Special

MmuINT0166399 @ mm9

Intron Retention

Gene
ENSMUSG00000039826 | Trub2
Description
TruB pseudouridine (psi) synthase homolog 2 (E. coli) [Source:MGI Symbol;Acc:MGI:2442186]
Coordinates
chr2:29631631-29634388:-
Coord C1 exon
chr2:29634252-29634388
Coord A exon
chr2:29633477-29634251
Coord C2 exon
chr2:29631631-29633476
Length
775 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGT
5' ss Score
10.24
3' ss Seq
TGTGTGTCTGTGACCCACAGAGG
3' ss Score
8.23
Exon sequences
Seq C1 exon
GTACTCCAACCTGGACCTGAAATCCCAGGAGGCCTATGAGATGGCTGTGCAAGGTGTGATCAGGCCCATGAACAAGTCCCCCATGCTCATCTCTGGCATCCGCTGCCTGCACTTTGCACCTCCCGAGTTTCTTTTGG
Seq A exon
GTAAGTCACCCAGGAAGCTGGAGTGATGTGATGGAGTCATGTGCGGCATGCCCAGCCCCGAGTGGCTTCTTTCCACCAGGAGTAGCACAAAGGCTCTGCTCTGTCTCCTGTCTATTCCCAAAGCATGTGAAACCAGCCCTTAAGAAACAGAGGCTGGGGGCCAGGCGGTGGTGTAGCACGCCTTTAATCCCAGCACTTGGGAGGCAGAGGAAGGCAGATTTCCCAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACAGGCAGGGATGCACAGAGAAACCCTGTCTTGAAAAACCAAAAAAAAGAAAGAAAAGAAAAAAAGGAAAAAAAGAAACAGAGGCTGGGTCTCTGGCAGCTCAGTTCCTTAGCAGTTCCACCTTGTTCTAGGCCCCTCAGGCATGACTGTCACTTCCTGAGTCTCACCCAGCTCTGCCCCAGCCTCTTCCCTGTTTCCGTGGGTTCTTCCCTGGGCTCTGACCAAAGACCCTGGTGGAGAGCCCCACATGACAGTGCTGTCTCTGACCTCAGTCCTGCTGCTGAGTAGACCAAGTGTGTGAGTGATGCTGCCAGAAGCCCAGCCTTTTTACAGCTCAAGCGGGGGGTCCAGAGCTGGGGTCTGCCCCCGCAGGTGCAGGAGGCCTGCAGTCAGCACCACTGCCGTGCTCTCAGCCCTACAGCAAAGCTCAAAGGCATCTCATGAAGGGACATGAGTCCACGTCAGCTTGGTCCCTGCAGCTGTTCCTGACGGTCACGTCTGTGTGTCTGTGACCCACAG
Seq C2 exon
AGGTGCAGTGTATGCACGAGACGCAGCAGCAGCTGAGGAAGCTGGTGCATGAAATCGGCCTGGAGCTGAAGACCAGCGCTGTCTGCACGCAAGTGCGGCGGACTCGGGATGGCTTCTTCGGCCTGGATGATGCCCTCCTGAGAACCCAGTGGGACCTACACAACATCCAGGATGCTATCCAGGCGGCAGCTCCCCGGGTGGCAGCGGAACTGCAAAAGAACTTGAGCCTAAAGCTGGGCCACCATCAGCTCCCCAGCACTGGGCAACCTTGGGGTCTCAAGGACCCAAGCTCCACTTTGGAGTTGGAAAGCTGTTCAGGGCAGTAAAGGGCCAGGTAGCAACCAGATGGAGAGCAAACAGGCTCTTCACAGGTCAGAACTGGTCACTCCGCAGGAGTAATGAGATCAGGGGCCCCTGAGCCATTATCCTTGAGACACAGACTAACTGCAGAGGCAAGCAGGTGTGGCCATGGGGGCCTATCGTCCCAGCTAATTGGGAGGCCCAGGTTAGAATCTTAACAGTTCAAGGCCAGCCTAGGGTTTCTTAGTAAAACCTTGACTCAGAGTCAGGCATGATGTCTCAGGCCTGTAATCTTAGCCCTCCAGAGGTAGAAAGGAAAATCGTGAGTTCAAGGCCAGCCTGGGCTACTTGCAGTGTTCAGCTTTTCAACTGATGGGAAATGCCGCTGCCTCAGCACTCCTTGGCCGTGAGCGATGATCTTTTCACAGAGGGAAAGTCTTTTTTGCTGTTTCAAGGTGTCTCACAGCTGAGATCTCAGTACTACTCAGCTGAGCCAGGAGGATGGCTCTGAGTTTAAGGCCAGTCTGAACAAGTCTCCTGGAGTACTTTGTGGTATGTGTCAGTATTTAATCCTGCCAGTCAATCCTGCAAACCTGTAATTAGCACCTGGGTGGTGGAGACTGGAAGATCTGGAGTTCAAGGTCATCTTTGGCTACATAAGTTCCAGGCTACATGAAACGTTATCTCTAAGACAATATAAAAAGCCCAGAATTATTTTTTAAAAGGTTTTCTTTCTTATGCATGTGAGTATTTACATGCATGTATGTCCACACCTGGTGCATCATGGAGGCTAGGAAAGGATGTAAGAGCCCTGTGGCTGGGCTTAAAGGCAGTTGTGAGCCACCAAGAAGATGCTGACAATGGACCACTAGTCCTCTGGAAGACAGCTTAACCACTGGTCCATTTCTTCAGAATTTAATTTAATTGCCTGCCCTGTGATACAATGCTGTAACTATCCCGTGCCCCGGCTGTAAACACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTAAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTTACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTTACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTTACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTTACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGCTGATGATTGTTGGTGTCTGCAGTGTGAACACTAACAGGACAGCAAGGGATGGTGTTCACTCAGTGGTGCCGGTGGAAGGCGTGGTGCAGAGAAGACATCGGGTTTATAAAATACAGTGGTTTTCCTCTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039826-Trub2:NM_145520:7
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=0.111
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0150913=TruB_N=FE(30.7=100)

							
A:
NA

							
C2:
PF0150913=TruB_N=PD(8.7=50.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000041848





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:128309876-128310886 
LOW PSI
HsaINT0173467
(TRUB2)
Human
(hg19)
chr9:131072155-131073165 
LOW PSI
HsaINT0173467
(TRUB2)
Rat
(rn6)
chr3:8339070-8339755 
ALTERNATIVE
RnoINT0156954
(Trub2)
Cow
(bosTau6)
chr11:98919786-98920586 
LOW PSI
BtaINT0153698
(TRUB2)
Chicken
(galGal4)
chr17:4989657-4990339 
LOW PSI
GgaINT0126190
(TRUB2)
Chicken
(galGal3)
chr17:5621025-5621707 
LOW PSI
GgaINT0126190
(TRUB2)
Zebrafish
(danRer10)
chr6:41026528-41026626 
LOW PSI
DreINT0168585
(trub2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CACTTTGCACCTCCCGAGTTT

				
R: 
CTGCCCTGAACAGCTTTCCAA

				
Band lengths: 
351-1126

			

		

	





	
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"