GgaINT0047673 @ galGal4
Intron Retention
Gene
ENSGALG00000010943 | SCN1A
Description
sodium channel, voltage gated, type I alpha subunit [Source:HGNC Symbol;Acc:HGNC:10585]
Coordinates
chr7:19122051-19123729:+
Coord C1 exon
chr7:19122051-19122530
Coord A exon
chr7:19122531-19123611
Coord C2 exon
chr7:19123612-19123729
Length
1081 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTT
5' ss Score
7.63
3' ss Seq
TTTTTTCTTTTTATTTACAGAAG
3' ss Score
9.64
Exon sequences
Seq C1 exon
GTACTGAACTTATTTTTGGCCTTGCTGTTGAGCTCATTTAGTGCTGACAACCTTGCTGTGACAGATGATGATAATGAAATGAACAATCTCCAAATTGCTGTAGCAAGAATGCAGAAGGGCATAGACTATGTGAAAAGAAAAGCACGTGAATTCATCCAGAAGGCTTTTGTTAAAAAACAAAAAGCTTTAGATGAAATCAAACCACTTGAAGATTTGAACAACAAAAACAGTTGTATTTCCAACCATACTGCAGAATTAAGCAAGGACCATGATTACATTAAAGATGTGAACGGAACAACTAGTGGCATAGGCACAGGCAGCAGTGTGGAGAAATACATAATTGATGAAAGTGATTATATGTCATTCATAAACAACCCAAGCCTGACTGTGACAGTGCCCATTGCTGTGGGTGAATCTGACTTTGAAAATTTAAATACAGAGGAGTTTAGTAGTGAATCAGACCTAGAAGAGAGCAAAGAG
Seq A exon
GTATTTAGATACTTTGTGCATTTCTCTGTGATCCCCCCTGCATGTTTTTCTTTACTCAGCCTAAGCCAGTGTATTCAGTACTTCACCATTTGTTATTTTGACACTTCTTCATACGTGGGCAAAAGTAAGTGTATAAAGGAGGGTTTAATTCTTGATGAGCAGAAGTGTGAGAAAGGTTTAAAAATTACTACAGTTCCAACAGGAGATAGGATGCGAAGGAATGAGGGATGAAGATAATAAGAACTGCTTATGACCTATGTTTTGTTGAGAACTGTGTTTTAGAAAAACTGTTAATTAACACTGTTGATTTTAAAGAACTTAATTTTAGTGTCCAAAATGCATGAAAGAGAATGGTGAATTAAAATGAAAAGTAAATATTTTTTCAAAAATGAAAAGGTTTTTGAAAAGTTTTGAAAAGTATTTTCAAAATTATTTTGTGTGGCCAAATACACTGCAAAGGACAAGTTATGAATATTGGATTGCTAGAAGAAAGTAGTATTTCTGTTAAAATATCAAAAAGACAATATTCAGGTGAAAATGGAATTTAAAAATAAAACCTCTATAAACTGTTTCTCATGAAAATTAATGACTGAACCTAGAACTGGATACCTCAACCCATTGTCTTGATAAAGATATTGTCCTCCACCTCTAAAATACAGCCTTCTATGCTTATCAGTGTTTTTTTCCCCTCATTTCTTTCAGCTGCCACCTCATTTATATATTTATATTTGGGCTGTTACCTGCTTTTCAGTAGGCTTAGCAGATTGCTGCATATATAAGTTGTATTCTGTCCAGGTCAAGAGATCTTTACCACTAATGGTTAGTTGTGGTCATCTTTACAGGCTTAGAATCATTATTCATATTTTGTAGTTTAAAATCTATTTTTCTTTAAACCTTATTTACCATTGATACAGTACAAAGGAAAATTTAAAAAACTGTACAAATTTCCCTTTAGTTTGTCAGCAATTAACTTGCACTGAATACCAGAACAAAAGAACTATTTAATTATTCTGAAAACTACTAACATTTTCCTAAAAATATTTAATGGAAATTTGTGATTCTTTTTTCTTTTTATTTACAG
Seq C2 exon
AAGCTAAATATGTCCAGTTCATCTGAAGGCAGCACAGTTGACATTGGACTTCCTGCAGAAGAGCAACCAGAAGCTGAACCTGAGGAATCCATGGAGCCAGAGGCCTGCTTCACCGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000010943:ENSGALT00000017814:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.177 A=NA C2=0.962
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(77.3=85.0)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(21.6=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:
TCCAACCATACTGCAGAATTAAGCA
R:
CCTCTGGCTCCATGGATTCCT
Band lengths:
346-1427
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]