GgaINT0047680 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19146882-19148580:+
Coord C1 exon
chr7:19146882-19147019
Coord A exon
chr7:19147020-19148475
Coord C2 exon
chr7:19148476-19148580
Length
1456 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
CTTTGATTTTATGTTTTTACTTT
3' ss Score
-0.01
Exon sequences
Seq C1 exon
GTGTTACAGCAACCCAAGTATGAAGACAACCTGTACATGTATTTGTATTTTGTCATCTTTATCATTTTTGGGTCTTTTTTCACCCTGAATCTGTTCATTGGTGTCATCATTGATAACTTCAATCAGCAGAAAAAGAAG
Seq A exon
ATAAGTATTGTTTCATTCCTCTTCTAAAGATATTGCGAAATAGTGACTTCCTGTAAGTGCATGATGTATGGAATGTATCAAAACTGAAAAAGCTGAAGAATACCAGAATATAAAATCTTACCCAGATGTTGCATACATTATCTTCATAAGATTTTACACTGTAGTGAACAGTACACACCTTTCTCCTTTCTGTTTTCAATTCTCCCAAATTCTATTCTGTGGCACTGAATTAAATAGTTATTTGTAACCATTGTAGGTTACAAAGGATACCCGTTCTTACTTTCATAGTGTAGCTGTGAATCTCACTGACATGGATGGTCTGAGTATCAGCTGCTTATCTTTAAAGCCAACTTATCAAATAAATGCTTATATTGCAGACACTGAGATTTGATAACTAAGAGATCTTCTTCAATTCAGTCATTTTGATTTTCAGGAAATTCCTGTCTACATCAAAATACTCTGTTTTCCAGGTTTCATTTGAAATTAATATGCAGCTCTTACTCAGAATATTTTTTTATATTTACCTCTCTTAATGTGTTAATTCTGTGAACACATTAAGGTTAGTTTATGTCAAGCAACAGGACCTAGATTACATTTTCTGTCAGTTCTATAAATTATAGGTACTTTAGTTATTGCTTGAACCTTTAATGTTACTCATCTGCAGTATTTCCATATGATGAGAAACTAAGCCAATACAAGATCTATAGAATCAGTTAGGACTCAAGTTGAGTATACACCTAATATTTATCAAATGAATGCAAAGGCTTTTTTTATGCAGAAGAAAGAACGATCATTTGGATCATTTGCATATCAACACTACTGTATACATAACTAAAATAAGTGCAATAACATGTACTTTATCTTTACACTGATTTTAGAAGACGGGCAGTCCCAGAACACCAATGAACATCGTCTGTCTTTGAAAATATTTGTGCCATTTGAATTTTCTGGAAGAAGAAACAAACATGCATGCACAATGTTTACTAGCACAAATTCTCCTTACCATTTTTCATCAATAATAGTATTGAATTCTCAGAAACTTTTGTCTGATCGCTGCTTCACCAAGTATAGCTTAGTATGGCAGTTAGTTTTCTCAAGCCATTGAAGCTGGCCATCCCATTTTCTTTCAACTTTCTGTTGACTCTAATATAAAAATGCCAGTAATCCTTGCCCAGATTCTTGAAGGGATATCCACGCTGCCTAACAAACTCTGGATTCTCTGAAGATGTTATAATTTCACATGAAAGAAAGTTAGCGGGGAATAGTGTAAGGTAAAAACATCCATTTTCTCACTGGATTTACTGTCATTTCTCCTGGAGTATTTGGTGCATTTTAACAAGACAATCAGAATAACACATATATAGTAAATAAATGTATTAATCACATTTCACTTTAAAAGCTTTTTCAACACTGCATATAAATGTGATTGTAACCAGCTTTGATTTTATGTTTTTAC
Seq C2 exon
TTTGGAGGTCAAGACATATTTATGACAGAAGAGCAGAAGAAATACTACAATGCAATGAAAAAGCTGGGATCCAAAAAACCACAAAAGCCTATACCAAGACCAGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:24
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=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
ACAGCAACCCAAGTATGAAGACA
R:
CCCTGGTCTTGGTATAGGCTT
Band lengths:
238-1694
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]