DreINT0079532 @ danRer10
Intron Retention
Gene
ENSDARG00000089212 | htr3a
Description
5-hydroxytryptamine (serotonin) receptor 3A [Source:ZFIN;Acc:ZDB-GENE-071012-5]
Coordinates
chr21:23101990-23102372:+
Coord C1 exon
chr21:23101990-23102099
Coord A exon
chr21:23102100-23102202
Coord C2 exon
chr21:23102203-23102372
Length
103 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
TTTCTTTCTGTCCTCTTCAGTGT
3' ss Score
11.15
Exon sequences
Seq C1 exon
CAATGGACAGATGAGTTCCTTATGTGGGATCCTGAGGAATTTGATGAAGTCAAAAAAATTTCCATTCCGACTGCCAACATCTGGATTCCAGATATCCTCATCAATGAATT
Seq A exon
GTGAGTAAACTTGACCTAACAAAAGAGAAGAATGACACATTAATGATGCATTTGCTGCTCTATTACTACTTAAAATGTACTTTTTTCTTTCTGTCCTCTTCAG
Seq C2 exon
TGTTGATGTAGGAAAGTCTCCTGATATTCCTTATGTCTACGTAGGCCATGATGGACTTGTCAGCAACTATAAGCCTATCCAAGTAGTGACTGCCTGCTCTCTCAACATCTATAACTTTCCTTATGATGTTCAAAAATGTAGCTTGACTTTCCAGAGCTGGCTACACACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000089212:ENSDART00000125907:4
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:
PF0293118=Neur_chan_LBD=FE(17.2=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(27.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCTTATGTGGGATCCTGAGGA
R:
CAGCTCTGGAAAGTCAAGCTACA
Band lengths:
253-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]