DreINT0131487 @ danRer10
Intron Retention
Gene
ENSDARG00000098738 | scn4aa
Description
sodium channel, voltage-gated, type IV, alpha, a [Source:ZFIN;Acc:ZDB-GENE-051201-2]
Coordinates
chr12:4851943-4852358:+
Coord C1 exon
chr12:4851943-4852097
Coord A exon
chr12:4852098-4852184
Coord C2 exon
chr12:4852185-4852358
Length
87 bp
Sequences
Splice sites
5' ss Seq
CTGGTGTGT
5' ss Score
4.96
3' ss Seq
CAATCTTTTCTCTTTGCCAGGCT
3' ss Score
7.51
Exon sequences
Seq C1 exon
GCTGTATTAGGCGATGTGCATGTTTGAGTGTTGACATCACAGAAGGATGGGGTAAAAAATGGTGGAACCTCAGAAGGACATGCTTCACCATCGTTGAGCATGATTACTTTGAGACCTTCATCATCTTTATGATCCTCCTTAGCAGTGGAGCACTG
Seq A exon
GTGTGTTTTTCAATTAGAATAAAAGAATAATCTTATGTAAATGGGAACTTTTCCTAACTTGACGTATCAATCTTTTCTCTTTGCCAG
Seq C2 exon
GCTTTTGAGGATATCAACATTGAGAGGCGCAGAGTGATCAAGACCATTCTGGAGTATGCTGATAAAGTCTTTACATATATTTTTATAGTGGAGATGTTACTGAAGTGGGTGGCATATGGCTTCAAGACCTACTTCACTAATGCATGGTGCTGGCTGGACTTCCTCATTGTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098738:ENSDART00000170961:17
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(23.4=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.1=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:
GCGATGTGCATGTTTGAGTGT
R:
ACTCTGCGCCTCTCAATGTTG
Band lengths:
180-267
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]