Special

MmuINT0010440 @ mm9

Intron Retention

Gene
ENSMUSG00000052374 | Actn2
Description
actinin alpha 2 [Source:MGI Symbol;Acc:MGI:109192]
Coordinates
chr13:12398541-12401253:-
Coord C1 exon
chr13:12401167-12401253
Coord A exon
chr13:12398629-12401166
Coord C2 exon
chr13:12398541-12398628
Length
2538 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TTTTCTTGCTGTTATTATAGAAA
3' ss Score
6.18
Exon sequences
Seq C1 exon
AAATAGTCGATGGCAATGTGAAGATGACCCTGGGTATGATCTGGACCATCATCCTCCGCTTCGCCATTCAGGACATCTCAGTGGAAG
Seq A exon
GTAAAGTTCATGGGGGTGGTCCACGTGTCTAATTTGGGAACTGAGCTTACAAATTAGATCTTGAATCGGATATTGTGACACTGAGCAGTCACTTGCACGATCAAACGGGAGGCATCTAAATTGAGTCTTTAAAATTTTTATATTTGTATGGGAAAAGACCGAGGCAGTGCTATTCTATTCTTGCGGTGGAATCGCTTTGCAAGAGATGCACACATGTCTGGAGCAGACGGTGTTTTTAACATAAGTTTCTTTACTGCATATTGTACTAGGGCGTTCACAAATGTGCTAATGCAATAGGCAGAGGGTTTTCTTTCTCCTTTGTATTCTCTATCCTTCCCTCCTCTCTCCCCTGTCCCTCCCTCCCTATTTCTTCTTCCTTCTCTTTCTCTCTTCACTGGGGATTAAAACAGGGCCTTGCAATTGCTAAACACGTGTCACCACAGAGTCATCCCTTCAGTTCCCTCGGGCAAAGATCATTAGGCTTACAGCTAGAACACTTTAGTAGTATTTAGTAATATTAATAATAAAAGTTGGGTGTGGTGGTTGACACCTATCAACCTAGCATTCAGGAAGCTAAGACAGGAGGATCACAAATTTGAAAGCCCCTCAGGCTTTGTAGCCAGCCCACCCAAGCCTGTGTAACCCCTGTTTCACCCCTAAAGCATTCTTTACATTCCTTCCAAAAAAAAGAAGAAAGAGAAAGAGACAAGTTTTCCTAGCCCAGCTACAGTGTGGATCAGTCTTCAAAACAGTGTCTACTCTACAAAGTGGGTTTAGCTGTTTAGGTATTTAAATTTAGTGGCTAAAAACTGACACAATTATGACAAATTACTGTTTTTCAATAAATTGGGAACCTCCGGGAAGCATCCTGTTACTTTCCTTAGCATGAAGAAATGCACGGTAATAGAAGCACCCTGTGCAGGAGTTTTCAGATGTAGACTGTGTGTTCTTCAAACTGGCTGTCATTTCTGAGCCCGAATTGAGGTTTAAATGGCATTATCTCTTGGTTTGATGTTTTAGATGACATAAGTGGGTTTGGTGTTCTAAAAAGGGAATCACTTAAGTGAGTTAGAAAGTTCTCTAAGGGCACATGCTGCAGTCTTCTTGTCACCTAGTACAGTGAGCAGGGACGTGGCTTGTTAAAAAGATCTATTTTAGTTTTAATTATGTATATGCATGTGCAGGTGTTCTTGGGGGCCAGAAGAGGACATCAGATTCCCTGGAGCTGGAATTATAGGTAGTTATGAGCTGCCCAACGTGGGTGCTGGGAACTGAAACAGATCCTCTTCCAGAGCAGTAGCACTTATCTACTGAGCCTTCTCTGGTCTCCATCTCCAGAGGGTGGGTCTCAATGATTGACTACTGAGCCTTCTCTGCTCTCCAGCCCCAGTGGGCGGGTCTTAATGGTTGCTGGCTGATGAGTCACTAAAAGCCCCAGAAAGACCAACATCCGGAGTCCCTTCATCCTGGGAAGACGATAAGAAACACCCCACTTCTCCATACTTAGATCTTACCACTCAGGCTAGGTTAGCTGTTGGTTACCAAGTTAACAGAGGCTGACTAATTGGCAGCCCAGGTTACCCTTAAACCTATTCTGCCTGCTGTGATTTGAGAGATAAATAGGTACTTCTAATTTTCAGAATGCCAAGTTTAATTTGGATTTATTTACAAGAGGTGCTGCTGAGATGACTTGTCATCCTAGCCTGGCAGCCTGAGTTGGATTTCTAGGACCCACAAGGTGGAAAAAGAATACTGCCTCTGACCTCCACATGTGCACTGTGGCACATGTGCATGTGTACATGCACATACACACACACACACACACACACACACATGCATTCACACTCATACACAACTTTTTAAAAATTTAAAGAAATAAATATTTAAGAAAAAGATTTAATTCCAGTGATCAGTTGTTAGGCTAAAAGGCACAGTAATACATTTTATTCAAAGAGGAAAGAAAGAAGAACAGTAATGATGAGGGGCTGAGACAGGGGAGGAGGGCCGTACTGGGCACACGGCACTGGTACACACTGATAAACATGGATGCTTTGTTTAGAGTTAGGGTCTGCCTAGCTCTCCTCTTGCCCTTCCTCTTTGGAGTGGGGGTTGTAGGAAGTCCACCAGATCTCCCTTCAGTCAGCATTACAGGGACTTAGGCTTTTGTCCGGCTTGTTGTTTTTGCTTTTTTATATTTTTTGTTGTTACTTGGTTTTCTCTTGGTAGATACTGAACTTAGGGCCATAGGAACACTAACCAGTAGCATTCTACTCATGAGCAACATCCCATAGCCCTGGTTATAATTTTGTAATTAGTGATAAGAGAATTTAAAATCTAATTTTTTTTCAGGTGTAGCTATGAGAATGGCATTGTCTGTGTTTCCCCTAAGTGACTTTTCATATATCCAAAATAAAATAGCCTTTTTTTAGCACACCCCACCACACACACACACACACACACACATACACACACACACACACACACACACACACACACACACACATACACACACACACACTTTTCTTGCTGTTATTATAG
Seq C2 exon
AAACATCTGCCAAAGAAGGGCTGCTGCTATGGTGTCAGAGGAAGACAGCTCCATACAGAAATGTGAATATCCAGAACTTCCACACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052374-Actn2:NM_033268:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (disopred):
  C1=0.055 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0030726=CH=PD(20.6=70.0)

							
A:
NA

							
C2:
PF0030726=CH=PU(24.0=83.3)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000106246





     
                   









    
Main Skipping Isoform:
ENSMUSP00000067708





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000129609
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:236720192-236725932 
ALTERNATIVE
HsaINT0003190
(ACTN2)
Human
(hg19)
chr1:236883492-236889232 
ALTERNATIVE
HsaINT0003190
(ACTN2)
Rat
(rn6)
chr17:66339710-66342224 
LOW PSI
RnoINT0012620
(Actn2)
Cow
(bosTau6)
chr28:9406780-9412604 
Chicken
(galGal4)
chr3:36983930-36984933 
LOW PSI
GgaINT0081776
(ACTN2)
Chicken
(galGal3)
chr3:39148747-39149750 
LOW PSI
GgaINT0081776
(ACTN2_CHICK)
Zebrafish
(danRer10)
chr17:20118428-20118742 
LOW PSI
DreINT0025709
(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"