GgaINT0047676 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19126510-19128633:+
Coord C1 exon
chr7:19126510-19126683
Coord A exon
chr7:19126684-19128510
Coord C2 exon
chr7:19128511-19128633
Length
1827 bp
Sequences
Splice sites
5' ss Seq
GATGTATGT
5' ss Score
6.31
3' ss Seq
ACTTTCCTGTTTTCATATAGGTC
3' ss Score
11.21
Exon sequences
Seq C1 exon
GCTTTTGAAGATATATATATTGAACAGCGCAAAACTATCAAGACCATGCTGGAATATGCTGACAAAGTCTTCACTTACATCTTCATTCTGGAAATGCTGCTGAAGTGGGTGGCCTATGGCTATCAAACATACTTTACTAATGCCTGGTGCTGGCTGGACTTCCTGATTGTTGAT
Seq A exon
GTATGTAGTGCATTTCCTAGGTGCTATTTTTACAATTTTTTTCATTACTTTCTCTACAGCCATAATATCTATGTGTATACCAACTAGTTTACTTTCCAGTTTAAAAAGTAAGGTAAATGGAAAAAAAAATCCATAGTTTTGGTCTTTCATTTTACACTTACACTACTACTTTCCTATACCACAGAATTAATAAAAATAAGGTCCAGCTAACAAAAGAATATAACATACTAACTCTGCAAGTATTTGCAGTTCATCCCAGCACTGCACATGCCTACCTTCAGGCCCCAGTTTCCTTCCTGTGGTGTAAATCACACCCAGCATTTAGATGGATGTCTGTTCTATCAGACCGTCATAACTGAAAAACAATTATCCAAACTATCCAACTACAAACTCCAGCATATGACTGAATTAAGTTTTTACAAGGAATGCAAGATGCATGTGTAGCATTGGTGGTGTGGCTTACTAAGTATAAAAGTCCACAAAATATTACTGAACTTACAATCTTCAAAGCTGTGTTTGAAAACAAACTCAATTATCTTTCCTTATGGGGTTATCTAATAGTTTTAAATCTACTGTGCTGTGTCATAAATCGTGGCAGACAATTTCTGTATGGATTGATGCAATTTAAAATTAGGATGACAATTTAAACCTCCAGTGTGCAAAAAAGCATACTGTACCAGTGGCTGGTAAAACTTGCAGGAAAAAGAAATATTAAGAAAGTTGAAATTTAAAATCAAGATGTATTTTGTCCTGCTTTCAGTGAATTAACAATGATATAGATATTTTCTTTAATTTGGTATTAGATTATGAGAGCATGAAAAATCAAGTTTTCAATAGCATAATGAAGGTATTGGAGAAAAAAATCAGATTCCAGAAGGTCCTAGTTTTGCAGGTTAGTAAAGATGAGGATTGGCAAGTAGAGAAAAGTTCAAGATTTCACATCTAATACTTGCTTCTAAATATGATTAATGAAGAGCACTGTCACAGGCTTTTCTTTTCGTATTGCTTTGTGGGTGGGTGTGTTTTGTTTGTTTGTTTGTTTGTTTTTAAATAATTAAATCATATATTAGACCATTAAACTATTTCTTTCCAATAACTAGTTTAGGAATTGGAACAGGATAATGAAAGACCATTCAGGGGAAATGGGATGAAAACTGAAAGTATTATTTTGTCATGAACCGTTGTGAATGTAGAGGATATGGTATATCTCATTGAGGAAGTGAAGGGATGTAGAATACATACAGGCAGGTGAAGATGTGACTTTAGTAGTTCTGTTGCCTATGGAACACATTCTGTAATGTCTTTTAAGAAACAGTGTATTCCAGGTTAATGTCAGCCTATAACGTACATAAATTCAATCGTCAGGCAAAAACTTAGTTAGTGTAACTGAATATAGAAAAATCAATCTACCAGTTTCCAGAGAAAGTGTTACTCTGTGACCCATCTGTTAACTCGAAACAGGCTTCAATCATTTCCCTTCCAGCTGTGGGCAATCAAAGGAGTATTATCAACTATAATTACTAATCCCAGCAACATTGTAAAACAGAGGGGAAAAGAAAAAATTTGGCCCTCAAATCACTATTAAAATAGGAAATTTCTAATTATTGTTTCCAGATAATAACTGTTACCCTATGGTATTTTTGTTTAACTATTTACTTATGCTTCTCTTCTTTCTCATTAATTCTCTTTTTTTTATTTAAAAGACTTCGTATTCCTGAAGAAAGTGGTCCAAAATTAGATTCTTCTAAAGAAGTTTGTGTCTCACATCTATGGTATGTAAAGTAGTATGTACAATATAATAATTTTTACTTTCCTGTTTTCATATAG
Seq C2 exon
GTCTCTTTGGTTAGCTTAACAGCAAATGCATTGGGTTACTCTGAACTTGGTGCCATTAAGTCCCTTAGGACACTAAGAGCTTTGAGACCTCTAAGAGCCTTGTCACGATTTGAAGGCATGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
ENSGALT00000017814fB11728
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:
TTGAACAGCGCAAAACTATCAAGAC
R:
CCTCATGCCTTCAAATCGTGAC
Band lengths:
278-2105
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]