Special

MmuINT0164492 @ mm9

Intron Retention

Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:112477240-112480758:+
Coord C1 exon
chr12:112477240-112477291
Coord A exon
chr12:112477292-112480653
Coord C2 exon
chr12:112480654-112480758
Length
3362 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGC
5' ss Score
9.55
3' ss Seq
CTAACTACTTTTCAATTCAGGTG
3' ss Score
7.87
Exon sequences
Seq C1 exon
CTCCTCCAGTCCAAAATGCACAGCGTGCCAAGAAAGCATCATCAAAGACAAG
Seq A exon
GTATGCTTACCCATTTCCTTCCTTCAGACAGAGGCTTGCTCTATAGTTCAGGGATCCCCAAACATAATGGACCTTCTTGCCCAGCCTCTGAGTGCAGGGGCACCACCCTTCTGGGCTTTTTAGATGGCTGACACATTTCACATAGCTTACGTTTGATGCTGTGTAAATCAGTTTATTTTTCTACTTGATTTATCATTGGGAGGAGGTGCATGCGTGCGTAGTGTTCACATGGATATCAGAGTACAACCTTGAGGAGTTCTGTCCTTCTTCCCTTAAGTGGGGTCTAGGGATCAAATGCAGGTTGCCAGGTTTGCACGGAAAGTGCTTTACCCTCCGGGCCACCTTGGTTTCCCATAGCTTTTGTACAATGCATTGAAGTTCAGTTTTGTTTTACTTTTAAAAATTAAGCTGGGTATGGTGTTGTACACCTTTAATCCCAGTACTCAGGAGGCAGAGGCAGGTGGATCTCTGGGAATTGGAGGCCAGCCTGGTCCTCATAGCAAGATCCAGGACGGCCAGGGCTATATAATTGAGACCTTTTCTCAAAAACAGTTATTACTTCCGTGGGGAGGTGAGGGTGGGAGTCTAGGTCAGGCTAGCCTTGAACTCACTTAGTAACGGAGGTCCTTCCTTCTCCGTCTCCCAAGGCCCAGGATCGCAGGTGTGCGCTCCCACATCTAGTTTCCGCAGTGCTGAGGGTCTTTCTCAGGGCTTCGGTGTGCTAGGTAAGCACACCACTAACTGACATACATCTCCAGTCCCTCGGGGTTGGTTGGTTTGCTTGAGATAGAGTTTTACTGTGCAGCTCTGGCTGGCCTTGAAATCCCAGAGATCTCTGCCTCCACACGTAGCAAGTCCCTTGGTTTTCCCCCCTTTGTTTTGATTTTTGAGATTAGAGTTTCCTATGTTGCCCAGGCTGGCCTGAAGCTCACGGCAGCCCTCCGCCTCAGCTCCTAGGATTGCAGCATGTTCCAGAACACTGACTTGCAGTTTTGTCAGTGGTGCAGCAGGCTCCACGGCCCAGCACGTGCTGTGTGAGCACCCGGGCAGACTGGGTGTGGAGGAGGAGCCAAACACAGCTTCAGCTGTGCCTCCTGCAAGGCGCACTGGCCTCTACTGTCCTCTAGCCTTAACAGTCTCAGTCTGACCTGTTCATGCCGTGGGAAGTCCTATTCGGAGTCTGTCCGGAGCTGTGAGAAGTGCTGAGGTGCCTGTTGTGGCAGAATCGCTGCCATCTTGTAGTTTTCTGTCTCATACAGCTTATACTCAACTTGGAGACACTAGCTTTTACCTCAGACATGCCAGTGGGAGGCTGTTTAAATGTGTTCTTGCTCCCCCTTACCAGTGTCTTGAAGTGTGTAAGCAATGAATGAGATCAGCTGCTGTGTGCCCACATGGCTGTCAGCATTGGCAAACTTAGAGTGGGGACCACTGAGGGGACCCTACCTTTTTCCAGAAGAACCTGATCCCTCCCCTTTTCTCTGGCACACGGCCACTCACAGACTGCTAAGCCCTTCCAGGTACATTTGTAGCTTGAAACAGCTCATTCTCAAGGACTTAAATATCAATAAAAATGCGTGTGATTCCAATATTTTGATTAATGAACCTAACAATTTTTAAGTGTAAGCTATTAAATTCCACACTAAGAATCTTGCTCTGGGGTTTCCTGTCAAAAGTATTTTCAAGTGCTGGACTTGCTGGTCAGGGCAGCCCAGGTGAGGCTGCTGGCCACAGGCCCTGACCCCTGGGCGCTAGGAAGAATGACCTCTGATGGAACTTGTTCTGGGTAGGAGCGGGGAGTCAGCCAGCCCTCAAGCTTTGTCTTATCAAACTGCTGCCGAAGACCTCAGTCACTTGTCACAAGAAGTAGGTCACAGCCTTTTCTTATTTATTTATTTTTTTATTATATGTAAGTGCACTGTAGCTGTCTTCCAGAAGAGGGAGTCAGGTCTCATTACGGATGGTTGTGAGCCACCATGTGGTTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAACAGTTGