Special

MmuINT0020243 @ mm9

Intron Retention

Gene
ENSMUSG00000027104 | Atf2
Description
activating transcription factor 2 [Source:MGI Symbol;Acc:MGI:109349]
Coordinates
chr2:73680417-73683610:-
Coord C1 exon
chr2:73683496-73683610
Coord A exon
chr2:73680504-73683495
Coord C2 exon
chr2:73680417-73680503
Length
2992 bp
Sequences
Splice sites
5' ss Seq
CCAGTAAGT
5' ss Score
9.09
3' ss Seq
TTTAAATATGTTTTTCACAGCTT
3' ss Score
6.93
Exon sequences
Seq C1 exon
TCCTGTACCAGGCCCATTTCCTCTTCTCTTACATCTTCCTAATGGACAAACCATGCCCGTTGCTATTCCTGCATCAATTACAAGTTCTAATGTGCATGTTCCAGCTGCAGTCCCA
Seq A exon
GTAAGTTGGAAAGTTAGACCATTTAAATTTAAGTCTTTGTATCTAAACTGGTCTGGGTAAAATAACCAGAAAATATATTTGAACTGCTTGATTGGCTTACAAAATGGAATTTATCAAGTGTTTATTAATTGGGAGTAGTATTTATTCATCATTACCTGTAATCGACTATAATATTCTAGGCAAACATAATTGGATTGAAACCTTTCTTTACCCCCAGCCCACTCTTGTTTTCTGTATTCTTATTGCATTATTTCTTGATTCACCTCACTCCAGTTTGACTAGGTTTATGAAATTCAAATATTTCTTAAGATACTTGTTTTGGAATGCTGGCAAATAGCTATGGTGTTTATAGTTATAAAAATTCTTCAAAAAACACACTTGTCCTTTATGGTTACATGAAGTTTAGTGGCCCAGGCATGTTAAAGTCCAAACATTCATATCTTGGCCTGATGACACATGCCAGGAATCCCAATAGTCAACAGATAAAGATAGGGTCAGAAGAAGGTCATAGCTAGCCTCAGCTAAATAATACATTTTAGGCCAGCCTGGGTTACTGTTGTGAGAAAATCCAAAAAAAAAAGTTTTATGAGAAACACACTAAATACTCAAATTTTGGGAAATAAAGAAAAAGTAATTAACTATATTGAGTTGTCTAGTGAACATTTAAAAACATAATGTTGGGCCAGGCGGTGGTGGCGCACGCCTTTAATCCCAGTGCTTGGGAGGCAGAGGCAGGTGGACTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGATAGCCAGGGCTATACAGAGAAACCCTGTCTTGAAAAAACCAAAAAAAAAAAAAATGCTGGAGCTGTGTGGTTAAGAGCTTGCACTGTTGTTGCAGAGGACATGAGTTCAGTTCCCAGCACCCATTGCAGATGGCTCACAACTGACTATTGCTCCTGCCATAGAAGATGTGAGAACTTGGCACACATGCCCACCCATAGATAAATACATGTACACACAATTGGAAAGATTAAATTGTTATGTAAAAGCACTGTATTTGAAATGATGAAAATTTTCTTTTTCATATCATATTTCACAAAAATAGTTTTATTCATACTTTCAAATTAGTCTTCCAACATTTTACATTTTCATCCTGAAAAGAACTTTTAGATATCTAGCAAAGTTGTCTAAAACATACTATTTTCATTTTCCCTAAATTATTTATGATACATATATAATTTGAAACTTTCTTAAAGAATACTTTAAGCCTTAGTCATTCATGTAATGAATATAGTTGGAGGGTTTTGTTGTTGTTTTTTTCCCCCCCCCCGGGACTAGTGAGATGTGTCAGTGGATAAAGATACTTGTCACCAAGTTTGACAACCTTTGTTCCAGTCTCCATGTCCCACATGGCAAAAGAAGAGAACCAATGCCAGCAATTGTCCTCTGACCTCCATATGTGTGCCATGACATGTATGTGGAAACATATATGCAAAGTAAAGAAATGTAAAAATTTTATTATTACATGGATAAATAGTGTTGATTCATGTGGTATAATCCTTTAGTATATAGCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAATTTATTTATTGGTTATATGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGTGTCAGATCTCATTACGGATGGTTGTGAGCCGCCATGTGGTTGCTGGGATTTGAACTCCGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGCCCAGTATATAGCTTTTTGAGATTATTTTTTAAAGCTTACTTGTAGCAACATTCTAAAATTTGTGGTTTGGATATGCTCCTCAACAAAATTAGTAACATATTAAGTATTAAGTTTATTTAAAAAACCTTCCAACCTACCTTCCTACCTTCCTTCCTTCCTTTCTTCCAGTTTTGAAGCAGGATCCCACTATATAGCACTGGCTGGTCTGGAACTATGTAGACCAGGCTGGCCTTGAACTCACAGAGATCCACCTGCCTCTCCACATGAGTGCTGGAATTTTTAAGTAATCTAAATGTCCAAATTATCATTGATTGAGGTATTTCCAAAATATTTTTCTTCTTTAAACAGAACCGTGTTATTCAAATTGCATTACTTAAAAGTCTTAGTGAAGACTCGGGGAAAGGTTTGCTTTCTCTTTTTTGAAGATATTTTTAAAGCAGGAAACATTCTTGCTTTGTATTTGAGATAAAATGATTATCCTTTTGAATGTGCCTGTATTAACGGCAACTTGTAATGAAAAAAAGAGATTAATTAACCTTACTCTTCTAAAGTGAAAAGCGAAAGTGGCAAACCCTGTTAAAGTATCACCTGAGGCATTATCAGGGGGCACCGGCTTCTATGTTAGTACACAGTACATTAATACATCAGTGCACATACATTTTAGAAAATTCATGTACTTATTTTAATAAATTACAGTTTGTGTTGAAATTATTTTAATTTTTATTGTCACAGATTTGGTAGTCCTTTTAATTGCAAAATTGGAATGTAAAAGATAATCTACACATTTTTGTATCAGTCACTTTGAATATTATGGGTTTATAAAAAGGAAGTTAAAGCCAGGCCAACTGACACAGGCCTCTTACCCCAGTTACTTAACAGGCTAAGACGACAAGCTAACCTGGACTACAGAGTGGGTGCAAAGCCATCCAAAATAACTTTATGAAATCCCATCTCAAAAAAACAAAAGTGGGTAGTGATAGAGCTTTATAATAGAGCACTTGACTCATATGCCCAAGACCTTGGTTTTGATCCTTGCAGGTAGATTGGGAAGGAGAATACAATCCTTTGAGAAAGGTTAAAACATGGAGATTATTATTTCAGAGAAATTGACAACTTTTGAAAGATAAATTTTCTAAATCCAAAGTTACAAATTAAGAGTCATATGTAATAAAAAAGGTACATCTTGTTTTATAAATACTGAATCAAAGTTATTTTAAATATGTTTTTCACAG
Seq C2 exon
CTTGTTCGGCCAGTCACCATGGTGCCTAGTGTTCCAGGAATCCCAGGCCCTTCCTCTCCTCAACCAGTCCAGTCAGAAGCAAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027104-Atf2:NM_009715:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.657 A=NA C2=0.947
 
                        

				
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, ENSMUSP00000107638, ENSMUSP00000107641, ENSMUSP00000107648, ENSMUSP00000114828, ENSMUSP00000118560, ENSMUSP00000118719, ENSMUSP00000126034, ENSMUSP00000133632
  



Associated events






Conservation


Human
(hg38)
chr2:175111655-175113993 
LOW PSI
HsaINT0013801
(ATF2)
Human
(hg19)
chr2:175976383-175978721 
LOW PSI
HsaINT0013801
(ATF2)
Rat
(rn6)
chr3:60744830-60747626 
LOW PSI
RnoINT0022303
(Atf2)
Cow
(bosTau6)
chr2:21796189-21799168 
LOW PSI
BtaINT0022499
(ATF2)
Chicken
(galGal4)
chr7:16179780-16179944 
ALTERNATIVE
GgaINT0046059
(ATF2)
Chicken
(galGal3)
chr7:17811243-17811407 
LOW PSI
GgaINT0046059
(ATF2_CHICK)
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"