Special

MmuINT0079596 @ mm9

Intron Retention

Gene
ENSMUSG00000032269 | Htr3a
Description
5-hydroxytryptamine (serotonin) receptor 3A [Source:MGI Symbol;Acc:MGI:96282]
Coordinates
chr9:48709523-48712851:-
Coord C1 exon
chr9:48712682-48712851
Coord A exon
chr9:48709684-48712681
Coord C2 exon
chr9:48709523-48709683
Length
2998 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CCTTTCGTCTTCTCTCTCAGTCC
3' ss Score
10.17
Exon sequences
Seq C1 exon
TGTGGACGTGGGGAAGTCTCCGAACATTCCTTATGTGTACGTGCATCATCGAGGTGAAGTTCAGAACTACAAGCCCTTGCAATTGGTGACCGCCTGTAGCCTTGACATCTACAACTTCCCCTTTGATGTGCAGAACTGCTCTCTGACTTTCACCAGCTGGCTGCACACCA
Seq A exon
GTGAGTACTGGGCTTGTGAGTGGGGCAGAGGTTGGGGCTCACAGGGACTGGGGAGCCAGGATGTATCCTCTCTTCATCAAGCCATCACTATTTCCTCCCTCCTCCCCACCACTGCTCCCTTACCTGTCTCTTTCATTTGTCTGGTTCCTTTGTAGTTCTGGGGCTCTAACCTAAGACCTTGCACATGCTAGGCGAACACTCCACCACTGAGCAATATATCCTGCCACTTCTCTTTTTAATGTCAATGAGCCTCTGCTTCCTCTCCCTCCAGATGGACACAGTATTGCTGTTCTCACTGCCTCTGTTAGCTGTTTCAAAGATTAATGAGGCGGTGTGAATCGGCTCCAAGGCACTCAGCAAGGGACACTTCTTACCTAGCATCTCAAAGAAGATCTGACAGGAAGTGCGTCTCAGACCCACCAATGCCCCCTGCACAGGTGTCCTCATTCCCTTCCTACCCTGGCTCTCCCCATGCACCACCCGCACTGTGGTTCATGCTCTCCACAGCAGCCACTGAGCTCTTATTAAAATGCAAATCTGATCATGTCATTTAAAGCCCTCAATGGCTTCCCAGCAGTCCTGGGACCCAATCCAAAACCTTGACCTGGTCCTGCCCACAGTGTCCCACAGCAGCTACATCTGGTGTGTGCCAGCCCAGCTGCCTTCCTCTGGATGCCTAGAGGTCCTGACTGTTCTTTTTTATCACAGGCTGTTTCCTCTCCTAGGCTACCCACTTCTCCTCTTTCTCCTGCTCCCAGCACCCCAGCCACAGCCTGGTCAACTCCTCCAGTCATCTAATTATGCCGAAAGGCTCATCAGCTCCTGGAAGGACTTTCCATGGCTCCCTAGACTAGCTTTCTTTCATGCAGTGGTTAAAAACCCTGGGTTTTCTTACAAACTTCATCACTTGTCAATACTTGTTTAGCCCATGTCTAATTTGCTCATGGATATAATTTTGGAGGAATGGAAACATGGTTTCTGGCTCTCCAGCACAGTGTCTGATCCTGAGAGATTTTCTTGAGTGTAAACGTGCCAGGTACTCAGTGGAGGGCTAGGAAAGGCATGCTGTCTGACTATAGCAAGGCAATCCTTCCTTCTCTGACCTATTCATTACATTAAATTTCAATTACAGGGGCTGGAGAGGTAGTTCAACAGTTGAGAGCATTTGTTCCTCTTCCAGAGGACCCAGGTTCAGGTCCCATCACACCATATGACAGCTCTCAACTGTCTTTCTGTAACTCTAGTTACATAGGATAAAATGTCTTCTGGCCTTCACAGGAACTGCACATACACAGTACACAAACATACATGCAGGCAAAACACTCATATATACATATATGTAAATGTATACACACACATATACTTTTAAAAAAATACAACATGACATGATAGAGTCTTCCAGTTCCTTCTCTCTGCATTTCCACCCGCATGCACGTGCACACACACACACACACACACACACACACACACACACACACACACACACTACCTATGAAGAGCACATATTGCATACACTATCATACACTGTTACTTGTATGCTTTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTCTTTTCTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTACCAACAATGAATCCCTGACTTTTCTTCCAAGTTAGTGTGTGTGAGCTCTTCCTCATAAATTTTAATTGCAATAGACTCAAGTGCATATATCATTGGACACCTGGTATTTTATCCATCAGTGGACAGTTATTCTTTCTTTATTTCCCTTGAAGTGTAAATGTGCGCGCACGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTGTGTGTGCGCGCGCGTGCACATGGTGCTCATATATGTGGGCATCAGAGATCAGCCCAAGGTGTCTTCCTCAGCTCTTCTCCCTCTTGTCTTTTTTTAGGGAGGCTCTCTCACTTTTTCCTGTACTTGCCATTGAGGCTAGGCTGGCTGGCCAGTGAGCCCAAGGGATTTGGTTGTCTTCACCTCTCCAGAGCTGAGCTGACAGTGTGCTCTGTCACACCCTGTTTTCTTATGTGGCTTTTGGGGACCAAACTGAGGTCCTCATGCTTGAGCAATCAACAGGTTCCAGGTCCACTGGAAGAGCAACAAATGCTCTTAACTGTTGAACTATTTCTCTACTGGCCACCCCAACACTTTACTTTTTGGCTTTGAACTCAATATATGAGTTCAGACTGGCCTCCTAGACTGTCCTGGGAATCCTCCTGGCTCTGTCTCCTGGGTACTGAGATTATAGGCATCTGCAAATAAGCCTGGCAGGATATTTAGATCTTTTCCAATGTTTTGGTTCAGTGGATATTGTTGTGTTTCCTGGTAGACAGACAGACAGACAGACAGATAGATAGAAAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGGTAGATGATAGGTAGATAGAGGAGGATTTCTTTTATTTTCTTAATTCTTCAAAGACAAGTAGTTAATTCTATGAAGGCAGAGGTAAAAGATCATCGTGTTTTGTTCATTTTCTAGATGCAAAACTAACAAAGAAACATAGAAGGCTGTTTGGAAGGTATGTGTAAGCAAGTGAGAGACAGAGAGAGAGAGCTTTCTAGTGGATGCTTCCTTGGTTCTTTGCACTGTGTTCTCACTACAGGCTTGTGAGATAGACACCATGTGTTCTATCACTCCTCTGTGTGGCTGAGGAAACCCAATCTGAGAGTTAAGGGCAGAGATCTGTAGTCTAGAGATCTGACAACAGGGCCCCTCAGGTATTGTTCATCCTACACTCCACCTTCTATGCTCGAAGGTTCTATGATTGAGATTCCAAAGCTTTTCTGGCCTTTCGTCTTCTCTCTCAG
Seq C2 exon
TCCAGGACATCAACATTACCCTGTGGCGATCACCGGAAGAAGTGAGGTCTGACAAGAGCATCTTCATAAATCAGGGCGAGTGGGAGCTGCTGGAGGTGTTCCCCCAGTTCAAGGAGTTCAGCATAGATATCAGTAACAGCTATGCAGAAATGAAGTTCTAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000032269-Htr3a:NM_013561:5
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(27.3=100)

							
A:
NA

							
C2:
PF0293118=Neur_chan_LBD=FE(25.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000003826





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:113983290-113986014 
ALTERNATIVE
HsaINT0078174
(HTR3A)
Human
(hg19)
chr11:113854012-113856736 
ALTERNATIVE
HsaINT0078174
(HTR3A)
Rat
(rn6)
chr8:53214090-53217112 
ALTERNATIVE
RnoINT0072288
(Htr3a)
Cow
(bosTau6)
chr15:24845613-24848405 
BtaINT0073936
(HTR3A)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr24:4492728-4492867 
ALTERNATIVE
GgaINT0138733
(F1NGS5_CHICK)
Zebrafish
(danRer10)
chr21:23102373-23104011 
LOW PSI
DreINT0079533
(htr3a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
Functional annotations
(Submit an annotation)

	


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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"