MmuINT0079595 @ mm9
Intron Retention
Gene
ENSMUSG00000032269 | Htr3a
Description
5-hydroxytryptamine (serotonin) receptor 3A [Source:MGI Symbol;Acc:MGI:96282]
Coordinates
chr9:48712682-48714497:-
Coord C1 exon
chr9:48714388-48714497
Coord A exon
chr9:48712852-48714387
Coord C2 exon
chr9:48712682-48712851
Length
1536 bp
Sequences
Splice sites
5' ss Seq
GTTGTGAGT
5' ss Score
6.59
3' ss Seq
GATCCCTCTTCCCTGACCAGTGT
3' ss Score
7.68
Exon sequences
Seq C1 exon
TACTGGACTGATGAGTTTCTGCAGTGGACTCCTGAGGACTTCGACAATGTCACCAAATTGTCCATCCCCACAGACAGCATCTGGGTCCCTGACATCCTCATCAATGAGTT
Seq A exon
GTGAGTCCTTTCATCAGATCATAGTGGGCTGGGAGGCTGTGGTTAGAGAAGCCAGGAGCAGTGACAATTTCCTCTCTTGATCAAGTTAGCATTTGTTCAAGCTCTCCTTTATGCAATTCTCTGTTTTTCCTTGATTAACCTCTCTCTTTCTTTCTGTACCGGATGCTACAACCTTATACTTCTTAGTCCTGGGACTCCATCATAGGAACAGAAGCCAGTGAGTGATGTCACACTGAGTTCTAATAACTTAATGGAGACAGCTGCATTTGTCAGAGGGAATGGTTACTTTTTTTTTTTTGTGTGTGAAAGGAGCAAAACTCTGATGACAGCCAATGCTTCTGGTCACAGATGAGGATCAGGAGCCAAGGAACATATTCAAACCTCCCGAGGCACACGTGTGCCTAAGGGGGCACAGTTGGCACCTCTAGCATGAAGTGGGTCCCATTAGCTTTTGTTCTCAGCAGCTCAACATGCTCCCGTTGCCCTCAGCCAGCTGACTTTCTCTCCATTCTGCAAGTTCATCCAGGGTCCACCAACTGGACATCTGAGTACAAAGGCAAAGAAAATACATGGGGAAAATACAGATAGAATGGGGAAAGTAGGTTGGGGCTGTGATTCAATTGGTAGACTATTTGCATAGCATGATCAATGTCTGGGTTCCATGTCTAAAGCCAATGTGATGGCATCATCTTAGCCCATCATCTTAACACTTGGGAGACGGAGGCAAAAAGTTCAAGGACTACTGGAGATGCCAGAGGTATTCATGCGGTACCAATTGCATTGTCCAACTCCTTGACATTTCCATAAAGAAGGCCATTGAATTTGATCCACCCTTGAATGTCCCCCCCCCAACATAGCACAGGTGGAAAATGTTCTAGAAATTTCTTTCTGCTCTTTTTTTAGCTTCTATCTTTCAGTCTACCTCAAAGAAGGCCTAAGGCCAGGCCCTGGGCTCAGCCTACCTCATGCCTTAGGGTCAGGCTTAGTAAAGACAACAGGCTGAATTCTTGTTGGATTTTCCTAGGCCCCTCTACTCCTTATGAACTCTATGCTCTTCCATCTAGAGATGACTGCTCTCATTTGGGGGGCTTCTAGAAATGGGGAGCAAAGCAAACGTCAGAGAATGGAACGTATGATTCTTCTCTCCTATCAAACCGCTGGCTAATCTGGGGACCAGCTCTGCTCTGGTGTGGGGCTGGTGTGTCAGCCTGGAGACAGCTGAGCCAGCTGCCTTCAGAGTTGGCTTTACAGTCCATGGATCCCTTCACTGCCTTTGAGAGCTAGGTTGCTAAGGGAGTTGAAAATAAGAAACATCCTTCATTGTTTGGAGCACAGCCTCGATAACAGTGGGTCAGAAAGCTAAGATTGATAACATTGGAAAAGTAAGGCCAGACAAAATGTCTGGATTATCTTGGTCTCTAGATCCTCTCTAAGTTTCTTTCCTTACTTACAAATTTCTTACTCAAAAGATCTTTAGCCTTCCATGGTGAGGGTCTGCCTCTTCAGCCCACAAACTGATCCCTCTTCCCTGACCAG
Seq C2 exon
TGTGGACGTGGGGAAGTCTCCGAACATTCCTTATGTGTACGTGCATCATCGAGGTGAAGTTCAGAACTACAAGCCCTTGCAATTGGTGACCGCCTGTAGCCTTGACATCTACAACTTCCCCTTTGATGTGCAGAACTGCTCTCTGACTTTCACCAGCTGGCTGCACACCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032269-Htr3a:NM_013561:4
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:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACTGGACTGATGAGTTTCTGCA
R:
GTGTGCAGCCAGCTGGTG
Band lengths:
278-1814
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: