HsaINT0078173 @ hg19
Intron Retention
Gene
ENSG00000166736 | HTR3A
Description
5-hydroxytryptamine (serotonin) receptor 3A, ionotropic [Source:HGNC Symbol;Acc:5297]
Coordinates
chr11:113851925-113854011:+
Coord C1 exon
chr11:113851925-113852034
Coord A exon
chr11:113852035-113853841
Coord C2 exon
chr11:113853842-113854011
Length
1807 bp
Sequences
Splice sites
5' ss Seq
GTTGTGAGT
5' ss Score
6.59
3' ss Seq
AACCCCTTTTCCCCCGCCAGCGT
3' ss Score
7.03
Exon sequences
Seq C1 exon
TACTGGACTGATGAGTTTCTCCAGTGGAACCCTGAGGACTTTGACAACATCACCAAGTTGTCCATCCCCACGGACAGCATCTGGGTCCCGGACATTCTCATCAATGAGTT
Seq A exon
GTGAGTACCGTTATCCATTGTGAGGTGGCTGGGTGGCTTAGGAGCTGGAGAAGCCCGGGGACAGAGAGACAAGATTGTCACTGTTGCATTTGAGATGTCCCACCAGGAATTGCAGACTGTAGATAAAGCTGGTGTGAGTCCAAATTCCCTTTGTCTTCCCCCCCGACCTTTTTCTGTTCTTTTCTTTTTGAAAACTCCTTCTTTTCGGTGCTTGATGTTGAAATTCCATACTTCGTAGTCCAGGGGCCCCTGCCACAGGGAAAGAAACCAGTGAATGAATTAACACTGAGTTATAATAACCTAATGGGACAGCTGCACTTATAAAGGAGACAGTAAATGTTTATTTAAAAAAAATGGAGCACTTGGCCAGACTCAGTGGCTCACACCTGTAATCCCAGCACTTTGGAGGCCGAGGCGGGTAGATCACCAGAGGTCAGGAGTTCAAGACTAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCCAGGCGTGGTGGCGAGCACCTGTAATCCCAGCTACTCGGGCAGCTGAGGCAGGAGAATTGCTTGAACCTGGGAGATGGAGGTTGTGGTGAGCCGAGATCACACCATTACACTCCAGCCTGCTGGGCGACACAGCAAGACTCTGTCTCCAAAAAAAAAAAAACAAAAAACTGGAACACTGATAGTGGCTGCCACTTCTGGCCCGCAAAGGAGATTTGGAGCTGGGGGACATGTTCAGACCTCCCAAGTTACCCATCTACCTGACAGGCCACAGATTGTTTCTCCAATACGAAGTGGGTTCCACCAGGCTTTACTCCTGGCAGCCAAACACGGTCCCATTTGGCCCCAGACAACATTCCTTCTCCCCATCCTGCAGGTTCATTCAGGGCCCACCAACTGGGTTTCAGAATTCAAGGGCAGGGAAGATGGCTGGGGAGACGGAGGAAAAGGGAAGGTGACAGGTGGGATCAGCCATCCTCTACCCCATACCCACAGCATTGTCCAACTCCAGGGGGTGCCACTGACATTTTTCCAAGGGGGTAGTTGACCTGGACCACACACCATCCTCTACATAGCTCAGGCTGGAGGGCTCTGGGAAATCCCAGTTTCTGCTGGCTCTCCAGTTTCAACAGTGAAGTGGCCTTAGTCTTGACTTCTCATCTCTCAGCATGAACTCACAGAAGGCTGAGGGCTCAGCCTACTCCATGCCACAGTGGTCACTCAAGAGGGCCTACCACTTTGACATCAGCTGAGAGAGTGGAATGAGGTCTTGTGGGGCTTTTCTGGCTTTCCCCAATTCTTATCCATTTCTCTAGCTCCTTTTCATCCAGAGATGATTATTTTCATTTCAAAGGACTTCCAGGGGTGGGAAGCAAAGAGAAGCCAGAGTCAGGATGGAACACAAGATCCTGCTCTTTCACCAAGCCTGCCTGGTCCCGCAGGACTGGCGATCCTGGGAGCCAAGCTTTGCCCAGCCCAGGGCAGTGACGGGTTGGGGCCACTGGGCACGCTTCCTACTGTCCATGGCTTTTGGGCCCATGGGTTTTCCTCCCTGCCTTGTGTGGCCAGGAGCCAGGGGAATAAAGGAGAAATGCCCATGACTGCTTGAAAACTAGCCTTGACAACGGCAGGTCAGGAAGCCTAAGATAGGAAGGTTGGAAAAACCGAGGCCAGGCAAAACATCCAGGTTATCCGGCTGCCTATACCCTCCCCGAACTTCACTCCCTACCCAGTTGTTCCAAGATCTTCAGGCACCCAGAGCTTGCCCTGTCTCTTGAGCTCCCAAACTAACCCCTTTTCCCCCGCCAG
Seq C2 exon
CGTGGATGTGGGGAAGTCTCCAAATATCCCGTACGTGTATATTCGGCATCAAGGCGAAGTTCAGAACTACAAGCCCCTTCAGGTGGTGACTGCCTGTAGCCTCGACATCTACAACTTCCCCTTCGATGTCCAGAACTGCTCGCTGACCTTCACCAGTTGGCTGCACACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000166736-HTR3A:NM_000869:4
Average complexity
IR-S
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
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGGACTGATGAGTTTCTCCAGT
R:
GTGTGCAGCCAACTGGTGAAG
Band lengths:
278-2085
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)