DreINT0079533 @ danRer10
Intron Retention
Gene
ENSDARG00000089212 | htr3a
Description
5-hydroxytryptamine (serotonin) receptor 3A [Source:ZFIN;Acc:ZDB-GENE-071012-5]
Coordinates
chr21:23102203-23104172:+
Coord C1 exon
chr21:23102203-23102372
Coord A exon
chr21:23102373-23104011
Coord C2 exon
chr21:23104012-23104172
Length
1639 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGC
5' ss Score
7.47
3' ss Seq
AACCTTCTCTCATCTCGTAGCTA
3' ss Score
7.95
Exon sequences
Seq C1 exon
TGTTGATGTAGGAAAGTCTCCTGATATTCCTTATGTCTACGTAGGCCATGATGGACTTGTCAGCAACTATAAGCCTATCCAAGTAGTGACTGCCTGCTCTCTCAACATCTATAACTTTCCTTATGATGTTCAAAAATGTAGCTTGACTTTCCAGAGCTGGCTACACACAA
Seq A exon
GTAAGCAACCACATTAAAGTATTTCTAAGTAGTCAGTGACAAAATGCATGTCTAAAATTTTTAAAAGATGTGATCTTTAAACATTTTTATAATGCCCGATGAAAGCTAATTAAAGCAAGACACTACAGGTAAAATATATATATATACATATATAATGCACTTGTTAGTTTTTAGATTTTGAGATATTTGGCTATCCATATGATGTCTTTTTCAGTTAATGTAAGAAAAACATCCAACATACACTTTTAAGAGTTTATTTTGCTCAACTTTGTATGTTTTTGTCTGTAGATTTCCATTACAATACATTGTAAAAAATGCTGGGATCCACAAAATTCCTTCATGCTCTCCCAACACAAATTGATTAAGTTAACTTAATCGTTTTTTTTTTATTTTTTATTTTTTACAAAATTTAAGTGGATTGAACATAAAACAATTAATTAGTTAAAAAAAACTTAGGAATTGCGTTGTTTTAACTCATTTTAAATAAGTAGTTTGAACAAGCAGCAAAAATCATTTTTTTGTGTTTATTTTTAAGAGTGATTTCCTGAAAATGAAAAAAAAAAGCAAGAATTTTAAATCTGACTTCTTCCGACGATTTTTGTGCAAGAAATATATGCAAATGAGTGGGTTAATAAGTGGCTTTCATTAAACAATGGCTTTCATTAAACAATGCCTTGTTTGCATATTTTAACAGCTTTTATTATATATTTTATAATCAACAGGGAAAATATAATATCATTTTTTAAAATATCTTTTTATTGACCTTTAACTTAATAAAACAAAAATTTCAAAAAGATTTGAAACAGAAACAAATCCTCTTTTCTCCAAAAGAGCTCCTGGCCCAACTGTACCATTGCAATGCATTAGTTTTGCACATTTTAAATCTGATTTACACTATATTATTATAGATATGTACATAAAAAAAAAGTATGCACATAAAGACAAATAGATAAAAGTACACTTATGTTCATTTATATATTGTTCACTCATATACATAAAATGAATCAAAATTAACTTAAAATAATCAAATAAAAAAAATGGAGGGAGAAAAAAAGAGCAAAAAAAAAATCTTTAGCTTTGAACAAGTATTAATCTGCTGTTAATGTGAATTATATTTTCTGCTATTTGTATTTCCTTCATCTTCATCAGACAAAACAAAACAAAATGAAACAAAACTAAACTAAACTAAATCAAACCAAACTAATCAAAACTAAACTAAACCAAACAAAATGACTAATCGAAACGAAATGAAACTAAACCAAAGTAAATCAAACTAAACGAAACTAATCGAAATGAAAGGAAACAAAATGAAACGAAACAAATAAAAACTAAACGGAACAAAATTAAAACAGCAAATATTAAGTTTGCTTCATTCTGTACATAAGCACTGGCTGTCAGATAGTATACAATTTTTGACTGCAACCTTTATAGGAGTTATCAGACATTATTTTACCGTTCACCTGCAGTGTCTTTCGTATTTACTGAAACATTCAGTTTTTATTCAGTTTTTATTTTATTCCAGTTTTTATTATTCTGGAAATGCATTATTGGAGAAATGATTCAAGCATAAGAAAAAAAAACAAAGTGTCTTTTTCGTAAAGCCACACGAACTGACCTTTAACCTTCTCTCATCTCGTAG
Seq C2 exon
CTAAAGACATCAACATCACACTAATGAGAAGCCCTGAGGCTGTCAAGACAGACAAGAGTGTGTTCATGAACCAGGGAGAATGGGAGCTGCTTCACGTCCTCTCCACATACAACGCGTTCAGCATTGATAATGATGATTACTACGCCGAAATGAAGTTCCAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000089212:ENSDART00000125907:5
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(27.3=100)
A:
NA
C2:
PF0293118=Neur_chan_LBD=FE(25.4=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:
GGAAAGTCTCCTGATATTCCTTATGT
R:
TGGAACTTCATTTCGGCGTAGT
Band lengths:
320-1959
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]