Special

MmuINT0023078 @ mm9

Intron Retention

Gene
ENSMUSG00000033488 | BC026585
Description
cDNA sequence BC026585 [Source:MGI Symbol;Acc:MGI:2448516]
Coordinates
chr1:159388713-159388983:+
Coord C1 exon
chr1:159388713-159388776
Coord A exon
chr1:159388777-159388874
Coord C2 exon
chr1:159388875-159388983
Length
98 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCAA
5' ss Score
2.83
3' ss Seq
CTCCCTTTTCTTTGTTGCAGGCA
3' ss Score
11.91
Exon sequences
Seq C1 exon
GACTTCAGCTGGCCATGGCAGCAAGGCTGTGTACGCGTTGCCTCCCTCCGGTGTGGCTCTGCAG
Seq A exon
GTGCAAGCCCAACTCCCCCCCCCCCCGCCCCCCCCCCGGCCCCCTTACAGACCCCAGGGGTACTGCTGAGAAAACCAGCTCCCTTTTCTTTGTTGCAG
Seq C2 exon
GCAAGCCTGGCAGGGCCAAGGCCGGCACTACCGAGCTGCACTCTGCACCGAGTTGAAGCAGCCCCTGACCATTCAAGAGGTGGCTCCCCGCCCCGTCGGGCCACAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033488-BC026585:NM_001033284:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.027
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF082407=ADH_N=PU(1.6=5.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000044945





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000044945f3144A, ENSMUSP00000113664
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:178037802-178037896 
HsaINT1039802
Human
(hg19)
chr1:178006937-178007031 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr16:60866083-60866163 
ALTERNATIVE
BtaINT0008970
([1])
Chicken
(galGal4)
chr8:6585977-6586446 
LOW PSI
GgaINT1000603
([2])
Chicken
(galGal3)
chr8:6914851-6914875 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GACTTCAGCTGGCCATGGC

				
R: 
GGAGCCACCTCTTGAATGGTC

				
Band lengths: 
151-249

			

		

	





	
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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