GgaINT1024527 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19321010-19322366:-
Coord C1 exon
chr7:19322229-19322366
Coord A exon
chr7:19321115-19322228
Coord C2 exon
chr7:19321010-19321114
Length
1114 bp
Sequences
Splice sites
5' ss Seq
AAGATAAGT
5' ss Score
2.82
3' ss Seq
TTTTTGTCTCTTTGCTTTACTTT
3' ss Score
1.74
Exon sequences
Seq C1 exon
GTTTTGGATCAGCCTAAGTATGAAGATAACCTGTATATGTATCTATACTTTGTCATCTTTATAATCTTTGGATCATTCTTTACCCTAAACCTTTTCATTGGTGTCATCATAGACAATTTCAACCAACAGAAGAAAAAG
Seq A exon
ATAAGTATTTCATCATTACTCAGAAAACAAAGCTAAAAGTTGATCTTTTTGGTCCACAAACAATGACTTTCTTTTCTTTTCAGGCTTTATTTTAAGATAAATTAACCCACTTTGTATATTAAATACATTAAGTTGATTAAAGCAGTACAATTTGTCTCAATAAATGTTTGACAGACAAGTGACACCATAAGTCTTTCCATGGTTAGTGAAATATTCAATGCTAATGTAAAGATGTGAATTTCGGATTGGACTCTTTAACAAGATCAGAAAAAGGCTAACCATTGAAATACTTAAATGCAGCTGTAAAACCTCTTAGTTATGTTATTGTCAAGTCTCAGAGCTCAGCAGCCTAGATTTCTGAATCATAATAATAAATATTTAAATAAATTTATTTGTCCTCTCTTTAGTCTTCATATTTTGTCAACGCTGCCTCAAAAGGCATCAGTGTTTCAGCAACAGAACTTAAAGAAATTATCTGGCAGGACAATGAACTGGTGGAAATGCTGCTGGAGTCATATATTAAAATTTGAGATTTGATATTAAAAGTTGAGATGGAGAGAAATTGGCTTTTTTTTCCTACTCAATCCATGTAATAGTTCCAGGATCTTCTGCTTCAAGTCCTGCATTTGCAGTTAGAAGATAAAAGTTGTGAGATATAATTGTATGCCTAACTTCTCATCTTCCTTTTGTATCATGGAAGTCAATTCTAATATTTTGCCAAAATTTACTCAAAAAGAAAAACAAGAGCACAGGATTGGAATGTTCTGTTCATTCATATCTCCATAATAACTTCAATAGAGCAAAGAAAAAGCACCTCTCTTTCCTGAAGATTCCTATTACCTGTACCACCCAAATGAATACCGGAAGTCTATCACAAACATTTACAGTGCAAGAGTCTTTTAAAAAAAATCCTAAACTTTGAAAGCGACATTTCTAAAGCATTTTTTTGTTACTCATATACTAATAATCAAGATAAATGGAAACTTAAATGTCTATTCTAATTTTCCCACAGCTTAGAACGTTAATAAGAGTGATTATTACTAATATGTATTCCTGTTTATAAGTAATCAATAGAAATATGTGATTATGACCAGTTTTTGTCTCTTTGCTTTAC
Seq C2 exon
TTTGGAGGTCAAGATATTTTTATGACAGAAGAACAGAAGAAATACTACAATGCAATGAAAAAGTTGGGTTCAAAGAAACCACAGAAGCCTATACCACGACCAGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:21
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=PD(15.3=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTTGGATCAGCCTAAGTATGAAGA
R:
TGCTGGTCGTGGTATAGGCTT
Band lengths:
241-1355
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]