Special

MmuINT0164497 @ mm9

Intron Retention

Gene
ENSMUSG00000021277 | Traf3
Description
TNF receptor-associated factor 3 [Source:MGI Symbol;Acc:MGI:108041]
Coordinates
chr12:112490875-112493574:+
Coord C1 exon
chr12:112490875-112490967
Coord A exon
chr12:112490968-112493433
Coord C2 exon
chr12:112493434-112493574
Length
2466 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGC
5' ss Score
10.08
3' ss Seq
ATTGAAGGATTTTTCCTCAGGTT
3' ss Score
3.89
Exon sequences
Seq C1 exon
GGTACAAACCAGCAGATCAAGGCCCATGAGGCCAGCTCCGCGGTACAGCACGTGAACCTGCTGAAGGAGTGGAGCAACTCCCTGGAGAAGAAG
Seq A exon
GTAGGCTGGGGGCTCCTGGCTTCTGTCAGGTTTATAATGCTTCAGACTATTTATAGAGTAAATCTGTTTTGTAATTATCCGTGGTTTTTAAATGAAAGGGTCATTGTGAAGCGTTAGTTCTTTTCTGGAATCTTAGGCTTCTGTGTAGAAGTGTTTGCTCCTGTTCAGCTACCAAGTGGCATGCAATGGCCCTCTTTCTTTCTTTCTTTCCTTTTCTTTGTGGGTTATCTTAGCACTTATCCAGAACAAAGATTGTCCCAACTTCCATCCTCTGGTCCTCAGCTCCATGGTTTTGTGAACAGTGGCCACCCACAGGTGAATTAATTGCCTCTGGTTGCCTTGGCACTAATAGCATAGAGACTGGTGGGCTGGACCACTTAACCCCAAATACTGGCCGGTTCCTCACAAAGCAAGTTTGCCAGTCCCTGTAAGTCTGGTTACTAGTGTCGCATGATCTACAGCTATGTCTTTTGTGAGACCCAGATAGGAAGCCTTTGCCTTCTTCTCCCAGTTGCTTGCAGTTGGTTCTCTTGGCAGCTGTACTGGCTTCATAGACAGCACCACTGTCAACAGCCCCTCCTCCCTGAGAACCAGGTTCTTCCAGTCAGAGTGCACCTGGCTCAGGCACTTGTTCTGTGGTGGTCACCCCACTGCAGGAACGTGTTTCCATGAGAGAAAGGCGAAACAAAAAATAGTTGTGGGCTCACACTCATTGTGGCTCATTTACATTCAGTATACATTGATTAAAAACTTGTAGCAGGCTGGTCGTGGTGGCGCACGCCTGTAATCCCAGCACTTGGGAGGCAGAGGCAGGAGGATTTCTGAGTTCGAGGCCAGCCTGGTGTACAGAGTGAGTTCCAGGACAGCCAAGGCTACACAGAGAAACCCTGTCTTGAAAAACTAAAAAAAAAAAAAAAAAAAAAAAAACTGATAAAGGATAAAAAAAAAGACTGCCAAAGACTGCCAAGAGCTGTGCGGTGGTGACACACACCTTTTTAACCCCAGCACTTGGGAAGCTGAGGCAGGTAGGTCTACGGATGGAGTTCTAGAACACAAGGCTACACAGAGGGACCTTGTCTCAAAGGCTCTTCCTTTTACTTAGTTTTACCCAGGTGGTGCAGCACATGCCTGTAATTCCAGCCCTAGGGAGGTAGACGGATAGAAGGTCAGAAGTTCAGGGTCATATTTAACTACAGAGCAAGTTCAAGGCCTATGAGACATGCAAGTTTGGTCTGCTCTGTTTGTTTTCTTTCTATTTTATTGGTTTGGTAGGTTTTGGTTGGTTGGTTGGTTGGTTGGTTGGTTGGGTTTTGCTTTTTCCAGACAGGGTTTCTCTCTGTGTAGCACTGGTTGTCCAGAAATTCACTTTGTAGACTTGAATTCAGAGATCCACTCACATCTGCCTCCCAATTAATGGGACTAAAGGTGGCATGTCGTCACATCTGGCTCACTCTACTGAGTTTTTGTATCAGGGTCTCTCTGGGTGTGAGCTCTGTCTGTCTTTGAGTGGGCCCAAGGGTGAGATTACGTGTCTGTGCAACCTCAGTCCAGCCACGCTCCTTGTGTTTGGGGATGTAGCATTACTGGGCAGGGGTCTTGCAGGGTGTGAGATCATATTCATTGGGCCATGATTGGGTTTTAAAGATCTGTCGATAGAGACTGTCTATCTTCATGGAGGTGCATATGTTAGGAAATGGTTTTAAAAGCTAGTTTGTTGAAAGGCCTGAGATGCTTCGCTGTCTCCGTGGTGTGAACATTTCACATCTGTTCTCAGCAGCTCGGTGTGCTGATTACGTTGTTGACAGTTGTCACTGTGCTGACCAGGGGGGTCTCAGGAAGAGTTCTTTAACTGGAACTGTGATGTGGCAGTGGCTCCCGTGCCTCCCAAGTCCCACGGCCCCTACCTCTGCTTCTAGGCTCAGCTGTTGGGTTCCAGTTGTGGGAACAGGCAGTGTCTGTCTTGCTGTGCCTGCCCTGTTCAGTTAGTGATGTCCTTCAGGGACTAGCTTTTTATTGTGATTTCATATCAAATAGAAAGAATAAAACAGAAAATATCAAGTCCATTGTGTTAGAGCAAATGTGACTCTGTAAGGACCGTGTTTCAGATATACCTTCTGTGAGCTGGATAAAATATAAAACTAGTTTTTATTATGTGTCCTGGCCAAAAGTTAGAATCTACACTGCTGTAAGCTTTGTTTACAGTAAGCGCTTTCAAAACCAGCTCCTTGTTCCGACATTCAGTTGCCCCTGCCCCAGACCTCCCTCAGCTGCAGGAGAGCCAGAAATGGCTCACAGGGCTCCCTGCTAGCTCTCCAGAATTCCCCTTTTTGTGTAGAGGGATTTTTCTCCTGGGCTCCTTTTAAGATGCCAGTAGAAAGCTTATATTGTGAAAGTTTAATTACTATCATTATTGTTAATTAACACCAAACCACTTTTTGTTAAATTAATTGAAGGATTTTTCCTCAG
Seq C2 exon
GTTTCCCTGCTGCAGAATGAAAGTGTTGAGAAAAACAAGAGCATCCAAAGCCTGCACAACCAGATCTGCAGCTTTGAGATCGAGATTGAGAGGCAGAAGGAGATGCTCCGAAACAACGAGTCCAAGATCCTTCACCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000021277-Traf3:NM_011632:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.065 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0314511=Sina=FE(43.5=100),PF0149614=V_ATPase_I=PU(4.5=25.8),PF0205011=FliJ=PU(13.9=61.3),PF101744=Cast=FE(19.6=100)

							
A:
NA

							
C2:
PF0314511=Sina=PD(0.1=0.0),PF0149614=V_ATPase_I=FE(26.0=100),PF0205011=FliJ=FE(33.6=100),PF101744=Cast=FE(30.1=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000021706





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000058361, ENSMUSP00000112517, ENSMUSP00000132750
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr14:102891418-102897260 
ALTERNATIVE
HsaINT0171698
(TRAF3)
Human
(hg19)
chr14:103357755-103363597 
ALTERNATIVE
HsaINT0171698
(TRAF3)
Rat
(rn6)
chr6:135705752-135708642 
LOW PSI
RnoINT0155205
(Traf3)
Cow
(bosTau6)
chr21:69242967-69247586 
LOW PSI
BtaINT0152146
(TRAF3)
Chicken
(galGal4)
chr5:49769027-49773539 
ALTERNATIVE
GgaINT0054795
(TRAF3)
Chicken
(galGal3)
chr5:52373643-52378155 
ALTERNATIVE
GgaINT0054795
(TRAF3)
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"