Special

MmuINT0020240 @ mm9

Intron Retention

Gene
ENSMUSG00000027104 | Atf2
Description
activating transcription factor 2 [Source:MGI Symbol;Acc:MGI:109349]
Coordinates
chr2:73688646-73689039:-
Coord C1 exon
chr2:73688921-73689039
Coord A exon
chr2:73688775-73688920
Coord C2 exon
chr2:73688646-73688774
Length
146 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TTTTTTATCATTTGTATTAGATG
3' ss Score
6.89
Exon sequences
Seq C1 exon
ATCAGACTCCAACGCCAACAAGATTCCTAAAAAACTGTGAAGAAGTGGGTTTGTTCAATGAGTTGGCAAGTCCATTTGAAAATGAATTCAAGAAGGCTTCCGAAGATGACATTAAAAAA
Seq A exon
GTATGTTGTTAACCATGAAATTATAAAAAGAATACTTCTATTAGGAATACAATGATGCTTTTCACTTCCTGGTTTCTTAAACATTTTGCTTGGCTGTTTTTTATAAACTTTTTACAAAGTTTTTTTTTTTTTATCATTTGTATTAG
Seq C2 exon
ATGCCTCTAGATTTGTCCCCTCTTGCAACACCCATCATAAGAAGCAAAATTGAGGAGCCTTCTGTTGTAGAAACAACTCACCAGGACAGCCCTTTACCTCACCCCGAGTCGACTACCAGTGATGAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027104-Atf2:NM_009715:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.378 A=NA C2=0.808
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000058521





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000058521f2052A, ENSMUSP00000088311, ENSMUSP00000097586, ENSMUSP00000097586f2051A, ENSMUSP00000097588, ENSMUSP00000107636, ENSMUSP00000107638, ENSMUSP00000107641, ENSMUSP00000107647, ENSMUSP00000107648, ENSMUSP00000118357, ENSMUSP00000118560, ENSMUSP00000126034, ENSMUSP00000130822, ENSMUSP00000133632
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:175118119-175118250 
ALTERNATIVE
HsaINT0013798
(ATF2)
Human
(hg19)
chr2:175982847-175982978 
ALTERNATIVE
HsaINT0013798
(ATF2)
Rat
(rn6)
chr3:60752876-60753018 
ALTERNATIVE
RnoINT0022300
(Atf2)
Cow
(bosTau6)
chr2:21790186-21790310 
LOW PSI
BtaINT0022496
(ATF2)
Chicken
(galGal4)
chr7:16171880-16173364 
LOW PSI
GgaINT0046056
(ATF2)
Chicken
(galGal3)
chr7:17803342-17804826 
LOW PSI
GgaINT0046056
(ATF2_CHICK)
Zebrafish
(danRer10)
chr9:2351095-2352575 
LOW PSI
DreINT0034495
(atf2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ATCAGACTCCAACGCCAACAA

				
R: 
ATCACTGGTAGTCGACTCGGG

				
Band lengths: 
242-388

			

		

	





	
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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