Special

MmuINT0163996 @ mm9

Intron Retention

Gene
ENSMUSG00000026849 | Tor1a
Description
torsin family 1, member A (torsin A) [Source:MGI Symbol;Acc:MGI:1353568]
Coordinates
chr2:30816081-30819122:-
Coord C1 exon
chr2:30818995-30819122
Coord A exon
chr2:30816718-30818994
Coord C2 exon
chr2:30816081-30816717
Length
2277 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
CACCTTTCTGTCTTTCCCAGGTG
3' ss Score
12.47
Exon sequences
Seq C1 exon
CAATGCAGGGGCAGAGAGGATCACAGACGTGGCTCTGGATTTCTGGAAAAGTGGGAAGCAGAGGGAAGAAATCAAGCTCAGAGACATGGAGCCCGCCCTGGCCGTGTCGGTCTTCAATAACAAGAACA
Seq A exon
GTAAGTATGGCAGTCCACCCCCTAACCGTGCACCCCTACTGCTCCCCGGACCCGACGGAATCCTCGAGTGACCACTGTTAATGAGCTGCAGGAGGCTTTATAGATGAGTTGGTTAAGACAGGGTTTGCGCTACATTCCTTGTGGAGGAAGAGCAGGCAATTGAAGCAGAAGGCCACTGCAGATGGCTGCAGGAGGCAGTAACAGGGAAGGCCTCTCCCTTTGCAGTGTCTTCCCTCTGTCACAGACACTTGCCCTACCTTGTGGGGTAGGTAGATGCTGGCTGGCTGCTTCTTACCGAGGACACAGGCGGCAGGAGGATCTTGTACAGCACCAGGCAGCCAGTACTCAGAGCTTTTGACTCTCAGCTCAACTGCTTCTCTGGCTACTGTCATGCAGACCTTTGACCTTGAACCCTACAAGGCAGACAGCCACGAAGGTTACTCACTGGTTATCTCACCAGGTCGAAGGTTACTCACTGGTTATCTCACCAGGTCGTTGAGGTGACAAAAGGCTACAGGCCCCACTGGAAACATGCTCACCAAGAAATCCGCATTGAAGTTAGGTGACTAGCTAGCACAGTGCGTTCTGTTACTCTGTGCAGATGGAATATTGAGAAAAGACAAACCTTTTTGCTCTCTCTTGATGCTATAAAGGATGGCTGCACACAACAGGAAGAACAGATTGATGGGCAGCACTGTGTGTGTGTGGGCGTGCGTGGTGTGCTTGTGTGGTGAAGGCAGGAGGAGCTCCTGCGGGGCTGTAGCAGGGATAAGGGATAATTGAGAACTCTGTCATGGCTGGTAGACAGTAGTGCTGGGGTGGACAATGAGAGCAGTCTTGGGAGGAGGACACATTGGGCCACCTTGAAGGGAGACATTTGCTGAGGACACATATCTCAGTTGGCGGTATATGGGTGGTTTTGCTTTTATGTGGTTCACACTTTTGCTTTTATGTGGTTCACACTCAAACCCAGGGCCGTGCACACGCCAGCTAATTGCCCTACCACCAGCCCAGCTGGTATTTTTAAGCCGTGTGACCATTTGAAGTCACTGGTTCTGCTGAGCGCTTGTGCTCGGGGTCACCTCCCCAGCCAGGCAGATGCCCCCAGCTACACCCTTAGGGTTCTGGCGCAGAGGCACTGGTGACTGCTCCACAGTCGGTTTGCTCTTTGCTGTGGCCACAGGTCCTCCCCCAAGTACATCAGTGCAGAGCACCGTTCTGAGAAAACAGACCCTGGGCTCTCTGCACAGCTTGCATTGGGAGCCAGAGCACAAAGACTAATAGGCTAGGCAGGACACCAAGACATGTCACGGGCTCTTTAGGGCATCCTGCAGGTACTGAATCAAGTGTTTCCAGGACTGGACGGCTGAGCTATGCAGAACTAGACTTTTGTAGGGAAAATGTTGTCAGAATCCCGACCCTTGAGGTGCACAGCCTTGCTGGCACGCCTTATTACTCAGGGAAGTCTAGGTGTTGCTTCCGGAATGCTCTGCAGGGTTTAGGAACTGGCAGGCAGCAGCTGTGGATTCCTTAATTGCAGGTCCAGCTATGGAAGCTCTAGTTGGAGATTGGCTGGTGGAGTCTGTGGCTGGCTCTCCCTTACCTCTTTTTTTCGAACTTCTTCCAATCTGTCCACCAGCTTCTCACCACTGCCTGGGGCCCAGCACAGTGTGGTGCAAGTGGCCATCTAGTCTGCCTCCCATCTCAAAGGCACACAGGAGAGGCCTTTCCAAGCCCAGAGCTCTAAAGTGTCTGTTTTAAAGCTTTTTTGTGTGTTTCTCATTTTTGTATGCCTATGTATGTGTATGTCAGTATCCAGAGAAGGTTTTGCATCCCTGGACCCAGAGTTGCACGTGGTTGTGAGCAGCCTGAGGCGTACTGGGACCCAACTCAGGTCCTCTGCAGTGAGCAACAAGTGTTCATGTTGGTTTGTTTTCGTGTAACATGGTTTCTCTGTTTAGCCCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCAGATCCACCTGCCTCTGCCTCAGGAGTGCTGGCATTAGAGGTGTGCACTGTTAAAGGCATTCTTAACTAATGAGCCCCAAAGGTGTCCCCTTATGTCACCCTGCCCTTGCTGTCCCTGCTGCATCCCAAGGCAGTACTCATGGGCAGTTCTCAGCTTGTCTCTCTTCCTCACTGTATGGAGATGGGTAGCATGGCCCCCAGTGAACACCTGGTAATTATCCTGTCTGGACCGATCATTGTTATGTGTCACCTTTCTGTCTTTCCCAG
Seq C2 exon
GTGGCTTCTGGCACAGCAGCCTCATTGACCGGAACCTCATAGATTATTTTGTCCCCTTCCTGCCCCTGGAGTACAAGCACCTGAAAATGTGCATCAGAGTGGAGATGCAGTCCCGAGGCTATGAAGTAGATGAGGACATCATCAGCAAGGTAGCGGAAGAGATGACGTTCTTCCCCAAGGAGGAGAAGGTCTTCTCTGACAAGGGCTGCAAGACTGTGTTCACCAAGCTGGACTACTACCTGGATGACTGAGGCCGGCTGCCAGGGCTGTGTCAGTCCGCTCCTCCCCAGAAGAGGCTTGGACACTTCCTGCTGAGGTTAGCGGGAGAATCCTGTTTCTGCTCCTCAGAGCCTGCAGGTGACCGCGCTGTAGGGACCACAGATGCAACATGGACCTGAAGCTCCTGGAGCCTCCAGAGATGAAAGCAGCTCCCAGCATTCTGGACTTGTGATTTTTTTAAAATTATGTTTTAATTTCAGGTGTTTCTGTTTTGAGGCAGAACAAGTAAGTTTTACTGCAAATGTGATAACGTTTTATTTAAAATGGTTTTTAATACTATAAGAAGCTTTCAGCGGTGGCTTTGTGTGTCTTTTGAAACTGTTGGATGACATTACCAGTATTTCTACTTCAGAAACCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026849-Tor1a:NM_144884:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028200





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000128959
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:129809033-129809341 
ALTERNATIVE
HsaINT0171026
(TOR1B)
Human
(hg19)
chr9:132571312-132571620 
ALTERNATIVE
HsaINT0171026
(TOR1B)
Rat
(rn6)
chr3:9796549-9796784 
ALTERNATIVE
RnoINT0154643
(Tor1b)
Cow
(bosTau6)
chr11:100219830-100223038 
LOW PSI
BtaINT0151632
(TOR1A)
Chicken
(galGal4)
chr17:5697065-5697369 
LOW PSI
GgaINT0125856
(TOR1B)
Chicken
(galGal3)
chr17:6258057-6258692 
LOW PSI
GgaINT0125849
(TOR1A)
Zebrafish
(danRer10)
chr21:3634087-3634906 
LOW PSI
DreINT0166561
(tor1)
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"