Special

MmuINT0020234 @ mm9

Intron Retention

Gene
ENSMUSG00000027104 | Atf2
Description
activating transcription factor 2 [Source:MGI Symbol;Acc:MGI:109349]
Coordinates
chr2:73661258-73666735:-
Coord C1 exon
chr2:73666529-73666735
Coord A exon
chr2:73661364-73666528
Coord C2 exon
chr2:73661258-73661363
Length
5165 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
GTGAGTTGTTTCTTCTCCAGAGC
3' ss Score
7.32
Exon sequences
Seq C1 exon
GCTTCTCCAGCTCACACAACTCCTCAGACCCAAAATACAAGTGGCCGTCGAAGAAGAGCAGCTAATGAAGATCCTGATGAGAAAAGGAGGAAGTTTCTAGAACGAAATAGAGCAGCAGCTTCAAGATGCCGACAAAAAAGGAAAGTGTGGGTTCAGTCCTTAGAGAAGAAAGCAGAAGACTTGAGTTCACTAAATGGCCAGCTGCAG
Seq A exon
GTATGGGCACAAGCAGTTTGCTTCTATTTATTAGTTAGCAACATAGGTGTTGCTTGGTTTGTTGGTTTGGTTTGGTTTGGTTTGGTTTGGTTTTTTGTGTGTAGCTTTGCAAGACAGGGTTTCTCTGTGTAGCCCTGGTTGTCCTGGAACTCACTCTGTAGACTAGGCTGGCCTCGAACTCAGAGATTCTCCTGCCTCTGCCTCCTGAATGCTGGGATTAAAGGTGTGCACCACTGCTGTCTGACTAGGAACATAGTTTTTTCTAGATGATCCTGCAAGTATTTTAGGACATGATATATACGACACATATGTAGACTCTGTAGTAAGCCATGGTTTCCTAAACCTTGTGAATTCTGACCTGAAGTGATACCAAACTTTCAACCCTGACACAATGAAGAAATTTTATGTGTAACTGTTTAGTTGTGTGGTACAGAAATACTGTAATAACCTTGCTTGAACTTTATAAAGTTCAAAACTTTTTTTAAAAATCGCTATTTTTTGTTTATTTGTTCTGTTTATTTGTCATTTTACCTTTATATTAACCATAAAGTTGTTCCAATGGCAGTTTTTTACTTTCTTTCTTTGAATTACAATTCTGTTGTTCTTTCTTAAGTAACTAGCACATGTGAAAGGAGCCAGATTGACAGCTTTGGAAACTGAAGGATTCTAATTATCCACAAAATAGGTAATATTCGGCCAGTGGCATAACAAATTATTTCATACTGCCCTGCCGATGTGCCTCAAATACATTTCTTAGGATCTCATGTGTTATAAAGATTTTAAGGCTCCATTCAAGTCTTGGGTAAGATTTTTAATAAAAGTATTAAGGTAGCATCAAATGTGTTTCTTTCCTTCCTTCTCTCCTTCTTTCTTTCCTCCTTCCTTTATCTCTTTCATTCTGTTTTCATCATTTTGCTTTTGACATTGTGAATATTCTCCAGTAGTAGCTTTTGAACTAACAAGTAACTAGAAATTAATAAATTGTAGTTGTTTATTAATATAGGTCAAGTTTTTGTGTGTTTAACAACAGGACTAGAAGTTGAAATTGGGGCTTCAGTGGTCTACCACTAGTGCCTCCTTTAGTAATTTTGAGTTTTAGCATAGGGAGCTAAATTGCCCAAACTTGCTTCAAACTCAAGATCTTCCGGTCTCAGCTTTCCAAGTAGCTGGTATTGTGAACATATGAGTAGATCAATCTTTTGAATTACCCATTTCCAGTGAAAACAAAACTCAGTTATTATGAATATATGCTGTGCGCCTAGATTAGGCAGATCTACCACTACCCTCCATCTTCCACGTCTATGAGACTCCTTAGAACTTGAGATTTCTCCAGGCCATGTGCTTCTGCTCTACTTTTCTTCTTCCTCCTCCTCTGCGTCCTCTCCCTCTTCCATTTTCTTCTTCTTTTTCTCCTCACCTTCCCTTTTATCTGCCCAACCATCAACTCTCCTTTATTTTACAAATTAAGGCGGGAAGCAGGTTTACAGGAAATCACCTGAGTGCTGACCTGTTTCTTGTTCTTAGCCCCTCTACAGGAGAATGGGATTAACATCAAATATAATTACCCCCAGGGCTATCCACAACAGGGCACTTGTTTCTTAAATCTATCTTAAAAGTGTCACAAATAAAATTGTTAAAATACTTAGAAAGCTCTTTTTAACATCCTGTATCGCACTTACCCAAACTAAATTTTATAGCAAGTTTTCATATGTGAGACAGACATTCTTAGAAGCCTTTGTTGCATTTTGCATATTGTTTTGGTTATTTTAAGACGAACTGATTGCCTCTTACAAAACTTATTTTTAGCCATCTAACTTATAATATGAAAAAATGATTATTCATGACTTACTAAACAACATAAACTTCAAATATATACTAGAATTTAGTTACAAATTTTATCGTTATCATCCTAACAAATGAATTTACTAAAAAACTTAGAATAAAATTCATTTCTCATTTAAGTGAAATGAAACATTGTACATATACTGATTTATGTGTAGACCATGAAAACTATTCTTTGCAAACCTGATAGAATATCAATTACTATTACTTACATATCAACAAAGTGATTTAAATGTTTCTTTTTATTGTTCTTAACTAATAAAACTTTTTTAAAAATTTTTTGAAATTATAATTTATTTATACTTTGCTCTCCCTTTTCTCCCTCCAAATCCAGAATAATGCCCTTTCCAACTCTCCTTCAAATTCATGACCTTTTTTTTGTTTCAACAAATTACTACTTCATGCATATATGTATATGCATAGATGTTCCTAAATATAACCTATTGAGTCTGTCTAATACTACCTGTATGTATGTTTCGAGACTGACTTTTTTTTTTTTTTTTTGGTTTTTCGAGACAAGAGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTCACTTTGTAGATCAGGCTGGCCTCGAACTCAGAAATACGCCTGCCTCTGCCTCTGCCTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCTACCACACCCAGCTGAGACTGACTCTTTGACACTAGACAACCAGTTGGCATATTCTTCCCTGAGGAACACCATCTCTCCCATTCCCAGTTTACCTCAGTTACCTGTAGTTCTTGGTGTATATAGGGTTGTGGCCTTGGGGTCAAGCCATCTAGTTTGGCATGTTCATTGGTGTCATTCCTGTTCAGCTCACATTTGGACAAAATCATGTTGGTGAGACTTTATGGATAAGAGAAGGAATTAGTAGAGTACAGGTGAACTATCTGATCAGGGAAATGAAAAAGAGAAGGGGGCTCCTTAAGGAGAGGCAGAGAGGTTGATACAGAAGAACGGGTGGAGAGGAGGAGGGGAAAGGAAAAAGCAGTGTACAAGCTGTCTGATGGGGAAGTGGGAAAGGGATGCTCTTTAGTAAAGGGGAGGCAGGTCTATACAAAAGAAGAAAGGTGGGTAAAATAACAAAGATGTCTGAAAAAGCCACAACTGGTCATACTATTATCTATTTCCAAAATTTAACTTAAAAAACTATAATATTCCATGCATGAATATACATACACTTTTAATGAACCTTTCTCATCTGGGCAGACGAAGCTTCTTCCAAGAGCCAAAGACCACCTAACAAAACCTCCAATGCCAGACATGAGATACTCTCTTTTTAGTTGTTGTCCAAGAGACTCACAAAACATACAATCTATTGCTGTTGCCCTTGATAAGCCCCCAGAGGTAGAAGGTAAGTTTGTATTGCTAAGACACCGTGCACTTTAGAAGTAGGGCTGGAGAGATGGCTGAGTGGTTAAGAGCACTGACTGCTGCTGTTCCAGAAGTCCTCAGTTCACTTCCCAGCAACCACATAGTGGCTCACAACCATCTGTAATGAGATCTAATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTGTGTGTGTGTGTGTGTATACATTTACACACACACACATACATAATTCATAAAAACAAACAAACAAAAAAAAGAAGTAAGGCCCAGAGATCCCTCAGCTTGGACTGACCTGTGCCCCTTCCCTGAAGACTAGCTTTCATATCAGAAATCGCCATGCATGCTGCCAAAGGAAGGAGGCAACCAACAATTTACCCAGCTGTGATACCTGTGTACCACAGCATGACACAATAACCCTGATCATGCAGTAGTGACATGCATACTTTGGTAGTAACCAACTACTCTCTAATTTGACTTAAGACTTAAGAGGGAGATCAAGAGGTACTGGCAACCTAGCTCGGTGCTAGTGAATTCATGGTTATTGGAGAGAATTCTACAACCACCTATACTTTTTTTTTTATGTGCATTGGTGTTTTGCCTGCATATATTGTCTATGAGAGAGTGTTAGATCACCCTGGACTTGGAGTTACATGCAGTTGTGAGCTGCTATGTGGATGCTGAGAATTGAACCCTCGTCCTCTGAAAGAGCAACCAGTGCTCTTAACTACTAAGCCATCTCTCCAGCTCTTACCATCAATTTTGAAGTACAGTAGTCTAAGGATTCTTTAACCTCTTACTGATTAGGGATATGCTAGCATAAATTGTGTTCTGTGCTTTAATACAGTGTTGCTAGTTTTGTTGGGCTGTAGAAAACTATTTGTACTTGATTTTTTAGATTGCTTGACTTTTTTTTTTTTCGTGGTTTTGTCTTTAGGAAGGCCTAAACACTAATTTGCTAAAAGCACATTCAGCTTTCTAGTTTAAGAGGTAGGGTAGAGGTTGGGTTTGGTGATGCACACTGAATTATAATCCCAGCACTTGGGTCTAGGGCAGGAGGATTGCTACAGTTTAGAGGCAAACCTGGGATGCACTGATACCCTGTCTCAAAAAGTGAGATGTCAGTAGACTGTGTGCCTACAATTTTATGTATGCCAGCTTCTTAAATATTTGCATTTGTTAATACTTTGGGTTTCATGGGTGAAACCTAGATGGTTATAGTTAATGTAAATCTAAATGAGAAGAAATATTCATAGTGACTTTTTTAATGTTACTAATTTATTAGGTCCATAGTATTTCTTAACTCATGAATGTTGGTAAAATAGTCATTCTATTGTAAGGAATAAGACAGAGCAGCACTGATATTAAAATTTAGATGCCTATATCACAGGCAACAAACCCATTTAACAGCACTGTCACTGGTTCTGGTGCCTAGCACAGTGCTCAGCAATAAGTATAAAGACCCGTGAGTCTTGAATAAGTGTAATTTCTTTTTTTAAAGTATGAACTTGCATGATTACATTTCCAGGATACATTTTTAATTTTTAAAAGGTGAATGGAATCAATGAAAATTCATTGATTATTGATATTTTTAAGTTTTCAAATAATCAGAAGAGCATATGACATATGTACAAAAGAGCTCTTCAGTGAGTAACCTATAATGCATACGATTCCCGTGGCAAGTAGTGAGCAAGGCTACCCAGTTATGGTATTCATATGATTTTAGTTTTTAAACTAAAAGACTTACATAGATGCTTAAGCAAACCAGTGTATACTGATTAAATTTATTTAAACAGCATATGTCCCTTATTGTTCTGCCAAAGAGATCCAGTTTTCATCCTGTAAGCCTTGCTTTCTTTAAATAGTAAAATATGTGTCTATCTAATGCTGCTAAAGCATGTGAGTTGTTTCTTCTCCAG
Seq C2 exon
AGCGAAGTCACCCTGCTGAGAAATGAAGTGGCCCAGCTGAAACAGCTTCTTCTGGCTCATAAAGATTGCCCTGTAACTGCCATGCAGAAGAAGTCTGGCTATCATA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027104-Atf2:NM_009715:12
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.937 A=NA C2=0.663
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0017016=bZIP_1=PU(70.8=66.7)

							
A:
NA

							
C2:
PF0017016=bZIP_1=PD(26.2=47.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000058521





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000058521f2052A
          









    
Other Skipping Isoforms:
ENSMUSP00000088311, ENSMUSP00000097588, ENSMUSP00000107636, ENSMUSP00000107638, ENSMUSP00000107641, ENSMUSP00000107647, ENSMUSP00000107648, ENSMUSP00000126034, ENSMUSP00000130822
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:175080766-175093060 
ALTERNATIVE
HsaINT0013792
(ATF2)
Human
(hg19)
chr2:175945494-175957788 
ALTERNATIVE
HsaINT0013792
(ATF2)
Rat
(rn6)
chr3:60726822-60732125 
ALTERNATIVE
RnoINT0022294
(Atf2)
Cow
(bosTau6)
chr2:21813672-21825529 
ALTERNATIVE
BtaINT0022491
(ATF2)
Chicken
(galGal4)
chr7:16190535-16196929 
ALTERNATIVE
GgaINT0046062
(ATF2)
Chicken
(galGal3)
chr7:17821999-17842016 
LOW PSI
GgaINT0046062
(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"