DreINT0131513 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22176447-22176876:+
Coord C1 exon
chr3:22176447-22176728
Coord A exon
chr3:22176729-22176822
Coord C2 exon
chr3:22176823-22176876
Length
94 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGC
5' ss Score
6.64
3' ss Seq
TGGTTTTGTTTGGTTTCTAGGCA
3' ss Score
8.44
Exon sequences
Seq C1 exon
GTGGTGGTGAACGCCCTGGTGGGTGCAATTCCCTCTATCTTCAACGTTCTCCTGGTGTGCCTGATCTTTTGGCTCATCTTCAGCATCATGGGAGTCAACCTTTTTGCTGGAAAGTTCTACTACTGCTTCAATGAAACATCTGAGGAGGTCTTCGATCACAATGTGGTCAACAATAAGACTGACTGCTATGAGCTTATGGAGTTTCATCCCGAAGTGCGATGGATGAACGGAAAGATCAATTTTGATAATGTGGGCATGGGCTACCTCGCCCTACTGCAAGTG
Seq A exon
GTGAGCGCTGATATTAATCATCAACATGTGTACACGGCAAAATCAAATATACAAAACTGGATGTATTAAAAATGTGGTTTTGTTTGGTTTCTAG
Seq C2 exon
GCAACATTTAAAGGATGGATGGACATCATGTATAGTGCTGTGGATTCACGTGCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:19
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(40.6=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.4=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:
TGGTCAACAATAAGACTGACTGCT
R:
GCACGTGAATCCACAGCACTA
Band lengths:
172-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]