Special

MmuINT0142231 @ mm9

Intron Retention

Gene
ENSMUSG00000071350 | Setdb2
Description
SET domain, bifurcated 2 [Source:MGI Symbol;Acc:MGI:2685139]
Coordinates
chr14:60045299-60050105:-
Coord C1 exon
chr14:60049980-60050105
Coord A exon
chr14:60045392-60049979
Coord C2 exon
chr14:60045299-60045391
Length
4588 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGA
5' ss Score
8.55
3' ss Seq
CTCTCTCTCTCTCTCTCCAGACT
3' ss Score
12.94
Exon sequences
Seq C1 exon
GTGATGCAAAGACTTTCTGGATGGAGCTACAAGATGATGGTAAAGTTGACTTAATGTTTGAGAAAACACAAAATGTCCTACATTCACTGAAACAGAAGATAAAGGATGGGTCTGCCACAAATGGAG
Seq A exon
GTATGAAAAATGAAGATTTCTGACACTTTCTACTAATGCTATATACTGGATATGCGGTATAATGCTACTGTTGTTTATTATAGACAATAAATAAATGCTTTTCTAAGGCCCTAATGTGAATTTTATCTGCTTTATGTATTATAAACTTGCTTTCCCCATATGTGATGGTTTGTATATGCTTGGCTCAGGGAGTGACACTATTAGGAGGTATGGCCTTGTTGGAAGAAATGTCACATGGGGGTAGGCTTTGAGACCTACCTCCTAGCTTCCTGAAAGACAGTCTGCTCCTGGCTTCCTTTGGTTGAAGATTTAGAACTCTTAGCAACTCCAGCGTCATGTCTGCCTAGATGCTTCTGTCTTTCCTGCTATGCTGCTAATGGACTGAACCTTTGAACCTGTAAGCCAGCCCCAATTAAATATTGACCTTTATAAGAGCTGCCTTGGTCATGGTGTCTTTTTAGAGCAATGGAAACCCTAACTAAGATAGAAGTTTGTACTGGGGTATTACTGTGATAGGCCTGGCCATGCTTTTGTTTGGAGGAATGTAGATTTTGGGACTTTGGAAAGCAGTGGAATGCTTTAAGTGGGGCTTAATGGGCCATATTAGTAGAAGCATGAAAGACAGTGTTCCTGAGTGTGTTTTGAACTGTGGGGAACCAGCTCAAGAGGTTTCAGAGGAGAAGACTATGTGGCCTACAGACCAGTTTTTGTGATATTTTGGTGAAGAATGTGGCTGCTTTTTTGCCATTGTCTAAAGAGTCTGACTTAGGTTAACGTGAAGAGATGTAGACTAATTACTTTGACAAAGGAAGTCTCAAAACAGCCTGGTATGCATTCTGTTGTGTAGTTACTAAAGTTCATTCTTATAAAAGCATTTTAATGAAAAGTAGCAAGCATAGAAAGGAAAAACACAAATATATGGTTCAAAGAGTAAATGAACACGAGGAATGAAGCTAAATCCTGTGTTCAAGGATATTAAATGGAATTAAAGGAGTGGTGACCTTTGAGCAAGATCTCACCTGCTAAGCTTATGCTTTTGAAGTTGAAGAAGAGATATAGTTATATCTAAGCATTATTATGACCTGGTTATTGTTTTTATTTGGACTTTTAATCTGAAATGAAGTACAATCCAGAAATGGAGAGCATAGCTGTCATCCAGATCTTGAAGCTGGAAGATACAGCTTTTGATCCTGACCTTAAGGAATAGTGGCTATGAAAAGCTTAGGACCAGGTATGATGGTGTACACCTTTAATCCCAGGAGACAGAGGCAAGCAGATCTCTGAGTTTAAGGCCAGTCTGGTACAGAGCAAGTTCCAAGACAACCAAGTTTAGGCAGTGAAGGAGTTGGAAAACAGAAAGCTGGTAATAGAATAAGGATGCCATGTTTCAGCTCCAGTAAGCTGCAGAAATAAGCAGCTTTGGTCATGTGGCTCTGGCTTTAGAATCAAGACTAGAAGGCGACTACTGGGACAATTGGTGATGCTGGTTAGCTGGAGCTAAGAAATTAGCAGTGATTAAGCAGAGACCAGCATCACTGAGGGGAAGTATTTTCTGAAAGCACAAAGAAACTGTATCCCAGAGATAGCCAACGTTGTACCTCGTGCTGCAGCTGTACTTAGCAATGTGTAAGAGTCGCCCAGGTAGTACTGGTTTTGAGTGCCTGAGGGTTCATGGAGAGCAGGTGAGGTTTGGAACTGTGAGAGGTCAGGGAGGTACATTTGTGAAAGTGCAGCCTCATTTGCAGTTGACAGCCCAGGACTGAAGGGGTCATGTAAAGAAGTTGAGGCTTGGCACCATAAAGGGTGCCTATGAGAGGCTGTTGATGAAGCCTAGTTGCAATGAAAAACCCCAGCATGTTAGAAATGTCAGGACCATGGGATGACCACCAAGAACAGCAGCAGCAATGGAATGGAGTCAACCAGAGCCTAGAGTGCTACTACAGAGGGCAGAGCTACAGATGTGACTTAGACCCTTAGGAGGAGCCCAGAAGATTATGTATGGATCCCAGACATAGGAACAAAAAGCTTTAAAGTTGAAATTGCCTTGGATACCCAAAGATGTTACAGATGCCAGAGCTGTGCAAAGCCTGCTGAGGAAATCTGCTAGCAGGGAATGGAACCAGTTCAAGAGAAAGAAGTGTGTTGCAGTCAACAAAGCAGAAAGGAGTTGGGCATCTGAAGAATACTTTGACATCAGACACAGAGATACAGAGTTTGGAGTTTGCCTAGTTAGTTTTTGGTCTTGCTTTTGTCCAGGATTTCCTATCTGTGTCCTTTTGGAATGGTAATATATATCCTGTGATATTGGAGATATGTGATCTGCTTTTTTATTTTGATTATATAAGGGATTACAGTTCAGCTATTGGATGAATCTCAGAAGAGACTTTGAACTTTGAAACATTGTTGAGACTGTGATAGGCTATGGGAACTTTTGAAGTTAGATTAAATGTATTTTTTATTATGCTGTGTCTAGGTATGGCCCCCATAGACTCACATGTTTTAACAAGCATATGGGGCCAGGGAGTAGAATGTGGTGGTTTGAATATGCTTGGCCCAGGAAGTGGCATGTGACATGTGGCCTTGATGGAGGAAGTGTGTCACTGTCGAGTGGACTTTCAGACCTTCCTCCTTGCTTCCTGGATGACAATCTGCTCCTGGCTTCCTTTGGTTGAAGATGTAGAACTCTAAGCTCCTCCAGCACCATGCCTGCCTAGACACTGCTGTGCTTCCTGCCATGATGATAATGGACTGAACCTATGAACCTATAAGCCAGCCCCAATTAAATACTGTCCTTTATAAGAGCTGCCTTGGTCATGGTGTCTCTTCACAGCAATGGAATCCCTAACTAAGACACTATACATCTTATAGAAGTGGATAAACCTGAGCTTTGGAAATGATAGTTACTGATGATCCCCTTCACCATGTGTAGCCTAGAACTCTTAAGCACTGGCCTTAAGCACTCTTCCTTCTTTAGCCTCTGTTGGAGCTGAAAACAGGCTACGATTTCCCCCTTTGTTTATACTTTTTCCTTTTATACCTTCATACCTGAACTGGAGGGGAGGAATGTTGCATAAGTAGTACCTGCTTCTTGTATAATTTTGGCATAAATAGGAAAATCCAACAGAATTTTGTTTACTCCACTTAAACAACTGGTGTATGTATATATGACTCATTAGTGGTAGAAGTCATGATCAGCATGTGTAAAGCCCTACCTAGGTTCTATCCCACCATACAACAGCATAAAAATTTCCTACTTCAAACAGAACTTAATATACTAGTTTTGAAAGCAAAATTTTAGGGTTTTGTTTTTCTGTGTGTTTTCAACCCTAGTTGTTTAAAACTTGAGACTCTAAATTTAAGCTCTTCCTCTAGCTCATTAGGATATTGTAAAGCAAAAATGTTCCCAACTGTTAATACTTTTGGTTGCTCTCACTAGGTAGTCTGTAGCCTTGATATTGTGAAAACCCGAAGATGGGTGGGGACGTGCAGTGGGAGGGGTTGTTGGTTTTATCTTGGTTTGTTTGTTTACAGTTTTGTTTAAAAGTGGGAAGAGAAGCATTCTTGTTTCTCTGCCTACTCTGAAACAGGGTTATAATTGTGTGGGAAAGATGAGGTAAAGCCAGCAAATAACGTATATGTAGATTTAGCGGAGGCATGGGTTCCTCCTGTCACTCACTGCCAGAGGCTTTCTCTCAGCATGGGATCTCTGCTATACTATGCTAATGACATTTCATACACTCGTGATCATGTATTAGTTTTTTTTCTTCTTTAAGAAACTTGTAAAAATTTTAGAGATTATTTCTCAAACTTTCTTGAGTGAGCTAGATGTAAGTTTGAATACAGCTCTCAGTTTTAGTAATAGCTGACTTCCTGGCCTCATTTCCTTGGTCTCTGTCACAGATGATCATAGGCTCTTTCCAGGGAGGTGGAAAGAATCGATGTCAGTTGTTTCGTATTGGAGTTGGTAACCTAAATGGAAGTGATGATGATTGTCTCTCTCTCTCTCTCCTCTCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCTCTCTTCTCTCTCCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCCCCTCCCCTCCCCTCCCCTCTCTCTCTTCTCTCTCCCTCTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCTCTCCCCTCCCCTCTCTCCTCTCTCTCTCCTCTCTCTCCTCTCTCTCCTCTCTCTCCCTCTTCTCTCTCTTCTCTCTCTCTCCCTCTTCTCTCTCCTCTCCTCTCTCTCCCTCTTCTCTCTCTCCCTCCTCTCTCTCTCCCTTCTCTCTCTCTCTCTCTCTCTCTCTCTTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCTCTCCCCTCTCTCCCTCTTCTCTCTCTCCCTCCTCTCTCTCTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCCAG
Seq C2 exon
ACTATGTCCAAGCAATGAATCTAGTAAATGAAGCCACTCTGAGTAACACGCAAACACTGGAAAAGGGTATGTTCATTACTTATTCCAATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000071350-Setdb2:NM_001081024:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.366 A=NA C2=0.423
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF127032=plasmid_Toxin=PU(73.6=90.7)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000093450





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000106884, ENSMUSP00000124696
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:49460233-49461096 
LOW PSI
HsaINT0148384
(SETDB2)
Human
(hg19)
chr13:50034369-50035232 
LOW PSI
HsaINT0148384
(SETDB2)
Rat
(rn6)
chr15:39735167-39738541 
ALTERNATIVE
RnoINT0133868
(Setdb2)
Cow
(bosTau6)
chr12:19118273-19119623 
LOW PSI
BtaINT0131673
(SETDB2)
Chicken
(galGal4)
chr1:168507421-168508462 
ALTERNATIVE
GgaINT0112300
(SETDB2)
Chicken
(galGal3)
chr1:173508030-173509071 
LOW PSI
GgaINT0112300
(F1N8V8_CHICK)
Zebrafish
(danRer10)
No conservation detected
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"