DreINT0131468 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10052817-10053331:-
Coord C1 exon
chr6:10053190-10053331
Coord A exon
chr6:10053024-10053189
Coord C2 exon
chr6:10052817-10053023
Length
166 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GTGCGTTGTGTCTCTTACAGACT
3' ss Score
10.39
Exon sequences
Seq C1 exon
GCAGTGCCCTGAAGGTTTCACGTGTATAAAAGCAGGGCGTAATCCAGACTACGGCTACACAAGCTTCGACACGTTCAGCTGGGCTTTTCTCTCACTCTTCCGACTCATGACCCAAGACTTCTGGGAAAACCTCTACCAGCAG
Seq A exon
GTACAGCATGAACACATCGCATTACTCTGTAGGCAAGTCTTCATCACTGACTCTGTGATTCTTCCTGTTACTGGGAAGCTGCCTTGGAACAATCTATATTGCGTAAAGCACGATACAAACTGTTTTAATTTGGTTTGTTTATGTATGTGCGTTGTGTCTCTTACAG
Seq C2 exon
ACTCTGCGTGCAGCTGGAAAGCCCTATATGATCTTCTTTGTTCTTGTGATCTTCCTGGGCTCCTTCTATCTGGTTAATCTCATCCTGGCTGTGGTGGCCATGGCGTATGATGAGCAGAACCAGGCCACTATAGAGGAGGCTCAACAGAAAGAGGAAGAGTTTCAGGCCATGCTGGAGCAGTTGAAGAGACAACAGGAAGAGGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:9
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=0.217
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(18.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(12.1=44.9),PF0293211=Neur_chan_memb=PU(33.7=89.9),PF0310514=SPX=PU(15.9=50.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGTTCAGCTGGGCTTTTCTCT
R:
CCAGCATGGCCTGAAACTCTT
Band lengths:
246-412
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]