GgaINT0046956 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19333352-19334678:-
Coord C1 exon
chr7:19334524-19334678
Coord A exon
chr7:19333526-19334523
Coord C2 exon
chr7:19333352-19333525
Length
998 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGT
5' ss Score
10.65
3' ss Seq
CTCAAAAATCTTTTTCACAGGCA
3' ss Score
6.54
Exon sequences
Seq C1 exon
GCTGTGTGCGGAGATTCAAGTGCTGTCAAGTCAGTGTAGAAGATGGGAAAGGGAAAATCTGGTGGAATCTTAGGAAAACGTGCTATAAGATTGTTGAACACAACTGGTTTGAGACCTTCATTGTCTTCATGATTCTCCTCAGCAGTGGGGCTCTG
Seq A exon
GTAAGTTAAGGTGGAACAACTGTTTCTATTATAAGCAACAAGCATTTGGAGTTACAGTTAATTTTATAGCTACAGTAAACATCAGAAATTAATATCCAATTCAGTGATGTTCTAATGCCAGTGTATATGAGCAAATATTTGGCATATATTATGGTGTACTTGTAAATTTCTCTCAGGCTATGAAAGAAATTGTTGGATGAGTTCAGAATGTAGCTAGCGTTCAGAAAAATATGAAATCAGCTACATCAGACTGGTGCTCACATCTCCATATTCTTTTTATATATTAGCAACTCTTTTTTCTCAGTTAGAAATAGAATATGATTTGATAGCTGAGCTAGGAAGATATCAACAGTAACTTGAATTGCAAAATGAGATGTAAGGTATGATAATGATTCAATCTTTTTTTCTTTTTTGCCAAATTGATGTTAAATCAGGTACACTGAGTAAGTACAGAAGTAACTAGTTTCTCATAGCAGGAGCAAAATACAGTGTATTTGCTACACTACCATTTCAGGTCATAGTGATTCACCGTCAATGTAGATCTTTCCTTCTGAAATTTCTGTTCAGAATTGCTTTGTGGGTTGTGTGTATAGTTTGAGTTCAATTACTCATTTTGCAAAATTATATATCAGAGAGCCATTATTAAATTTCTAATATAATGTTAATAATTTTGATATAAAGTTTTGATACAAAGTTGGAACAATCACAAGGGAAATCCTTATGCCAATAAGCTATTGCTATTCATGGAAATGAATGAAAATGAGATTTGGAGAATTGTATTACAGTGAGTTTCATGAATCACTGTCCAGCTCAGCTGAAAGATGAGTACTACCGTGTTATGAAGACTACGGTATTAAATTAAAGAGAAAGGATATTGGGAAGGATATGTGGCTTATCATCACATATATCTTTTCAACTCAAATACTTTCTTGGCTACTACATCCTGCATTGCAAGTTAGGAATTCATTTAATTATGTCCTCAAAAATCTTTTTCACAG
Seq C2 exon
GCATTTGAAGATATATACATAGAGCAACGTAAAACTATCAAGACCATGCTGGAATATGCTGACAAAGTTTTTACTTACATCTTCATTCTGGAAATGCTTTTAAAATGGGTGGCTTATGGCTTTCAAACATATTTCACTAATGCATGGTGCTGGCTGGACTTCCTGATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:16
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:
PF065128=Na_trans_assoc=PD(19.8=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
GCTGTGTGCGGAGATTCAAGT
R:
CAACAATCAGGAAGTCCAGCCA
Band lengths:
327-1325
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]