GgaINT0046949 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19351077-19352485:-
Coord C1 exon
chr7:19352138-19352485
Coord A exon
chr7:19351210-19352137
Coord C2 exon
chr7:19351077-19351209
Length
928 bp
Sequences
Splice sites
5' ss Seq
GAGGTGATG
5' ss Score
4.44
3' ss Seq
TATCAGTGTTTTATTTTCAGGGC
3' ss Score
9.16
Exon sequences
Seq C1 exon
TCTTTGCTGAGTATTCGTGGCTCCCTATTTTCCCCAAGGCGCAATAGCAGAACAAGTCTTTTCAGCTTCAGAGGTCGTGCAAAGGATGTAGGATCTGAAAATGACTTTGCTGATGATGAGCACAGCACTTTTGAAGACAATGAGAGCAGAAGAGATTCTCTCTTTGTTCCTCATAGACATGGTGAACGGCGCAACAGTAACATTAGTCAGGCCAGTAGGTCATCCAGGACAGTACCTCCACTTCCAGTGAACGGGAAGATGCACAGCACTGTGGATTGTAATGGAGTAGTTTCTTTAGTCGGTGGGCCTCCAGCTCTGACGTCGCCTACTGGACAGCTTCTGCCAGAG
Seq A exon
GTGATGATTGATAAAGCAACCACTGCTAGCAATGTAAGAAAGTCTGCAATAGCTCAGGCATGATGTCCTCTCCCTGTATAATCAACTACTGTTTCTACAAAACCTAGTAACTTGGGAATAATTCCCTTTTTGTCCATGCTCCTTTCATATATTCCAGTTCAAAGTTGAAGCTGAAACTGAAGGTGTCTAGCTCTCATTAACTAGATATGTGTAAATGTATGTTAGGTCACTGGGAATTAACAAAATAGCAGTAAGCCATTAAATAACTTGGTTCACTGTGGTAACTGAAGAAGTTCTGTATTTGTATATCAACCAAGATATCAAAATGAAAAAGGAGTTATAAAGGAATTACTTAATGGAATATATTAAATGAGTATTTAACATCCTGCTGACCATACGTTATATTTTTGATATAATATTATATGATAAGACAACTTACATGAGTTAGAATTCCTATCAAATGTTTAATTTTTCTTGTGATATTTTTTTTGGTGTTGACAACATTAACAAATAATTTTCGCTTATTTTGTTTGAAAATATGTGTTAGAAAATAACATGAGTTATCTTAAGAAAATATACTCATTCTTTGTGCTCTTATAGCTATCTGTGTGCCTAATAAGAAGGATATTTATGGTTGAACTCATAGACAAACTTTTTGTAGTTTACAAACTTCTTGAATCTCTTTTAATGTTTCAGTCCCACTTCAGTAAAATACTTAAAAGCACCTTAGCACAACACCAGTCCTACTGACATATTTGACTATTTAGTGAGTTAGGTACACATCATTCTCTTGCAAAATCGTAACATAAATGGAGCATCGGGCAGATCACCAGGGTGTTTAAAACCATTATATCTTTATAATGATTTACAGTATTATTCTTATGAAATGAACATTTGATAGTCTAGTTTATCAGTGTTTTATTTTCAG
Seq C2 exon
GGCACTACTACAGAAACTGACTTAAGAAAAAGAAGGTCTAGTTCTTACCAGGTTCCTATGGACTACCTAACAGATCCTAGTGCAAGGCAGCGAGCAATGAGTATAGCCAGCATGCTCACAAATACGATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.750 A=NA C2=0.311
Domain overlap (PFAM):
C1:
PF119333=DUF3451=FE(51.3=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.5=82.2)
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:
GCTGATGATGAGCACAGCACT
R:
TACTCATTGCTCGCTGCCTTG
Band lengths:
343-1271
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]