GgaINT0046942 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19363262-19364199:-
Coord C1 exon
chr7:19364071-19364199
Coord A exon
chr7:19363354-19364070
Coord C2 exon
chr7:19363262-19363353
Length
717 bp
Sequences
Splice sites
5' ss Seq
TGCGTAAGT
5' ss Score
9.73
3' ss Seq
TGTGAACTCCCCTATTACAGATA
3' ss Score
7.61
Exon sequences
Seq C1 exon
ATACACATTCACTGGAATTTATACCTTTGAATCACTTATTAAAATTCTTGCAAGGGGCTTCTGCTTAGAAGATTTTACATTTCTTCGAGACCCGTGGAACTGGCTAGATTTCACTGTCATTACATTTGC
Seq A exon
GTAAGTCTACTGTTTGTTTCTTTTGGTTTGGTTTGTTTTTTTGTTAGATTGTTTTTGTTAGTTTTTTTTTTTTTTTTACTCTTTCAAATAGGATGAACTTAGTGACTAAAAATTGCCTGATATTTTGTCAACCAGAACATTTGGAGCCTGGACTTCCTGCAGTTTCAATATGTTTCTTCTACATCTTTTACACATTTTAGTATTTCTAACTGAGCATGTGCTGCAGAGGCCAACATGGTGTGTCAACCTATTAGGATTGTGAATGCCATCAGCCTGAACTGTTCATATCCTGTCTCCTTTCTGCATATCAGAATTAAATCATTTTGACTTCCTGCTAGAAGCTGACAAAATTAGGTTTCAAAAACAAGTCAGTGTGGCTTATTTTGATAAATGAATTTAATTTTACGATCAGAAGGACATGTATAACACAGGCAAAATACAGTGAATGGTGAAAAGGTCTTAATCAAAGACCCAAGCAATAAGGATAAAATCTGCCTCAATTCTGAGTAACTGTGATTTAATCCTACAGGTATGTAACAGAATTTGTAAACCTAGGCAATGTTTCAGCTCTTCGAACTTTCAGAGTATTGAGAGCTTTGAAAACTATTTCTGTAATCCCAGGTAAGATGTAGTTGGTGTAAGGTGTTAGGCCCCTCGTTTCTCCAACTGTTATTTGTGTGCTGTCATTGTGTTTGTGTGTGAACTCCCCTATTACAG
Seq C2 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTCCGAGCTTTGAAAACAATATCAGTCATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:2
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=FE(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACACATTCACTGGAATTTATACCTTT
R:
ATGACTGATATTGTTTTCAAAGCTCG
Band lengths:
214-931
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]