DreINT0131460 @ danRer10
Intron Retention
Gene
ENSDARG00000062744 | scn1lab
Description
sodium channel, voltage-gated, type I like, alpha b [Source:ZFIN;Acc:ZDB-GENE-060906-1]
Coordinates
chr6:10015516-10016011:-
Coord C1 exon
chr6:10015907-10016011
Coord A exon
chr6:10015787-10015906
Coord C2 exon
chr6:10015516-10015786
Length
120 bp
Sequences
Splice sites
5' ss Seq
GCGGTACAA
5' ss Score
2.55
3' ss Seq
GTCTCTATATTTCTCTCTAGAAT
3' ss Score
9.3
Exon sequences
Seq C1 exon
CTTGGAGGTCAGGATATCTTCATGACAGAAGAGCAAAAGAAATATTACAATGCTATGAAGAAGTTGGGATCTAAGAAACCTCAGAAGCCAATTCCCAGACCTGCG
Seq A exon
GTACAACACATTCAGCTTACTCTCACTAATCGTATATTTAGTACAAAATAAATTATACACTACAATTAGTATCATATCATCAGCATTATATGACAATAATGTCTCTATATTTCTCTCTAG
Seq C2 exon
AATAAGTTTCAAGGCCTTGTCTTTGACCTAATCACCAAACAAGCCTTCGACATAATCATTATGATCCTGATCTGCTTGAACATGGTGACCATGATGGTGGAAACCGATGACCAGACAGAGGATATGGACAATATTCTGTACTGGATAAACCTGGTTTTCATCATCCTCTTCACTGGAGAATGTGTGCTAAAGATGATCTCCCTGCGCCACTACTTCTTCACCATCGGCTGGAATGTGTTTGACTTTGTTGTGGTGATTCTATCAATTGTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062744:ENSDART00000151247:25
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGCCAATTCCCAGACCTGC
R:
GTGAAGAAGTAGTGGCGCAGG
Band lengths:
243-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]