GgaINT0046941 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19364071-19366026:-
Coord C1 exon
chr7:19365839-19366026
Coord A exon
chr7:19364200-19365838
Coord C2 exon
chr7:19364071-19364199
Length
1639 bp
Sequences
Splice sites
5' ss Seq
AGAGTAAGT
5' ss Score
9.35
3' ss Seq
ATCTTACATATTTTCCCCAGATA
3' ss Score
8.11
Exon sequences
Seq C1 exon
TAAATATCTCCTGATACTGGATATCTGCCAGACCAGGATCCTGTTTGATATTCTTTTAATGAGATTTTCTGGCTTACATTCCTTGACTCTTAACCCACATTATTCAGCATGCTTATCATGTGCACTATTTTGACCAACTGTGTATTTATGACCATGAGTAACCCTCCTGACTGGACGAAGAATGTAGA
Seq A exon
GTAAGTGAAATGGATTTTCTTTGAATTATGTTCAGTCATCTGAAATAAACTGCTGTTAATGATGTTACACTAATAAGGATAACATCTACTGACAGCAGCTACTTCGTAACATGTTTTAAACACCTATTCAGATGCTAGCTTCTTCTCTGTAATATTACATCAGTGTATTTTTCAAGGCTTCCTTCATTGCAGAATGTTGAGTTTGCATTCTCTGTTTGCAGTATTAGATGGGTAATGTAGGAACAAGATGCTAGTCTTACAAGTATGCAAAAAAAGTGGATGCATTGCAGGAATAAAGAGATAAAGAGTGCAGTAAAGACAATCTGTTAGTGATTTACTTTTTTTTTTTTTAATGAAAAAAAAGGTTTTTCAAAAGTATTTCAGTGATTGGCTAATCCTCCCATAGGAAATAGCAGCTAGAAAGAGAAAAGTTCCAAGACAGCATCAACCCCAGTCCCCATATACAGTTGATACATATTTTGTGATTGTTTCAAGGCAGTGCAAAATACTGCTCTTTATGATGCTTCATTTTTGTAATAACATCTTATGCTTCTGCTGTAACTTCACTTCTAACTGATTTGGATGATAAGTGCATGTTTAATCTTCAGTAATCAACAGTGAAATCATAGGACAATTAAAGTCAGTGTAGGCATTCTTGTTTTGAATTGCATATGAACATATATGTATTCAGGGTATCTAGCATACAGTATTTATGAACAAATATAGCTAGCTTGAATACTTACTTGTGTCATATTGTGCCCTATGTATATATAATGCAAATCTTAGTCATCTATTGAGTGAAGTTGTGTGGGAAAAACTTTTGTTTTTTTCTTAGTGACTGAACTGAAAAATATCATAACAGGAAAATTGGTTTCAGGTTGATTGTGTCTGAAAACCAGTGTGAGCCTTTTAAACAGTTTGACTTGAAACAGTCTGTTTTACCTTCTTTTTGATTAAAGATATAAATTAAACTAAATTTCAAAATGGCATCATTTGGAGATAGAAAATTAAAATGACTCAGAATGCCAGAATTAAGCACTTATGTTTCAGCAAAATTTTTTTAGTCTAAACAAGCACTGCATTTTATTGGAATCTATACAAAGTTTTGATTGGTCTTGCGCAGGATTTTGCATCTGAAAATACTGATCTTGTTCCAGTACTATGTTTGTCCAGCTGAGGGTGAACTACTGGGTACAGCTACTCTAACAAAGTGAATGAGTGCTGATGAGATTTGACACATTGACAGATCATGGTACTCTACAACATTTCAGCATAAAAATAATACTGAAGAAATTAATATTCAGATTGGAAGCAACTTCTGAAATTATGACTTCGTATGTTTTTTCTTGTAGAATTAGGTTGGACATAAATATGTGCCAATGAAATAACAGGGAATTTTGCAACTAACTTGTTAACATAGATTGTACCATTTGAACCTCAATTTATGGATTGTCACGTAGTCTTTTAATCATGGTTTGATTCTTCTCCTTTAAGGAAGAAATTCTGCAGATGTTTAAAGCTGGTTATGTCTATTAAATTCTTACGCTTCTCAAAGAGTAGAAAATGGGACTAGAGAGCATACTGTGTAGGGATAACATGAGTATGTTTTTATAAACTCTATCTTACATATTTTCCCCAG
Seq C2 exon
ATACACATTCACTGGAATTTATACCTTTGAATCACTTATTAAAATTCTTGCAAGGGGCTTCTGCTTAGAAGATTTTACATTTCTTCGAGACCCGTGGAACTGGCTAGATTTCACTGTCATTACATTTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(0.7=7.4)
A:
NA
C2:
PF0052026=Ion_trans=FE(16.0=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:
ATCTCCTGATACTGGATATCTGCCA
R:
AAATGTAATGACAGTGAAATCTAGCC
Band lengths:
310-1949
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]