DreINT0131510 @ danRer10
Intron Retention
Gene
ENSDARG00000034588 | scn4ab
Description
sodium channel, voltage-gated, type IV, alpha, b [Source:ZFIN;Acc:ZDB-GENE-051201-1]
Coordinates
chr3:22169564-22169972:+
Coord C1 exon
chr3:22169564-22169718
Coord A exon
chr3:22169719-22169798
Coord C2 exon
chr3:22169799-22169972
Length
80 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGT
5' ss Score
10.47
3' ss Seq
TTGTTTGTTGTTTTATTTAGGCT
3' ss Score
9.7
Exon sequences
Seq C1 exon
ACTGCATCAGGCGATGTCCTTGCTTGGATCTGGACGTTAGCCAAGGTAAAGGCAAAGCATGGTGGAACTTCCGGAAAACCTGCTTCGCCATTGTGGAGCACAGCTATTTTGAGACCTTCATCATCTTCATGATTCTCCTTAGCAGCGGAGCTTTG
Seq A exon
GTAAGTTGTTTGTAAAACCAGATCAACCCACTGATTTCTCTTCTTTTTAAATAAGTATGTTTGTTTGTTGTTTTATTTAG
Seq C2 exon
GCTTTTGAGGACATTTACATTGAACAGCGGAGAATGATTAAGATCATCCTTGAATATGCAGACCAGGTCTTCACCTATGTGTTTGTGGTTGAGATGCTTTTGAAATGGGTGGCCTATGGTTTCAAGGTCTACTTCACAAACGCTTGGTGTTGGCTTGACTTTCTCATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000034588:ENSDART00000044157:16
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:
PF065128=Na_trans_assoc=PD(31.4=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCATTGTGGAGCACAGCTAT
R:
GGCCACCCATTTCAAAAGCAT
Band lengths:
183-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]