GgaINT0046951 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19349179-19350485:-
Coord C1 exon
chr7:19350247-19350485
Coord A exon
chr7:19349353-19350246
Coord C2 exon
chr7:19349179-19349352
Length
894 bp
Sequences
Splice sites
5' ss Seq
CTTGTAAGT
5' ss Score
8
3' ss Seq
AAACTGTATTTTCCTTCCAGGTG
3' ss Score
10.42
Exon sequences
Seq C1 exon
AACTTGAGGAATCAAGACAGAAATGCCCACCGTGCTGGTATAAATTTGCTAACACTTGCTTGATTTGGGACTGCTGCACTCCATGGCTGAAAGTCAAACATATTGTAAATTTGATTGTGATGGACCCATTTGTTGATCTGGCCATTACTATCTGCATTGTTCTAAACACTCTGTTCATGGCCATGGAGCACTATCCAATGACGGAACAGTTTAGTGGTGTCCTTTCAGTAGGAAACCTT
Seq A exon
GTAAGTCTTCCGTGATGTACCATGTATGTCAAATACATTTTTCTTAAATGATACTTGTGTTACCTATGTATGTATGTTTAAAAGAAAATGCTGACTAAATATTTAAAAGGCTTGGAATGGTTGAATTTGTATTTAAGCTGTACTGAATGCCTTTTGTTGATATTTGTGTATTTCTCCATTCTTGTTATATGGACTTTAATTCTCCTTTGCAGAAGATTTACTGAGTCAAAATTCATTTTCTTTTTTAAATCCTTCAGGTTCCCTCATGGAAACTAGTTACAGAAATTAGTGTTTTCTCTTAAATGGATACTTATAAAGGGAAGGAACCTTCAAATCTGTTCCCACACCTGTTCTGCACCTCTCTAGTTCCTCTTGGTGTTCTAGATGTTCAAGGGGATGTAGAGAGGAAAGACCCAGTGAGCACAGAGTATTTATTGTGACTTAACAGGAGATGGTGTGACAGTGCTATTTGCTGGCTATCCCAAAGAAGAATAGTTCTGCTCAATGTTATTTTTTTTCTTAACTTTTTTTTTTTTATTATTATTATTATAAACTTATACTTATCCCTAGAAGAAAAAGCTGTCCTAAGGAGATCTGAGGAGGAAATTTGAGTACTAAAATCAGAAGTGATACAATATATCACTATTTATGTGTGCATATTAGCTAGATAGGAAGCATCCTATTTACCTCTTCCTTGTGAGGTAAATAGGAACTGCATATGTGAGCTTAAATCTGAATTTAATTCCTAACCTAATGTATGGGAATATAGAGAAGGTATTCAGATCCACCATGGATTGCTTACTGAGAATATAACTTAAAAAAAGTTAATGCTGTTACATTTTAAAAAAATAATTTCTTATTAAAATAGAGTAAGAAACTGTATTTTCCTTCCAG
Seq C2 exon
GTGTTTACTGGAATTTTCACAGCAGAAATGTTTCTCAAGATAATTGCCATGGATCCTTACTATTATTTCCAAGAGGGCTGGAATATTTTTGATGGTTTTATTGTGAGTCTTAGTTTAATGGAGCTTGGTCTTGCAAATGTAGAAGGATTATCTGTCCTTCGATCATTCCGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:11
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=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=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:
TGATTTGGGACTGCTGCACTC
R:
TCGGAATGATCGAAGGACAGA
Band lengths:
350-1244
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]