Special

MmuINT0142228 @ mm9

Intron Retention

Gene
ENSMUSG00000071350 | Setdb2
Description
SET domain, bifurcated 2 [Source:MGI Symbol;Acc:MGI:2685139]
Coordinates
chr14:60025483-60028355:-
Coord C1 exon
chr14:60028015-60028355
Coord A exon
chr14:60025572-60028014
Coord C2 exon
chr14:60025483-60025571
Length
2443 bp
Sequences
Splice sites
5' ss Seq
AATGTGAGT
5' ss Score
7.8
3' ss Seq
TGTTTTGTTTTGTTTAACAGCAT
3' ss Score
9.46
Exon sequences
Seq C1 exon
AGGACTTAAGTTCAAACCCAGCTGGAGATTCTGAAGACACACAGCTGACTGAATCAGACGTGATAGATATAACTGCAAGTAGAGAAGACTCTGCCCCAGCATACAGGTGTAAGCACGCAACCATAGTGGATCGTAAGGACACTAAACAGGTGCTTGAAGTCCCAGGAAAGAAGTCCCAAGAGGAAGAGCCTGCAGCCTCTCAAAGCCAGCAGGCCTTGTGTGATGAGGAGCTGCCAAGTGAGAGGACAAAGATTCCATCTGCTTCCCTGATGCAGCTCAGTAAGGAGAGTCTGTTTCTATTGGATGCTTCAAAAGAAGGAAATGTGGGCCGTTTCCTCAAT
Seq A exon
GTGAGTATCAGGGTTGAGATTACTATTTTTAAGCACTCATTTCTTTAAAGTTTATCAGGACATGTGTGTTGTTTCCTGATGTTTAATTCCTGCTGCTAATATGGGAGTAACAATTTGGGTTTTTTTGAGGATCATACTAATTTAATATAAATTGTTTGGAAGTGCTTACCATATAGTAAACATTTGCATTAGAAAACTTAAGAAATGTTGGGCATGGTGACTCATGCCTGTAATGCCAGCACTTCTCAGGCTGAGGCAGGTGAGTTTTCTGAGTCTTAGACCAGCCTGGGCTACATTGTGAGACCCTGTCTTTAAAACACAAAACAAAACAAAACAAAACAAACCATTAAACCAAAGAATGTCAGTACATCAAGAAGTTTACAGGGCTGGTGGATGACTCAATAAAGTGTTTGCCAAGCTAACATGAGGACCTGAATCTGGATGCCCGCACCCACATTTAAAACGAGTGTGGCTGTATGCATGCCTATAACCCTAGAACTCTTATGAGTGGAGACAGAAGGCTGGTTAGGTCCAGTTTCAGCGAGAGATACTGTCTCAAGGGATGATGGTAAAACATGAGCTGTGTACCCAAGATTCTCCTCTGGCTTCCTCATGCACATACACAGACATGTGCGTACACACAATACCACACACAGTATGTCTTATACAGACACACATATGCACACACACTCACACCCCAGGCATCATGACACACATACTTGTAATCCTAGTGCTGGGGAAAGATAGGAAGATGCTGGGGCTTACTGGCTTGCCTAGCCAATCGTCAAGTCCAGGTTCAATGAGACCTTGTCTCAAAAAATAGGGTTCTAAAGTATGAAAAACTAAGGTGAAGAGCAATCTAGACATCTGTCTTGACATTTGACTTACTGTGGAAGTACATGTGTGCATAAAATACACACGGTTTCCAAACAACTGTATAAGTTGCAAAAAATTGAATAGGAAATAATCATCATGATGCTAAATGATGTCCATGTACGAGGATATTGTAGAGGTTTGGTGGCCCTGTGAGTCTTATGATGGTAATAAAGATCAGTATTTGAGAAAACAGTGGGCAGCTAAGAATACTGGAATGGAGGCATTGAGAGTACCATTATGTTATGAGCCTTGGAAAAAGGTTATGTGGCTGTCTTGAGAGAAATCAACTTCTTTTTTTTTTAAGATTTATTTATTTATTATATGTATTTATTTATTTATTTTACATTTTTGAGACAGTGTCTTTTCTGTGTAGCCCTGGCTGTCCTGGAACTTACTGCCCAGTTAAAGCCTTCTCTTGAAAAGTATTATGCTATCAATTTCCCTGACCCCATTTTATAGCTCTTGTTTATTCTTGCTCTTTTTTTTTTTCTTTTTCCTTCTTTCTTTCTTTCTTTCTTTCTTTTTTTTTTTTTTTTTTTTTAGCTTTGCAAATACATTTATGGTGTTGGTTCTCTTTTATATAGCTTATTCACTTTGAGTGCATGGTAGCGACCTACCTGCACATGTGTTTGGGAGCCTGGGGTCAATCATGGGCATTGTTGCTTTAGTGCTATCCCCTTTGGTTTTTTAAAACAAGGCGATCCATTGGCCTGTATTTCACTAATCAGTCTGGGCTGTCGGCCAGCAAGCCCCAAGGATCATCCTGCCTCTACTGCTCTGGTCCGCATATGAGCATGAGCCACCACACCTGGATGTTTCACAAGGGGTCTGGAGATGGAGCTCAGGGCTCCATGCTTGCATAACAAGTACTTTGTTGACTGAGCTTTCTCTTATATTTAAACTTACAATACTATCCTGAAGTTTATTCTGTATCAGTACACGGGAGTTCCTGGTCCTCTCCTATTTTATACTCATATATGTTGTATGTGGGGGAGGGGATACACACATGCATGTGTGGAAGCTAGGGAATAACTTGGAGATTTGGTTCTCCCCTTTTTGCCATGTAAGTTCCGACTCAGATTATCCAGCTGGTTGGTAAATGGCTTTCCCCACTGAGCCATCTCACTGGGCCTGATTCTTCTTGTTAGCATGTGTCTCCCTTTACGCTGCATAGAATTCCATTTTGTCATTTTTTAGCTAGTTCCCAATAGGCAGGTATTAAGTTTACTTCCAAATGTGTCCTGGTTAAAAAACAATATTTATCAACAATCTTACACATAAATATCTGCGCAGATGGTCCTATACACAACATTTTAAATATAGTGTTGATGAGTCAGGAGATAAATGTGTTCATAATAAATAGCAATCCCCATTTGGGAGTTCTATGTTGACATTCTGTCAGCATGTCTGAATGGCTATACTAAATTGGTTCTTGCTATTAACTACATGGCTAAGAACTGTGGGAGATTGCATATTACTTAAACTGAGAAGGACAAAATCAGTGAGATGTGTAAGAAACAAGGATGCTATGTCTAACCTCTGGTTTTTGTTTTGTTTTGTTTAACAG
Seq C2 exon
CATAGTTGCTGTCCAAATCTCTGGGTGCAGAATGTTTTTGTAGAAACACATGACAGGAATTTCCCATTGGTGGCCTTCTTCACCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000071350-Setdb2:NM_001081024:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.588 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0085623=SET=FE(36.7=100)

							
A:
NA

							
C2:
PF0085623=SET=FE(9.4=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000093450





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000124696, ENSMUSP00000130483
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:49488631-49490821 
ALTERNATIVE
HsaINT0148382
(SETDB2)
Human
(hg19)
chr13:50062767-50064957 
ALTERNATIVE
HsaINT0148382
(SETDB2)
Rat
(rn6)
chr15:39715740-39718136 
LOW PSI
RnoINT0133866
(Setdb2)
Cow
(bosTau6)
chr12:19142900-19146543 
ALTERNATIVE
BtaINT0131671
(SETDB2)
Chicken
(galGal4)
chr1:168518817-168519931 
ALTERNATIVE
GgaINT0112311
(SETDB2)
Chicken
(galGal3)
chr1:173519426-173520540 
LOW PSI
GgaINT0112311
(F1N8V8_CHICK)
Zebrafish
(danRer10)
chr16:22093652-22093798 
LOW PSI
DreINT0133542
(setdb1b)
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"