GgaINT0046945 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19358966-19359717:-
Coord C1 exon
chr7:19359654-19359717
Coord A exon
chr7:19359108-19359653
Coord C2 exon
chr7:19358966-19359107
Length
546 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
CATTTCCTCTTCTTTTGTAGTCA
3' ss Score
8.36
Exon sequences
Seq C1 exon
ATCATTTCTACTTCTTGGAAGGACAAAATGATGCTCTGCTGTGTGGCAATAGCTCAGATGCAGG
Seq A exon
GTAAGAAAATCATTTTTCATAGTGCATCAAGAAAGTTAGCTACTTAGAATAGCTCATGTGGCTAATTAAAGTATCAGCTGTACCATAGAGTTTCAAATTACCAACATTCTGGAATATGAAACTATACCTAAATATAATCATCTATGTGATTTGAGTTTACACAGGCAATTTCTTCAGCACCTTAATTTTGTAAAGGTAATCCCATTAATACTATGTGCATAAAAGTTACTGCCAGCTGGCTGACTATTTACTACTAGCTGTGCTCGATGGCGATCTTCTCTTGTGCTGATGGAGATGTGTTGATAAGAAAAATTGTGGGGAAGGATAGATTACTATTAGCTATATTATTATAGCAATGAAATATAAGTAGGAGATGGAATTAAAAATTGAAATCCACTAGAATTTTTTTATCTTAGGTATGTAGAATAAAGTTTTACTTGTTCAAAATTTCATTTGCAACAGGTACTCCTGAAAAATTTTGTGATTTTTGTAGCATATCGTAATCTAGAGTAGTTGTTAAACATAGCATTTCCTCTTCTTTTGTAG
Seq C2 exon
TCAATGTCCAGAAGGATATATATGTGTGAAAGCTGGTAGAAACCCCAACTATGGCTACACAAGTTTTGATACATTCAGTTGGGCATTCTTGTCACTGTTTCGATTGATGACTCAGGACTTTTGGGAGAATCTTTACCAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:5
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(7.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(17.5=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:
ATCATTTCTACTTCTTGGAAGGACA
R:
CAGCTGGTAAAGATTCTCCCA
Band lengths:
206-752
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]