GgaINT0046955 @ galGal4
Intron Retention
Gene
ENSGALG00000011009 | SCN2A
Description
sodium channel, voltage gated, type II alpha subunit [Source:HGNC Symbol;Acc:HGNC:10588]
Coordinates
chr7:19334524-19335145:-
Coord C1 exon
chr7:19335025-19335145
Coord A exon
chr7:19334679-19335024
Coord C2 exon
chr7:19334524-19334678
Length
346 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGA
5' ss Score
9.45
3' ss Seq
CAATTTATTATCACACTTAGGCT
3' ss Score
4.08
Exon sequences
Seq C1 exon
AAATTAAATGCCTCCAGTTCATCAGAAGGCAGCACAGTTGATATTGGACTACCTCCAGAAGGGGAACAGCCAGAAGTAGAACCTGAAGAATCTCTGGAGCCTGAGGCTTGTTTCACAGAAG
Seq A exon
GTAGGAAAAGAAAATATACTCACATCATGAGACCTAATTTTGTTGGTATGGGCTGGGTTCTATTCTTAGTTGAAATCAATAAGCTGCCTTGTGATTACAGTTATATTTTCTTTTTGTATGAGTATCTCCTTCATAGGTGATGTTGTGGTGCTCTCTTTATCCTTGATAGATATTATAAAAGTTACAAAGCTTCCATTTCAAATATTGAAACTAAGGCCCTCAAATATTCAGAAAGATACAGCCATCTATTGTAGTATTTCTGAAATGAGCCAAATTGCTTTGTTCATTCGTAATTCCTAATTAATATTAACCTGATACTGACATCTCAATTTATTATCACACTTAG
Seq C2 exon
GCTGTGTGCGGAGATTCAAGTGCTGTCAAGTCAGTGTAGAAGATGGGAAAGGGAAAATCTGGTGGAATCTTAGGAAAACGTGCTATAAGATTGTTGAACACAACTGGTTTGAGACCTTCATTGTCTTCATGATTCTCCTCAGCAGTGGGGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011009:ENSGALT00000017933:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.707 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(18.0=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.8=84.6)
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:
AATGCCTCCAGTTCATCAGAAGG
R:
CAGAGCCCCACTGCTGAGG
Band lengths:
270-616
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]