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCCTAGCCTTTTCTTAAATGGCAGTGTGCCTTCCTTGTTCTCATGAATTGACAAGTGTGACGGAGAGAAAGAAGGTAAAGCTACAAGCTCAGGTACCTTTTAAAGTATCTCGGGCTCATTCCAGGCTGTCCTCAAACTCAGACTCACAGTCATTCTTCTGCCTTTGCTTTCTGAGCGCTGGGTCTAAAGGCAAATACTATGATACCAGCTTCCATCTTAAGTTTGAAACAGGGTCTGTCACTGACCCTGGGGCTTGCTGATTGGATAGACTAGCTGCCAGTAAGCTGCAGACCCTCCCACCCCCAGGGATTACAGGTGCATACCATCCCCCCAGGGGTTACAGGTGCAACCCCCCCCCCAGGGGTTACAGGTGCAACCCCCCCCCCCCAGGGATTACAGGTGCATACCACCACCCGTGACTTGTATGTAGGCGGCAGCACCAAAGCTCAGATCTTCATGCTTGCATAGCACGCACTTTACTGACTGAGGAGTCTCTGTTTTTAAAGCTTATCAGCCATTTGTTCTGTCTCTGCCTGGACATTTAGGAAGGACTAAGTTTTGATAGGTGGGAGTATCTCAAAAATGCCCGAGGACTAAGAGGCCATAGGCCGTTGTTAGAGACAGATTGCTTGTTTTCTAAGGGGAAATAAAATTAAAGACAAGCAGGTATTCATTTTGAGGAGAATAGTTCAGTCCCAGCTCATCCTCATAGCATTTATTTACAGCTTCCTTTGGACTGAGATGTGGCTCAGTGGTGGAATGTTGCCCTAGCATGCTCAAGGCCCTGGGAGTCCATCTCCAGTGCAAGGGAAAAGGGAAATTAAAAAGAAAAAGTCTTTGGTAAGAACTTGCACTAAGAGGAAACCAAAACTGTTTCGCACAGCGTTCTAAGACATCATGTCCACAGCTATCGGTCTGATTCTCTAAGCAGCATTCTGTATAGCGCATCAAGGAGCCAGCGTGTTGCCAAGTCCTGTGGTGAGAGGTGCACGCCAGGGCCATCTGCTCCTTGTTGGCTGGCAACTCAGGCCTACCTTGTCCAGAGGCCATGTGCTCAAAAATGTCTTCACCCCAACTGTCATTTGCTTACCTAATAAAAGATAGAGGTTAAGGCTATGTGAGTTAAATGGTGTCTCTTAGTGGGGCCAGCTCCTTCATTCTACTTATGGAAATTAAAATGGTCCTTAATGCTTTCTGAGGCCCACTTAAGAGTTGCTCTTAGGATCTTTAGAGTGGTTTAGCCTTGTCCAAAATTGCAACATGTGAAGATCAGGAAGTATTAATCCTCTAACTACTTTTCAATTCAG
Seq C2 exon
GTGTTTAAGGATAATTGCTGCAAGAGAGAGATTCTGGCCCTTCAGGTCTACTGTCGGAATGAAGGCAGAGGTTGTGCGGAGCAGCTGACTCTGGGACATCTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277-Traf3:NM_011632:4
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=0.007
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009720=zf-C3HC4=PD(23.1=50.0)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000021706





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000021706f953A
          









    
Other Skipping Isoforms:
ENSMUSP00000058361, ENSMUSP00000112517, ENSMUSP00000119010, ENSMUSP00000132750
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr14:102871969-102875623 
LOW PSI
HsaINT0171693
(TRAF3)
Human
(hg19)
chr14:103338306-103341960 
LOW PSI
HsaINT0171693
(TRAF3)
Rat
(rn6)
chr6:135691995-135695502 
ALTERNATIVE
RnoINT0155200
(Traf3)
Cow
(bosTau6)
chr21:69229950-69232838 
LOW PSI
BtaINT0152141
(TRAF3)
Chicken
(galGal4)
chr5:49757103-49759260 
ALTERNATIVE
GgaINT0054790
(TRAF3)
Chicken
(galGal3)
chr5:52359194-52361987 
LOW PSI
GgaINT0054790
(TRAF3)
Zebrafish
(danRer10)
chr17:29219065-29219211 
LOW PSI
DreINT0167132
(traf3)
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"