Special

MmuINT0023239 @ mm9

Intron Retention

Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128519950-128520559:-
Coord C1 exon
chr6:128520450-128520559
Coord A exon
chr6:128520109-128520449
Coord C2 exon
chr6:128519950-128520108
Length
341 bp
Sequences
Splice sites
5' ss Seq
ACTGTAGGT
5' ss Score
4.15
3' ss Seq
ACGCTTCTGCTTTTGCACAGCTT
3' ss Score
6.73
Exon sequences
Seq C1 exon
GTGTGCAGATGAGTAAAACACACTCGGTTTTTATCACTTCCGTGCTTGGCACTGTCAGCTTCGAGAACATGGACCCTTTCTACAGGAGAGGGATCACTTATTTTGGAACT
Seq A exon
GTAGGTTTGCCTGGTACTTTCCAAGGAACTTCTTTGGGTTTTTTTTTTTCTCTGTTCACAAATTATCCCTTGAAAATTTCCAGACACTTTGATTGTAGGCTTATAATCCATCTCTAATATTACTATGTCTGCTATGCTTGGAAAGTTCCAGGGCTAAAAGAAACCGATGTATTAAAACAGCAGCTTCTGCTCTATGTGTAAGCACATACGCCCGAGCAGTAGAATGGATATTTCTATTCACCGAGATTTCTGTTAAGTGACCGCTGTCATGGATGAAAATTTCCTTGTAGAAATGTGGAGTTTCGTGTCCTAAGAATATTAACGCTTCTGCTTTTGCACAG
Seq C2 exon
CTTAAATTTTCTGGTCCCAATAACACACCACTGGTGGACAAACTTTTGCAACTGGAACTCGACGGCAAACCTGTAGGAAATTACACCACAGATGAGAACGGGGAAGCTCGATTTTCCATTAACACTTCAGAGATATTCGGTGCACAGATTAGCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.019
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000059426





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr12:9693940-9694280 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr5:101151362-101151693 
BtaINT0106543
(OVOS2)
Chicken
(galGal4)
chr1:75843922-75844606 
LOW PSI
GgaINT0105024
([1])
Chicken
(galGal3)
chr1:79486280-79486964 
LOW PSI
GgaINT0105024
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAGATGAGTAAAACACACTCGG

				
R: 
TCAAGCTAATCTGTGCACCGA

				
Band lengths: 
263-604

			

		

	





	
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"