Special

MmuINT0164024 @ mm9

Intron Retention

Gene
ENSMUSG00000060519 | Tor3a
Description
torsin family 3, member A [Source:MGI Symbol;Acc:MGI:1353652]
Coordinates
chr1:158583748-158586727:-
Coord C1 exon
chr1:158586603-158586727
Coord A exon
chr1:158586075-158586602
Coord C2 exon
chr1:158583748-158586074
Length
528 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGT
5' ss Score
10.86
3' ss Seq
ACTCTGGGTCTTGGTTACAGACA
3' ss Score
5.86
Exon sequences
Seq C1 exon
CAACCTCGGAGGCAGTGTCATCAATGAGGTAGTCCTGAGTTTGCTTAAGGCTGGATGGTCCAGGGAGGAAATTACGACGCAGCACTTGGAGGTGCCCCTTCAGGCTGAGATCATGGAGGCTGCAG
Seq A exon
GTAAGTGGTCAACTCAGATACATACAGCCTTGCCAAGAGCACAGCCAGAGATGATTGGTATCAAATGTGAGGCAGTGAGGGTGTCTGGACAGTAGAGGACATAGGACAGCCTCACCCATCAACTTCTGGTGGCACGAGAGTATGCCTATACTCCTTCCCTGGAAATGCATTCTGAAGAGGGTCACAGGTCCAGCCCCGCCCTAGAAACAGCTGTGGTCTCTGACCATAGGCTAGCAGATCTCCCTGAGACAACAGTGCAGGTGAAGGTGGGGCAGCTCCACCTTTTTGCTACACCAAAGCCAGCCACAGTCCTGGTGGTCATGCCATTATCTGCTACTACAGCCACAATCACTGTGCTTCTCCATGCCTAGAATAGCCACCACCGCACTGTCCTTGGCAACAATGCACACAGTACTCCAAGAGCTTTGTGGGAGACCAGCTCTTGTGCAGGTTTCAATTTGGGGATCTCCAGCAGGGTTCAGTCCCAGGCTAGGTCAGACACTATGTAACTCTGGGTCTTGGTTACAG
Seq C2 exon
ACAGCAGCTTTGGCTCCAGCGGTCTCCTGAAGAAACACCTTATTGACCACTTTATCCCCTTCCTGCCACTGGAGTACTGCCATGTGAGGCTGTGCGTCCGAGATGCCTTCCTGGGCCAGGATCTCCCATACACAGAAGAGACCCTGGATGAAATCGCCAAGATGATGACATATGTCCCTGAGGAAGAGCGGCTTTTCTCCTCTCAGGGCTGCAAATCCATTTCCCAGAGAATCAACCTCTTCCTGCCTTGAAAGTGACTCCTGTGCACCCTAAACAATCCTCCTCCACAAGAGACAGCCATCTGCCAGGTGCCCTGGCGTCCAGCAATCACTGCTTTCAGCTGGTGTGCAAGAGGCAGTTCCTAACAGAGGCAGTTTCTAAAAACCACTTGGTGCCTTAAAAACCTACATTCTAGACAATCTAGACTGAGGGTCAGGAAGCCAGTGGAACGGAAGGTCCAAGTACCAAAGGATCCTCAGAACACTCCCTACAGTCTCCTGGCACCGTAGCTCTTCCTGGAAGGCAGCTGGAGTTCATATGAGCCTGAGGCTCTAGGATCTTTGGGCTACAGAACAAGGAATATGTGTGGACTAGAGGCGTGTGGTCCAGGTCTGCAGGTCTGGCTGGCTTTCCTTGCTTTCCGGCAACGTGGGGGAGAGGGGCAGCTTCTGCATGTGAGACCAGCAAAGGGCCTTAGGCTAAAGGACAAACTGAAGCTTTCAAAACAGGATGGGTGTGGCCCAGCACTGTAGTAGGCTAATATGGGAGAGAGAGCTAAAGAAACCTGAGCTGCCTCGTTTGAGCAGCCTGCCAGGCTTGACCAAAACTCATGTGTATGGATAGCTAAGGCATGTTCTGTTGTGCAGACTGAAAACTTTTTAAAGAGGCCTCGTCATGTGTAATTAAATCTTGTATTTTTCTAACATCCTTTCTTACTGAGACCTGGTCCTTGCACTGCCCTGGCAGGCTGGCACAGCACGTGCTGGTCTCAGGCTACTTTAGAGCTTCTTACTAAACTCCTCTGACTCAGCCCTCGAACACACGTGTTCTCCGCTCCAGCTCGGACAAGTGGTTCCTGAGGCTGATGTGGCGAGGCAGGTCAGTACCACCTGTCTTTAGAATACCATGGGCCATTCTTTTCTGGTCCCTTCACACTTTTTAAACATACAGGTCTTTGTGTTTTCTCAGAATTTCCCCCTCTTATTCAAAGTCCTGCTCAGCACTCTCACCTTTAGTTCTTGTAAAAATGGACCATTTCTGCAACCCCCACTTACCAGTACATGTGTACTCACTCACCTGCCTTAAGGCTAGGGACCACCTAGCCCAGCCATATTCAAATAACTGAAATAAAGGAGTGTGGTTTGGAAGTGGGATCTCAATTAGCAAAGGCAGTCACAAAGTTCAAAAGCTTAGGAGTTCTGCTGCCACAAACCCCAGGGACAGAAATTTAACAATTAAGGTTTCTTATAAAGCAAGACCACATGGTAATTAATAAGCATAAAATGCCCAATGAGACTTAGATTCTTGTTCAAGCCAGGTGCTTCCATGCTGTCCTTGAATATTCAGGAGGACAGAGCGGGATGGGCACAAAGTGAGAACCAAGTGAACTGTAACAGGAATACTAGTGAATCCCTCCCATCCAAGAGCCAGACACACCGTTCTCCCTCTCGACAGGGGATGCTGGAGCGCTGAGCAGGTCTTACCTGATCTAACAGAACTGAAATCCGAGAATACCCTGTGGTCACGAGTATTATAGGTAGGAAAGCAGAGCAGGGATTATAAGCAGAAACTTACAGTTCCAGAACAACCAGCAGGTCAGTGGTTAGAGTGAAATGGAAAAATCTTAATTTTGTGAGGCAAAGCCCATGAGGAAAACAGCTCTGAGAAACTGCAACACACACACACATCTCAGACAGGCACTGTGCCCAAAGGACTAGAAAAACACTAAACTCCAAATTAGTATAATAACGAGCACTACAGTGGTGAAAAAGCTCCATGACTCAAGCACTCCGAAGACTGAGGCAGGAGGCTGTCTAGTGAATTTGAGACTGGCTAGGGATATACAGCAAGACTGTCCCTGTCTTTTTGAGACAGTGTCTCACACAGCTAAAAATGGTCTTGAACTCAGTACGTAACCCTGAAGTGACTTTGCTTTTTCATCTTTCAAGTGCTATAATTACAGGCATGTGCCAGTACACCTGGCTTTATCTGGTGCTGGGCTCAGATCCTGGGCTTCTTGCTAGGCAAGGACTTTACTGATGCCCAGCCCCAAGACCCTGTTTCTAAGAATGACACTGGACTGGACAATAAAAACAAGGTCAGTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000060519-Tor3a:NM_023141:5
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:
ENSMUSP00000078572





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000113984
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:179094218-179094967 
ALTERNATIVE
HsaINT0171036
(TOR3A)
Human
(hg19)
chr1:179063353-179064102 
ALTERNATIVE
HsaINT0171036
(TOR3A)
Rat
(rn6)
chr13:74253274-74253764 
ALTERNATIVE
RnoINT0154652
(Tor3a)
Cow
(bosTau6)
chr16:61884800-61885329 
LOW PSI
BtaINT0151650
(TOR3A)
Chicken
(galGal4)
chr17:5697065-5697369 
LOW PSI
GgaINT0125856
(TOR1B)
Chicken
(galGal3)
chr8:6547705-6547952 
ALTERNATIVE
GgaINT0037395
(TOR3A)
Zebrafish
(danRer10)
chr8:16562492-16564870 
LOW PSI
DreINT0166578
(tor3a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATTACGACGCAGCACTTGGAG

				
R: 
ATGGCTGTCTCTTGTGGAGGA

				
Band lengths: 
356-884

			

		

	





	
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"