGGGCTCCCCTTTCCTCTCCCGACACAACAGCAAGAGCAGCATCTTCAGCTACAAGGGCCGATTCCGCGACCCGGGCTCGGAGAACGAATTCGCCGACGACGAACACAGCACGGTGGAGGAGAGCGAAGGCCGCAGGGATTCCCTCTTCATCCCCATCCGCGGCCGCGACCGACGGAGCAGCTACAGCGGATACAGCGGCTACAGCCAGGGCAGCCGCTCCTCGCGGATATTCCCCAACCTCCGCCGCAACATCAAGAGGAACAGCACGGTGGATTGCAACGGCGTCGTGTCCCTCATCGGCGGCCCGCCTTCCAGCATGCCCGGCGGGCGCCTTCTGCCTGAG
Seq A exon
GTGAAAATAGATAAGGCAGCTCACGATGACAGTGTAAGGAGGCTGATGTGTAGCTAGTGTAGGCATGGCGGCCTTGTCGTCCTCCTCTACTTCCCCGTATGCCGCCCTCCGAGCCGTCTGGGCGCCCCGATGCGTTGAGTGTTGGTTTGATTGACCGCAGGCGGCAGCATCTCTTTTGGGTTCCAATCCTCACGCTTCGGCTTTCCCCTTTCTTCCCTTAATCAGACTTAATGACCCCACCTCCTTTCTCCCATCTGCCAAAAAAAGGGCTTGGAATGTAACGACCCTCAGTACGTCAGGGTGCTTCTCATGGAGCTTTTTTGGATAGGGGTCAAACAAAACTTCTTGCAAATGCTCTGCACAGTAAGATAAACCTGGGAGCTTAAAGGGAAGTAGAGACAGTCATTTACCCTCACTAAAAGGCCTCCTTTCTTCAGAGGAAATGGCGGTACCTTGGAGTATCAACACAGAACTTGTCTTACCAGAGAATAGATTGGGTTGGAAAAGACCTCAAAGATCATGGAAGCGTGGAATGGGTTGGGCTGGAAGAGACCTTAAAGAACATCCAGTTCCAACCCCTTCCATGGACTGGGTTGCCAACCACTAAGCCAGGCACTTGGTCAGGTTGCCCACCTTGAAGTATGTCTAGGGAAATACCTGAGGGATTCTACTAGTTTCAGAGCTGTTATGGTTTCAAAGGCTTGATTTTCCAAGGGAGGCTGTTAATATAACAAGAAACTTCTTTAATTTTAATTTTTGAGTTTTCCTGGGTTTCGGTTTTTCTTCAATTAGTTGACTGAATTGGTATTGAGTAACCTTCTAAGTGTATCAACAACAATTAGCTCAGTAAGGGAGGGCTGATGAGAATACTGAGAAGATCAAAACAATTATTTCTGAGCAAAGTCTGGTTACCACGCCTATAAATTCCAAGCAATTTTTAAAATCTGTTTCAGTTCTTGCAACCTAATTGACCCTAATGAGTTATGTTAAGCATTGGTTGCTACCACTTTTATTTTTCTTCCCCCATTAGCATGTTAATACAACGTTTTGCTTCAGTATTTAATTATCTTTTTAACACAGCATGAGCGTGGTAGGAATCGTAACCCGCATGATGCATGCGTAAAGGAGAAAGTTTTAGTTGGCAATCCAAGAACTGCTTTTATTGCTGTTTTCAGGTGCAGATTTCGAAATGAATGTCAATTCCATGAAATATTCCAGTGGTAAACTGTAACAGTTGCCTCTAATGAGGCTGGGGTTGAATTCTCACTGACCAGACAGGATGAAGCATGGGCTTGTTAGGAGTCATTGCTTGCCTGCTGTTAGTAGTAGAGTAGAAACTGCTTTGCGCTGTAGCAGGGCTCATTAGAAATGATTCTTAAGATATAATCCTCCCTTTGCCTGAGGCTGCAAAGCAATGATATGAGCAGAAATGAGGGCTTGAGTTTTGAATTGACCACTTATGTCGTATCATCATCTTCATCATAGAATGGGTTGAGTTGGAAGGGACCTCGAAGACCATAGAACCATAGGATGGTTGGGTTGGAAGGGACAACAGAGATATCCAGTCCCAACTCCCTTGCCATGGGCAAGGTTGCTACCCACTAGATCAGGTGGCCCAGGGTCCCATACAGGCTGGCCTTGAGCACATCCAGGATTGGGGCATCCACTGCTTCTCTGGACTGCCTGTAGGAAAGTGGAAAGACTAGCAATAATTTAAGATATTTGTTGATTTTTTTTTTCTCTCTTGGCTATACCTTGCATATTCCTAGGCTGGTAGCACGTGAAACACCGGGAAGATGAAAAGCTCATATTAATCTGCATATGAATGTTGCAG
Seq C2 exon
GGTACGACTGAAATTGAAATTAAGAAGAAACCTGGTGGGTCTCTCTTGGTCTCGATGGATCAGGTGAACGCCTCCTATGGAAGGAAGGATCGTACCAACAGCGTGATGACCGGCTTGACCAACACCCTCGTTGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006060:ENSGALT00000017935:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.500 A=NA C2=0.087
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(52.9=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.0=78.3)
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:
CATCTTCAGCTACAAGGGCCG
R:
AGACCAAGAGAGACCCACCAG
Band lengths:
356-2190
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]