Special

MmuINT0164483 @ mm9

Intron Retention

Gene
ENSMUSG00000026942 | Traf2
Description
TNF receptor-associated factor 2 [Source:MGI Symbol;Acc:MGI:101835]
Coordinates
chr2:25380387-25383068:-
Coord C1 exon
chr2:25382994-25383068
Coord A exon
chr2:25380669-25382993
Coord C2 exon
chr2:25380387-25380668
Length
2325 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
GCTCTTGTCCTGTCCCACAGGTG
3' ss Score
11.81
Exon sequences
Seq C1 exon
TTTCAGGACCATGTTAGAGCATGCAGCAAATGCCGGGTTCTCTGCAGATTCCACACCGTTGGCTGTTCAGAGATG
Seq A exon
GTAAGCCATGGGGCTGCTCTTAGGGACTAGGAACCTGGGTGGGTCTTTCCCTTATGATAAACAGTCTCCAGCTCTGGTTCCTCCTAGGTTCTTCCACCTCTCTGTTATCTCTCCTGGCTATCTCTCAGCACCCCTTCTTGCTGCCCTCAGGTGTCCAGGCTTGCCCTCTTGAGATCTAAGAACACACAAGTATATGTGCTCCTGGCACCTTGCACTTCCCAGAATGCCTAGTGGAGGCCTTAGAGCCACACCTTGGTCTTCTGTGTTCTTGCTGTCTACTTCTTCCCATCTCTCCCATGAAAGGAGAGCACACTTTAGCTCAGCTGCCTAGCCAAAGTCCCCGAGCCCAGAGGTCTGGCAGATCTTCCTCTTGTGTCATATTTCACATGCATACTGACAAATCCTTGGCTGTTGGCAGATGGATCCTGTCCCTCCAACTGCTATCTTGTCACCTCATCATCTCTTGCCTGGACACAGGCTTTATGTATTAGCCTATCTTGCCCCTTCATATTCAGCCTGTCACAGGCTATTTCTTTCTCTGTACAGTGGGACCCCCCATGTCCTTTCATGACGAGTGAACATGTGCTGGTCCACAGTGGGCCTATAGGATGTGAACATTCAGGGGAAGAGGAGGAGGCAAGCTGAGGATGCCGTGTCTGGGGCAGGGCGTCTCTGCTCTCTTATATGTAGTGGTGGGGATAGTTACAGCCTCGATTTCAAGGCAGCTGAGTTCCCTGCAGAAGGTAGATTAGAAGCTACCAGGAAACTGAGCTGCTGTAACCTTGAGCCTAGGATCTGTGCGTGTTCAGTTCGTGGGGAGCTCCAGTTCGTCTCTGACCTTGTTTGTGGGAACCTTGCTGACCCATGCTGAGGAAGCCACTAAGCTGACTAGTGCCTGCCCAGGAGGTGCAGGGTCACCTGCTTATGTACCCTGTCGTCCAGGAGGCTGTGCCCCCACTGGGAACACAGATGTCTTGCTTTCTGTTTACTTACGTTTTGAGTGTCTTTGTAAAATTATTTTATTTTGTTATGATTTTTATTTTTTATTACATCTGTGGGTACATGTAAGCCATGGCAGCATGCACATGAAACCAGAAGAAGCTTTTAGAGCTGACTCTGTCCTTCCAACACATGGGTCCCGGGCTGAACTCAAAGATCAGGCTTGCGGACAGCACATCTACATGCTAAGCCTTCCCTAGTGTTGCTTGAGATTGGGTTTGTTGGTTTTTGTTGTTGTCGTTGTTTGTTCTTTGTTTTGCTTTGTTTTTAAAGATTTATTTATTTATTTTATGTGAGTATACTGCTGCTCTTTTTTTTTAAAGATTTATTTATTATTATATCTAAGTACACTGTAGCTGTCTTCAGATGCACCAGAAGAGGGCATCAGATCTCATTACAGATGGTTGTGAGCCACCATGTGAGCCCTGAGTTTGTTTTTTTTTGTTGTTTTGTTTGTTTGGTTTTTTTTTTTTTTTTTTTTTTTTTTTGAAACAGGGTTTTTTTTTGTCCCCTGTATGTAACTCTGGCTGTCCTGGAACTCACTCTGTAGATCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCACCACCACTGCCCGGCTCCGGGTTTGGTTTTTAATTGACAGATTCTCATTATGTAGCCCAGGCTGGCCTTGCACTCATAGAAACTCTTCTGTCTCTGCCTTCTAAGTACTGGGATTGAATGCATTTGCCACTGTACCTGTTTATCTTTCTTAATTAGCATATAGTCTAATGGTACTATAGTCATTTTGAAATGTAAGACCTTAAATTTTTTTGCACAAGCTTGAATATGCTCAAATAGTGGCTTGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCTAATTTCTTAGTTCAAGGTCATCCTGGTCTACAGTGTGAGTTCCAGGACAGTCTGGACTACACAAAGAAACCCTGTCTCAAAAAAAAACAAACAAAAAAGCAAGTTTGAAAGTACCTAGTTGTGACTTAATTACTTTTCTGTTGCTGTGTAAAGATTTACACAGTTTCAGAAGGTTAGAATCTATGTCCATCATCATGGGCAGCACGGGAGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGCAGGTAGGCAGGCAGGCAGGTATGGTGCTGGAGCGATAGCTGAGTGCTCACATCCTGAGAGAGAAGCACATGTCCTAATGGATGTCAGTCCAGTGTGGCTCATGGTGCCGCACTGTTCAGGCTAGTTCTGTACAGACACCATGCCAAGAGCTCTTGTCCTGTCCCACAG
Seq C2 exon
GTGGAGACTGAGAACCTGCAGGATCATGAGCTGCAGCGGCTACGGGAACACCTAGCCCTACTGCTGAGCTCATTCTTGGAGGCCCAAGCCTCTCCAGGAACCTTGAACCAGGTGGGGCCAGAGCTACTCCAGCGGTGCCAGATTTTGGAGCAGAAGATAGCAACCTTTGAGAACATTGTCTGCGTCTTGAACCGTGAAGTAGAGAGGGTAGCAGTGACTGCAGAGGCTTGTAGCCGGCAGCACCGGCTAGACCAGGACAAGATTGAGGCCCTGAGTAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026942-Traf2:NM_009422:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0217613=zf-TRAF=FE(41.4=100)

							
A:
NA

							
C2:
PF0217613=zf-TRAF=PD(13.8=8.5),PF045827=Reo_sigmaC=PU(69.5=94.7),PF140731=Cep57_CLD=PU(67.0=64.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109872





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028311
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:136916616-136920233 
ALTERNATIVE
HsaINT0171684
(TRAF2)
Human
(hg19)
chr9:139811068-139814685 
LOW PSI
HsaINT0171684
(TRAF2)
Rat
(rn6)
chr3:2751416-2753584 
LOW PSI
RnoINT0155191
(Traf2)
Cow
(bosTau6)
chr11:106298599-106299868 
ALTERNATIVE
BtaINT0152137
(TRAF2)
Chicken
(galGal4)
chr17:536155-536862 
ALTERNATIVE
GgaINT1028432
(TRAF2)
Chicken
(galGal3)
chr17:917443-918150 
GgaINT0125454
(TRAF2)
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"