GgaINT0047658 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19094498-19099527:+
Coord C1 exon
chr7:19094498-19094782
Coord A exon
chr7:19094783-19099416
Coord C2 exon
chr7:19099417-19099527
Length
4634 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
CTTTTGTTTCTCTTTTTCAGACT
3' ss Score
12.07
Exon sequences
Seq C1 exon
AATGTGCAGGATGAAAAGATGGAGCAGCCAGTGCTTGTACCACCAGGACCAGACAGCTTCCAATACTTCACTAGGGAGTCTCTTGCAGCTATTGAACAACGCATTGCTGCAGAAAAAGCTAAGAATTCTAAACAAGATCGTAAAGACAACGATGATGAAAATGGGCCAAAGCCAAACAGTGATTTGGAGGCAGGAAAAACACTTCCATTTATATATGGTGACATTCCTCCAGGAATGGTGTCTGAGCCCTTGGAAGATATGGACCCATATTATATCAACAAAAAA
Seq A exon
GTGAGTCTAATATCATTCCCATTCTTATGAAAATGTTTGGAGAGCTTTATCATATTTGTTTCATTCTCTTACTATGACAAAAATAGTTTAATCGTCTGTTAACTGACAACAGTGTGGGAAAACATCATTCTAATAATGTGGGAACAGCTAAGCATTGTTAAAATAATTAGCGTACAAGAGCAGAAAATGTTTGATGCCATTGATAGATATGCATTCCACCTTCCAGAAAGTAAATACTGAAATTGTATGGGTCTGAAGAAGTGATACAGAATGAAGGAAAATTAGTATTTGCTAGAAAGAGTTAGGACAAGTATATGGATTAGCAGATGCCACTGTGGCTCATCTCTGTTAAGACCTCTGCAAAACTATATCTGATTCATCCATAGAACATTTGTAGGTTTGACTTCCAAGCATTCAAATAGCCTATAAAAATGGTTATCTATAGTGTTCGTCAAACGATGCTAATGATCATATTCACTGTGTTTTTTTCAGAAAATCTAATCAGCTGTACAAATACCTTCTTTATTCCAAATTTGAGTCATGAGAAAAATCATACATCAGTTGCTTCATACGCGTGTACTGCATTGCACTCATTGATCTGGTCGTGGGTTTTTTTTTTTTATTTGTTTGTTGTTTTTAGTTTCTTTGGAGGGGGAATAGGGAATCTTCTTTTCTGGATAATATGAATCAGCAGGGCTGAGCTCTTCCCTAAAGATTTAACTACTAAGTAATAATGGAAGTCTACCACCTATTTTGCCATACTCGGGCAGTTATATTTTCAGAAGGATACTTTTCACTGTACTGCATATGAGATCAAATTGAAATTATGTTTTGGTGTCTTTGTTTCTATGCAAAACTTATCACCAAAGAGGATGTATTCGTGCCCAATATTAACTTAAAGGAAAAGGCAAAAATAGCACCTAATAGCAGTATACATTTGCACTGTACTTTAGATAGCCTAAATGCCAGCAACTGTACCATGGGAACAAAATTTGTCTATTACAATTTAATACCCCTCCTTCTTATGGTTTTATTATAATGAAGTACCATTATACAAGATGTTCAGTAATGCTGGTCTTTGAAACTGTTAAGTTTAGCATTCTAAACCTTTGCTCACTTTTTGTATTCTACTCTTGTTTTAAGTGCGAATCTCTATGTTCCGGACACAATGGCAACTGCCTGTTCATGGTGAAGCTGCCATCACAAAGGATCAGGGAGGTTCATATCACTATCTGTTGAGAAAGGATCAGCTGGAACCCTTTCAGATCCTGATGTGCAGGCATGCTTCAAAATCTGGTCCTTTCTTACTTTAAAGTCTGGCTATTTTGTCTTTGCCTTGCTGCTTCATTAAAAAGGAGCAAAAGAATAGCTGGAACTAAATGGGCCCTACTTCACTTTCCTCCTGCTATAGTGTAGATTTAGCATTCCTGCTGATTGCCTCTGCCCACACTGCCTCTTGCCAGAAGGATGCAGATTGATGCCTGTCAGGAGAGCTCCGTCCTTTTGTCCTTGGCTACACCAGTTGCCTAATCCTATCAAACCATACCTTCTGGATTCCCAAACTGGATCTGTCTTGCAGAAGGAAACAAAAAAACCTATAAAATTATTCTATGTAACATCAGAAAAGGTGAATGCACTGGTGATCTTAGATATCTTTGGTGGTTTCAAATGAAAGAATTTTGAAGATAAAAGTTCAAGTAACACAAAAAACTAAGGTCTAGCTAGAAAAAAATGCTTTCAATAGACAGCCGCAAAACAAGAAAATACCAATTTCAGAAATGCTACAAAGTCTCTTGTGCTAGCCCTCTCCAGGGCTTTCCCTGAGAAGCTATTTGGCTGTAAGACTAAGAAGCTGGCACTACAGAAGGTGCTGTGGGTTTTGATATAGTGTTTATCTAGCCATAGGAAGTGGTAATGCAATGCAGTAGTGCTCAGCCTTCAAGAAACTGCTTCAAAGCCAAATGGAAGGAAAGAGAGGGGAAATAATGTTTAAAGAACTTTCTGTCCTGACTGGTTCTTGGAGGCTGCTTTTGTTTGGCTTCTTTACTCTTGGATGCATCAGTTTGAAATACTCTTCCTCCTCCTTTGCCCTGATAAGACTGTAGTTTCTCAGTTTGGGTCAAATATGGCAGAAGTTACGGAGCTGGAAGCCAGGTTACAGGCACAAAGCTGCAAATTGGACACTTCTCTTTAGGTATTTCATTGAATTTACATTCACACTGGAATACTTTCAGTCTGAGTCTTTATAACATGATAAAACACTTCATGAAACATAAACCCTGGAAAGTAAGCATAATCTTCCATATATGAATATGAATCTTATAATTTATTTAGAATTTATTTGGTTTTTCTCAGCATATGTCTACTTTGTCCTGGCAGATTTGGGTAGAAAGTTTCATGCTCATCCACACTGCCTACACACTGCCTTGGATCTGGGTTGAGACTGGGGTGCAAATGCAGGAAACTTACACAGGAGTTGGACATTAGCTGTAATCCCTGTTTTCTGCATTTTTAGGAAAATTCTCCTTGAGAGATGAGATACAATTTTAGTTCATTTTTAAGGCTAGAAGTCAGTGGACCAACGCAGTCATTTTCAAGGTTCCCATCACAGAGATGTTTTAGGTGAAAAATTAAAACCAAAATAGAAATTGTAAACCTTGCTGGTTCTGCTTATGCAGGGCAGCAGAAAGTGGAACAGCTAAAATAGCAGCAGCTTCCAACTGAAGCTGGAGTGGTGCCAGCATGCTGTTATTTTCCATAAGGCATGTTAAAAAGAGATGTATGTTTAATATGCTTGTGTTCAAAGATTTTTAAAGAGATGTAGGTTGGCTAAATGTAGGTGGTGTAGTTTTAGATTCAAAGCTAGTAGGAAATGTGATTTTTTATGTACTTTCTCAGCTACCTCATAGCTACAGAAGCTGTTACTGTGAGCTGTGAGGCCTGGGGGCTGGGGCCAGACCAGGGAGGGAAAACTCACCGTGCCTCTTGGTAAATGTACCAAAGCCCATCATTCATCTGTCTGGCTATTCGCATATTTAAAATGAAACCTTCATTTAAAGTCAAGTCAACTGCAGTTACCCTTGAAAGGTCATTTTTTATCTGTAATCTAACTGGAAATATAATTTAGGAATATTAGCTCAGTTCTTATTCTGTTGTTCAATTTCATCTGCAGATTCTCTATTTCTGTGCAGAAGCAGGGAAAACAGATACATCTCTTACAGCTTTCCTACACATCTTGAGTTTGTGCTCAAGATCCAGTGTTAATGACACTTAGTATTAAGGGCTTTGATCTGTATTGCCAGGTGTACTGCATAGAGCCAGGACAGAGGCAGCTCAGGGAAGAAGACAGCAAGTAATTTAGGGCTGGGAGAGCTTTTACTCAGTACTCATCCCCTTCTTTTTCCTCTGCCTTCTGTTTTTGGTGTCCACCACAGACTTGTGGAAACCCTTATCCTCTGCCTTCTGGATGCTCCTAGCAATTGGTGTCGGTACTTCCTGGTCTGTACATACTAAGCATTGTGAATGTAAGCAGATTGAAGAACTATCTTCTTTGAAAATATTTGGCATGTTTTTCCAGACTGACAGCCTTCCCAGAAATGGTTCTGTACGCTGCTTGCCATCAGTCGGTGGACTTTATGTCTCACTCCACACCTCACAGATACCACAAGAGATCAATATCTCCTTTTTCACATTTCCAATGGCATCCTAGCTTACAGCTCGCTTCTTCAGCAATGTAGTGATAAGCAAGAAAGCTTTATCATAGTATGTCCAAGAAGTAAGCAACCCTAACAAAAAAAGAAAAAGCATTTTTTGAGATTCATCATTCCTGGTTTCATCGGTACCTTTAATTCTGCTTGAATTTAGGCAGTAATTCTTGTGCATGCAGATTTCCTCCAAATTACTGATTCTTCCTTCTGCAGTGCTTTTTGTTCTGTTTTGTTTGTTTCTACAGCTGAAGATCACCTCAATGCCACAAAGAGACTTGGCAGTCTGCATTTCCAGTGTTGTAGTGTTAATGTTGTTGCAGCCACAATGGGCTGCAGCATAAGCAATTTTTTTCAAAGTTTCCCTAAACATTATACACTTGTTAGTGGTTAAAATAAGATCTCACATGATGTGTGCGTTCTGGGAAAGATTTACACCTGTAAACCACAGTTGTGCAGGGTGGTCTTCTGAGATGCATCTCCTGTTCTCCTCAGGTGAAGTGTACTTGGATGCCCACAGTCCTCAGAGATTCATGACTATGTGGGTTATTGCTATTTCCCTCTATCCTTAGCTTTTCCCTTACTTATGGGAAAGCCTTTCCCTTACTTATGGGAAAGTATAAACGCAATTACAATTTCAGTTAATTGTTTCTGCATCTTTTGCTACAAGTAGATTATATAACTGATATTGTTTAAAAAAGCAGTATTACAAAAGCATTAATGAAATGAATGTTCTATGTTTAAAAATATATTTTTGGACATCAGGTAAGTACTGGAAGTAAGTTTTATTTCAAAAGTGAGTCATGCTTTTTGTATATTAACTATTCAAAAATTCATGAATTTGCTGACTGTTTAAAATGAGAAAAGGTTTAAAATGAGCATCTACACTGAATACACACTTAGAAAATGTCTTTTGTTTCTCTTTTTCAG
Seq C2 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCAATCTTCCGATTCAGTGCCACCTCCGCCCTGTACATTTTAACTCCATTCAATCCTCTTAGAAAAATAGCTATTAAAATTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.421 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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]