Special

MmuINT0023263 @ mm9

Intron Retention

Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128492853-128493359:-
Coord C1 exon
chr6:128493269-128493359
Coord A exon
chr6:128492922-128493268
Coord C2 exon
chr6:128492853-128492921
Length
347 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
TCTTGTCAATCTCTTCAAAGCTT
3' ss Score
7.33
Exon sequences
Seq C1 exon
CTACACTGGAGCTCGTGAAAGCTCAGTTACAGTCCTTGTGGATGTGAAGATGCTCTCTGGCTTTACTCCTGTCGTCTCATCCACCGAGGAG
Seq A exon
GTAAATAAGGGTGGCCCTGCTCCCCAGCACAGAGAGAGTGAGAGTGCATAAAATAATAATGGGATAATGGAAATAATGGGATCCTTCATCATCTAAGCACATTTCTTCAGAGTTCACGTTTGTATTTAGTCTGTACTGGAATAGGAGAGATGATATTTTTATTCTGCAGAAATGCAGAGTCATTATGCCCACTGTTCATCATGTGTTTCTTTGCCGGGTTCCCTTGTAAATTCACCGAAACACTGAGGTACAAAGGGAACGTTCCCTGAACAGACAGCACAGAGCTCATTTCTAGAGGGGGACTCAGGTATTCTGACCCTCAACCCTTCTTGTCAATCTCTTCAAAG
Seq C2 exon
CTTAAATTCAATAGTCAAGTAACGAAGACGGACATAAAGAATGGCCACGTTCTGTTCTACTTGGAAAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:32
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF076779=A2M_recep=PU(25.3=71.0)

							
A:
NA

							
C2:
PF076779=A2M_recep=FE(25.3=100)

						

					

				








    
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)
chr12:9725690-9726061 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr5:101182905-101183267 
ALTERNATIVE
BtaINT0106534
(OVOS2)
Chicken
(galGal4)
chr1:75820041-75822314 
LOW PSI
GgaINT0105046
([1])
Chicken
(galGal3)
chr1:79459378-79464010 
LOW PSI
GgaINT0105046
([2])
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






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