DreINT0131446 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10047542-10048117:-
Coord C1 exon
chr6:10047776-10048117
Coord A exon
chr6:10047672-10047775
Coord C2 exon
chr6:10047542-10047671
Length
104 bp
Sequences
Splice sites
5' ss Seq
GAGGTATTT
5' ss Score
7.63
3' ss Seq
CAGTCTTTTTTTTTTCGTAGGGC
3' ss Score
8.31
Exon sequences
Seq C1 exon
TCTCTTCTCAGCATTCGTGGATCTCTCTTTTCTCCACGGAGGAACAGTCGTGCAAGCCTTTTCAGTTTTCGTGGCAGAGCTCGAGACTTTGGCTCAGAGAATGATTTCGCGGACGATGAGCACAGCACATTTGAGGACAGCGACAGTCGACGAGGATCCCTCTTCGTGCCTCGTTGTGTTGAGAGGCGAAGTTCTACCGTCAGCCACTGCAGCCTCACAGCACCCAGGATTATGCTGCCAGCCAACGGGAAAATGCACTGCACAGTAGACTGCAATGGAGTGGTTTCCCTGGTTGGCGGGACATCTGTGCCAACATCACCAATTGGACGTTTGCTACCTGAG
Seq A exon
GTATTTGAGTTGGATGTAAACAAACATGTTATCTATAAGAAAACTTCGCTTTATATGTAAACAGTATTGCGGTTGATTCTCATGCAGTCTTTTTTTTTTCGTAG
Seq C2 exon
GGCACAACAACCGAGTCTGACGTCCGTAAGAAACGTTCAGGATCACACCAGCCTTCTGATTACCTCGAGGAGACAGTAGCCAGGAAAAGAGCAATGAGCGTGGCCAGCATTCTCACCAATACTATGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.228 A=NA C2=0.455
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(15.2=24.6),PF0310514=SPX=PD(41.4=79.8),PF119333=DUF3451=FE(51.4=100)
A:
NA
C2:
PF0310514=SPX=PD(10.7=65.9),PF119333=DUF3451=PD(16.4=81.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAAGTTCTACCGTCAGCCAC
R:
TTCCTGGCTACTGTCTCCTCG
Band lengths:
242-346
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]