Special

MmuINT0002582 @ mm10

Intron Retention

Gene
ENSMUSG00000064308 | 2410137M14Rik
Description
RIKEN cDNA 2410137M14 gene [Source:MGI Symbol;Acc:MGI:1924047]
Coordinates
chr17:36978469-36978933:-
Coord C1 exon
chr17:36978651-36978933
Coord A exon
chr17:36978547-36978650
Coord C2 exon
chr17:36978469-36978546
Length
104 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTG
5' ss Score
5.56
3' ss Seq
CTCTCCCTTCTCTCTTCCAGAGC
3' ss Score
12.17
Exon sequences
Seq C1 exon
ACTCCCCCCAAAACAAATGTGGCCCATCATTCAACGCTTGAAGGTGATGTCACCCTGAGATGCTGGGCCCTGGATTTCCACCCTGCTGTCATCATCCTGACCTGGCAGAGGGATGAGAAGGACCTGACTCAGGACATGGACCTTGTGGAGACCAGGCCTGCAGAGGACGAAGCCTTCCAGAAGTGGGCAGCTGTGGTGCTGCCTTCAGGAGAAGAGCATAAATACACATGCCATGTGCAACCTGAGGGGCTGTCTGAACCTCTCATCCTGAAATGGAGTAAAG
Seq A exon
GTAGTGTGTGTAGGTACAGAGTCTGTCCTTGGGAAAGCAGGAACCCTTCTGCAGACCTTGAGCATATCCCTTAGTTCTATCCTCCTCTCCCTTCTCTCTTCCAG
Seq C2 exon
AGCCATCTTTTTCTCCCACCACACCCATCACGGGGATCACTGCTGGTCTGGTTCTCCTTCCAGTTTTGGTCACTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064308:ENSMUST00000039846:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.200 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0765410=C1-set=WD(100=87.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000044846





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000133725
  



Associated events







Other assemblies


mm9




Conservation


Human
(hg38)
chr6:29944398-29944499 
LOW PSI
HsaINT1015520
(HLA-A)
Human
(hg19)
chr6:29912181-29912276 
Rat
(rn6)
chr20:2047227-2047339 
ALTERNATIVE
RnoINT0122939
(RT1-M4)
Cow
(bosTau6)
chr23:27865130-27865244 
LOW PSI
BtaINT0026335
(BOLA)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGTCATCATCCTGACCTGGCA

				
R: 
AAGGAGAACCAGACCAGCAGT

				
Band lengths: 
256-360

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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