DreINT0131464 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10063995-10064405:-
Coord C1 exon
chr6:10064277-10064405
Coord A exon
chr6:10064087-10064276
Coord C2 exon
chr6:10063995-10064086
Length
190 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
CTCTCTATTTGATTCTACAGGTA
3' ss Score
10.45
Exon sequences
Seq C1 exon
ATACACGTTCACAGGGATCTACACCTTCGAGTCCCTGATTAAGATCCTGGCTCGGGGCTTCTGCGTGGGGAAGTTCACTTTCCTGAGAGACCCCTGGAACTGGCTGGATTTCAGTGTCATTCTGATGGC
Seq A exon
GTGAGTATCCGTAATGCATACTATTATTTTTCTTTTTTTTAAATGTAATAAGCAATCGAGAAATGAACCCAGAGTGTTCTCGGATAGTTTTGGACACATTGATGAAGGAAAAGCTGGTGAATCCATGTGGGTTGCGCTTGTGTGAGTTGGAGCGAGTGTGTTTGTGGTAACTCTCTATTTGATTCTACAG
Seq C2 exon
GTATGTAACTGAGTTTGTAAACCTAGGCAATGTGTCAGCTCTCCGCACTTTCAGAGTGCTCAGAGCTTTGAAAACTATCTCAGTCATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:5
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=FE(16.8=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(12.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACGTTCACAGGGATCTACACC
R:
CTGGGATGACTGAGATAGTTTTCA
Band lengths:
218-408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]