Special

MmuINT0112709 @ mm9

Intron Retention

Gene
ENSMUSG00000026790 | Odf2
Description
outer dense fiber of sperm tails 2 [Source:MGI Symbol;Acc:MGI:1098824]
Coordinates
chr2:29748521-29749089:+
Coord C1 exon
chr2:29748521-29748674
Coord A exon
chr2:29748675-29748963
Coord C2 exon
chr2:29748964-29749089
Length
289 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
CTCTAGTTTTGTCCCCACAGAAA
3' ss Score
8.43
Exon sequences
Seq C1 exon
ATCCATCTTTTTTGTGTTGCCCTCCCCTGCCTGCCAGAAGTGAACCATGAAGGACCGATCTTCAACTCCCCCCTTACATGTTCACGTGGATGAGAACACTCCTGTCCACGTCCACATAAAAAAACTCCCGAAACCGTCAGCAGCCAGCAGCCAG
Seq A exon
GTAGGAGCATGGCAGCGGGGCGAGGTCATGGCTGCAGATCCTGTCTCCCAGCCCAGTCTCCTCCCACTGCTGACTCCAAAGGTTTGGGAGACACATTTTTTTCTGGAGGTCAGTTGCCTGGTTAGAAGGTAGGCCTTTGGTTCCCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGCAGTAGCAGTAACATTACTCAGAAGAGGCCCCTCTGCAAAGGTGGCATATGCCACCTGAGTGACACTGGGCAGCTGGGCCTGGAGATGACTCTAGTTTTGTCCCCACAG
Seq C2 exon
AAATCTCATAAGCGCGGAATGAAAGGGGACACCGTGAATGTACGGCGGAGTGTCCGGGTGAAAACCAAGGTACCTTGGATGCCCCCTGGAAAATCATCTGCCCGGCATGTGGGATGCAAGTGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026790-Odf2:NM_001113213:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.898 A=NA C2=0.938
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109388f6171A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000049272, ENSMUSP00000109384, ENSMUSP00000109385, ENSMUSP00000109386, ENSMUSP00000109387, ENSMUSP00000109388, ENSMUSP00000117628, ENSMUSP00000121207
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:128460667-128460941 
ALTERNATIVE
HsaINT0117821
(ODF2)
Human
(hg19)
chr9:131222946-131223220 
LOW PSI
HsaINT0117821
(ODF2)
Rat
(rn6)
chr3:8452849-8454001 
ALTERNATIVE
RnoINT0105051
(Odf2)
Cow
(bosTau6)
chr11:99050256-99051433 
ALTERNATIVE
BtaINT0105361
(ODF2)
Chicken
(galGal4)
chr17:5112737-5114161 
ALTERNATIVE
GgaINT0124402
(ODF2)
Chicken
(galGal3)
chr17:5738572-5739921 
ALTERNATIVE
GgaINT0124402
(ODF2)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TTTTTGTGTTGCCCTCCCCTG

				
R: 
CTCCCACTTGCATCCCACATG

				
Band lengths: 
272-561

			

		

	





	
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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