Special

MmuINT0010445 @ mm9

Intron Retention

Gene
ENSMUSG00000052374 | Actn2
Description
actinin alpha 2 [Source:MGI Symbol;Acc:MGI:109192]
Coordinates
chr13:12383927-12386669:-
Coord C1 exon
chr13:12386577-12386669
Coord A exon
chr13:12384158-12386576
Coord C2 exon
chr13:12383927-12384157
Length
2419 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAG
5' ss Score
8.27
3' ss Seq
CTCTCGTGTTTGAAAATTAGCTG
3' ss Score
2.94
Exon sequences
Seq C1 exon
GCCGAGACAGCAGCTAACAGAATATGTAAGGTTCTTGCTGTGAATCAAGAGAATGAGAGGCTGATGGAAGAATATGAGAGGCTAGCGAGTGAG
Seq A exon
GTAAAGGAAATGGGGGCAGCTCCGTCCCATCTGCCTGCAGCCAGGGGTGAGGCAGAGGCTGCAAACGGACTGTCCATGTTTATTTTTTGCACTTTTCATCTCAGAGAGAGTGAGAGCAGAAAATACATCTGGTCTCAGGCTGCTTATCCTAAAGCAACATGCCGGGTACCTGGTGCCAGTGTCCCTGCCCGTCCCCCTGCCCCCACCGTGGCCTTGGCAAAGACCCCAAAGCTACATGTGTTGATGTGGTAGGAAGGGAATCTAGTCTTAGCTCTGTCCCTGTAAGGTCAGAATCGGTAACTTGTAGCCTGTGGGCTACTGCCATCTTGTAGGGCACTGTTTGTATCAAGGGCCCTGTTCAGCACTGTGACCTCATGTGAAAAGAATTTGCAAAGCCTTTTGGGAGGAGGAGGTGTGGTGTGCATGTGTGTGCGTGCGCGCACAGGCCCTGAGAGGGATCTGGGATGACAGCTCACCTTCCAAACCCTTTGAGCCTTAGGGACGAATTTTTGTAGCTCTTTATCCAAATTCTTGATTTGAGCAATGCATTTACAGTTCTTTTATTTATTTATTTATTTATTTATTTATTTTTATTTATTTTTGTCCTTAGCATAGAGGGTACCAGGACATCCTTGTTACTAACCCTGTGTTATTTTTGTAACACAAGCCCAGGCTGAGGGACCCAAGAGCTGTGTCTTCTGAGATAGAACTCAAGTACAGATCCATAGTCAAGACCAGATAACTTAAACTAAATCTTAAAAATAGTTTAAATGGTTAAAAAAGAATAAATGCAAGACTAGATAGTTTTTATGTTAATTTGATTCAACCAATAATTGCTATGTGCTGTGAAAAGCAATGATCAGCACAAGTGAGAGGTAAACCATCCCAAATACTTACTTGATGGGAACTCAATCAAGTAAACTAAATAAACTAAATATATACCTTCATGCTGCTGCTGTGGGAAGTTTAGCTGTTTGATTCCCTACCACTCTTTTTTTTTTCTTTTGTAATTGTTACTATTGCTGTGTAAAACAAAACAAAACAAAACAAAACAAAACAAAACAACCACCTCATTTGTTGGCATCAAGGAGTCCTTGACTTTACAAGAGAAGTCTATTCAGCACAGAAAGAATGCCAGGAATTTTCTTACTTCTTGTAAACTTAGTTTCTCCCTCACAGCTGTGATAAGACAATCTTACAGAAGCATTGTGGGGGAGACATGGTTTATTCTAACTCACAGTTCCAAGGGAGTGCGGTCCATTATGGGGAAGGAGGCATGGCAACAGAATCCTGAGGCAAGTCGGTCACTTTGTATCCACAGTCAAGAAGCAGAGAGAACAGGAAGCAAGGCCAGGCTATAATAACTTCCCAAAACAGCGCTACCTGCTGGGGAGCATGTACACACGAGCCTCTGAGGGACACTCCTGTTCAATGATGATTGGAGGTGTCATCACTGAAACTCCGTTTCATTCTAGCTTCCCACAGCATCAGTAGACATAAGAGTAAATAGAAGGGGAGCTGGAGAGATGGCAGAGAGATGGCTCAGCAGTTATGAGTCTGGCTGCTTTCCCACAGGACCTGGGTTTGAGTCCCAGCACCCACATGGTGGTTAACAACTGTCTGAACCCCCGGTTCCAGAAGGACCTGACAGCCTCTTTGGCCTCTGAAGGCACTTCATGCATGTGGTGCACAAATATACATTCAGGCAAATTGCCCATATGTATCAAATAAGAAGTAAAATTTCAAAACAAACTAAAAACTAGAAGAATAAACTAAGTGTCTAGGTCTCTGAGGCCTGGATACTGACTCAGGAGAAGGGCAGTCACTAGATTTTGGGGAATTCACTAGGATTTCACTCACTGCCTGTGGAGTTTCATAAAAACTAGGCGATGAAGCCTACCTGGCCCAGAATCTGCCCAGGCTTGTAGTACAATTCTCTAGCGAGTAAACTCATTAGATCTGAGCTTTGTTTTTTTCAACCGAAACATTTGACATTCAACCCAGTTCCTTGCTGAGTGCATCAACTCCATTCTTCTTGTTTTTTTTTTTTTTTTCCTTTTAATTTTGTTTTCCCTCTTAGAATTTGGAGGCTCCATCCAGCATTTGTCTGCTAATGTCTGGTTGCTGCGTTTCTTGTAAATGTCACATTTTTGTCAAACACGACTCCGTGTGCTGACCTGAAGTTCGAGTTAAACCTGTGTGTGGTCTCATCGGGGTGGTCACCGTGGCCCTGGGTGGACACTGTCATTCATTGCACCATGCATAGAGCTGCAGTCCCCAATTTAAGTCAGTACAGTTGTTACCATGCTCAGTCATTGGGAGCCTTGGGGGAGCTGGTCCCAGTTATCGGGCCCCTTTGTTCTTGAACTGGAAACAGTTAGCTAGTATCTTCAGTGCCACTCTCGTGTTTGAAAATTAG
Seq C2 exon
CTGTTGGAGTGGATTCGGCGCACAATCCCCTGGCTGGAGAACAGGACGCCTGAGAAGACCATGCAGGCCATGCAGAAGAAGCTGGAGGACTTCCGGGATTACCGTCGTAAGCATAAGCCCCCCAAGGTGCAGGAGAAGTGCCAGCTGGAGATCAACTTCAACACGCTGCAGACCAAGCTTCGGATCAGCAACCGGCCCGCCTTCATGCCCTCCGAGGGCAAGATGGTGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052374-Actn2:NM_033268:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (disopred):
  C1=0.323 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0043516=Spectrin=PU(9.9=35.5)

							
A:
NA

							
C2:
PF0043516=Spectrin=FE(68.5=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000067708





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000129609
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:236737215-236739301 
LOW PSI
HsaINT0003195
(ACTN2)
Human
(hg19)
chr1:236900515-236902601 
LOW PSI
HsaINT0003195
(ACTN2)
Rat
(rn6)
chr17:66325458-66327876 
ALTERNATIVE
RnoINT0012625
(Actn2)
Cow
(bosTau6)
chr28:9423648-9425476 
LOW PSI
BtaINT0013330
(ACTN2)
Chicken
(galGal4)
chr3:36971209-36972338 
LOW PSI
GgaINT0081781
(ACTN2)
Chicken
(galGal3)
chr3:39134767-39135896 
LOW PSI
GgaINT0081781
(ACTN2_CHICK)
Zebrafish
(danRer10)
chr17:20113110-20113197 
LOW PSI
DreINT0025714
(actn2b)
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"