GgaINT0047670 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19117661-19120378:+
Coord C1 exon
chr7:19117661-19117899
Coord A exon
chr7:19117900-19120204
Coord C2 exon
chr7:19120205-19120378
Length
2305 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CACCTGCCCTCTGAATTCAGGTC
3' ss Score
8.88
Exon sequences
Seq C1 exon
AACTCGAAGAATCAAGACAGAAATGCCCACCATGTTGGTATAAATTTGCAAATATCTTCTTGATCTGGGACTGCAGTCCTCATTGGTTGAAAGTAAAGCATATTGTCAACTTAGTTGTAATGGATCCATTTGTTGACCTGGCTATTACAATTTGCATTGTTTTAAATACACTCTTTATGGCCATGGAGCATTATCCGATGACTGATGAATTCAATAACGTACTTTCAGTTGGAAATCTG
Seq A exon
GTGAGTCTGTTGCTTTTTTTGTGTTTATGTTTTTAAAGGAAGTATGTCTGTTTGTACCTCTTTAGAAAGCAGATTCTAGCCATTTATTGCCCTCCTGATAGGACTCTATCATAACATTTTTGGAAATTTCACTGTCAACTCTGGGTCACATAACTTAGAATTCTGTAAAATCAATATTTTCCTGTGTTCCGGAAAACCAAATTAAATATTAAAAAAAAAAAAAAAAAAAACCAGCACCACTGCTACATTAAGTAAAGTCCATATTAAATAGAAGTTGATTTATCTAGCTACTAAACCAGGAAATGTATTACTTCCATGAAAAAGACACCTTGGGAATAAATGTGTTTCTTTTTCAATCAATACAATATAAATGTGTAAATTATGAATGTGTTTTTAATTGCTTTCATCTTTTTTCTCTGTTTCGTGAGTACAGGTTTACAATCACTAGAAGAGCCATTTAAAGGCATTTCTAGATTTTTCTTCTTTAAATGATTTTTTAATGTGTATATGTGGATTGTTCTCTGTATGTGCTTATTTTAAACATGAAAAATGTTCTGCAGTAATTTTTCTTCTTAGTCTTTATATTTTTAAGAATCAGATAATTAGTAAGATACCTTTTTTTATCTTATTGTCAACTATATTTTCTCCCTTCTACTTCAAAAAGGTAAATTATTAAAGAGTTCGGTAGTTAATTTTCTGTAGCTATGATGCTTTTGAACTGACAGGTTTGATCACACTGAAGTATCTGTGGCTGCAGTCCTACTTCATCTCTTATTTTAAGAATTGATTTCTTATAATGTGATTTTTTAAAATCCTTGTTTTGTAATGAAGGAAAAAATATCTCAGGTCAAATAAATAACACCAGAATTTGGAAAGGAAAAGTAATAGACAAATTCCTAACTGAATTTCATACACTTATAATAAAGGAAGCTCTGAATATGTTGTATCATAGCAGTTTGTCTTGTATTATAGCAATTTATAGTCTTGTTTGCCAATCAGGAAAATATCATATAAATCTTGGTGAACATCAGACTACAAAGAGAGTGTGAGAGAGATTGGCTGTAAGCACCATCCTCTTCCAATCTTAAGATGCTTGATTTAAGCCCCTTCTCCAATGCAGAAGCTTTCAGGGTTCTCCTACTCCCATAGTTCAGCTTTAAATGCCCTCGAGAACTTCACTGTCCCAATGGTTAGGAACTTTATTCATATTTTCACATGGTATTTATTCATTCCCACTTCTTCCACGGTGGTTTTAATTCTCTATCTTAAAAACAAGCAACTTTTCCTCTCCAGTGTTTGTATCTGTGATGTATTTAAAAGTAATAAAAACTATCTTGAGCATTCGTGTTCCTACGCTGAACAAGTCAGAATCTTGTACAGATCGTGATTATCCCAGTTATTCTCTTCAGCTGCTGCAGTTTCTGTTCAGCTTGAAAACTGAGTTATCAAAAAACAAAAGGAAAGACAAATAAGCAGTACAGTGCAGAGCTCAGGCAGCCTTTAATGGTAGCTTTAATACTTTCCTATCCTATAAGAAATTCTTCTAATACTCAGAATCACAACCTTTTTCTCTGAAACCTACTCAGGCTCAGTACCTTGGTGGCTCCCTAAATATTATTCCTGCTTCATTCAGAATATTGAATTCCATGATAGGAAATTATTACCAGAAATATCATGTTTAAAATGCACTTTTAAATGCTATTTCAGTTAAGACAATTGAGTCAATTGGTTTCGCTGAGCTTACTGGCAACACCCAAGTAGAAGTTTCCTCAGCTTTGCAAATTGTTGTATCTCTGCTGATCCCCAGCTGTTATAAATAATTTTATCTCTGTTGAACTGAATGGGATTATTATAGGCTGTCTAAGCAAAGGAACTACTCATCAGGAGTCTTAGACTTGGCCTCATTCATAATGCTGTATAATGTAATTAGTGTACCAAAAATTATGTTATGCCATGTAATTTCTTGGAAAGCATTCTGGTTTATGTCGTGAAAATCAAATTAAGGATATTGTTTGTACAGTACATGAGAAGGTCCATATCCTGATACAGTTGAAATTGGATTACAAATGTTATAAAACAGAAGTTTACAAAATTTCTTCTTCAGTGTAGAATGTAATTAATTAAAAAAAATTACTTGGTTTATATGACCTCTGTTAAGGTAAGGTGATCATAATATATCACTACAGTGAACTATTTTTAAGTATCTGTTTTGGATGAAGCTAATTCCAGATAGGTAGCCTAAACAACAGCTAAACCTACAATATTATATTTCACAAAAAAATAACCACCTGCCCTCTGAATTCAG
Seq C2 exon
GTCTTCACTGGAATCTTCACAGCAGAGATGTTTCTCAAGATAATTGCAATGGATCCTTACTATTATTTTCAAGAAGGCTGGAATATTTTTGATGGTTTTATTGTAACCCTTAGCTTGGTTGAGCTTGGTCTTGCAGATGTGGAAGGACTCTCAGTTCTTCGATCATTCAGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:14
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=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=100)
Main Inclusion 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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]