Special

MmuINT0164470 @ mm9

Intron Retention

Gene
ENSMUSG00000026875 | Traf1
Description
TNF receptor-associated factor 1 [Source:MGI Symbol;Acc:MGI:101836]
Coordinates
chr2:34813479-34814131:-
Coord C1 exon
chr2:34814033-34814131
Coord A exon
chr2:34813627-34814032
Coord C2 exon
chr2:34813479-34813626
Length
406 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TCCTCTGCTCTACTTAACAGACC
3' ss Score
8.85
Exon sequences
Seq C1 exon
ACATAGGGTAGCCAAATGACAGTGTGAGAAAGTGACATTTACTCAAGGCCACCCAGATATCCTGGAGGACCCAGAACCCTGGAGATTCCCATCAGAAAG
Seq A exon
GTGAGCCCCATTGTTCCAGAGGTACTGGGGGGGTGGGGGGCACAAAACAGCCTTGGCCTCTCCACCAAGGGTCCGGGAGGAGATAGAGAAGGCAGCCCGTGGTTCTCAGGCGGAGGAATTGTGACTCTGCTGGAGAGCCAGGGCACTACTCTCTTCCTCTGATTCTGTCTCTTGCTCGTTCTCACTCTGAAAAGTGTCTGGACACTCCTTAAAGTTTTTAGCCTCTGTCCAGGGGATTTTTTTAACCACAAAGGGTAATTCCTACTCCACCCTTGCTGTGACTCAGCTATGACGTCGTACCACACAAGCCAGAGAGGAGAAAAAGTCACCAGAAAGGGTGGCCCGGAGCCAGAACCCACCTCTCTCTACAGACTCCACAAGGCTGGTCCTCTGCTCTACTTAACAG
Seq C2 exon
ACCTTCTGGCCACCTGAAACCCCAAGATGGCCTCCAGCTCAGCCCCTGATGAAAACGAGTTTCAATTTGGTTGCCCCCCTGCTCCCTGCCAGGACCCATCGGAGCCCAGAGTTCTCTGCTGCACAGCCTGTCTCTCTGAGAACCTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026875-Traf1:NM_009421:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=NA A=NA C2=0.169
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000130759





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000130759f2019A, ENSMUSP00000132284
          









    
Other Skipping Isoforms:
ENSMUSP00000028234, ENSMUSP00000108687, ENSMUSP00000131375
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr9:120926302-120926549 
ALTERNATIVE
HsaINT0171669
(TRAF1)
Human
(hg19)
chr9:123688580-123688827 
ALTERNATIVE
HsaINT0171669
(TRAF1)
Rat
(rn6)
chr3:14019346-14019589 
Cow
(bosTau6)
chr8:112214611-112215069 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACATAGGGTAGCCAAATGACAGTG

				
R: 
TCAGGTTCTCAGAGAGACAGGC

				
Band lengths: 
246-652

			

		

	





	
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






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