Special

MmuINT0112700 @ mm10

Intron Retention

Gene
ENSMUSG00000026790 | Odf2
Description
outer dense fiber of sperm tails 2 [Source:MGI Symbol;Acc:MGI:1098824]
Coordinates
chr2:29914734-29915317:+
Coord C1 exon
chr2:29914734-29914919
Coord A exon
chr2:29914920-29915207
Coord C2 exon
chr2:29915208-29915317
Length
288 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
CTGCTGTCCTGTGTTCCCAGGAC
3' ss Score
10.1
Exon sequences
Seq C1 exon
AACTTAGAGCGCAGTGGGAACCAGCATAAGGCGGAAGTAGAGGCCATCATGGAGCAGCTAAAGGAACTGAAGCAGAAGGGAGACCGAGACAAAGAGACCCTAAAGAAGGCCATCCGAGCCCAGAAAGAGCGAGCCGAGAAGAGTGAGGAGTATGCCGAGCAGCTGCATGTGCAACTGGCCGACAAG
Seq A exon
GTAACAGCTGGGCCCTGCCCAGCTTCTCCCTGAGGAGGAGCCTCGTTATGTAGGGGGAGCTGGAAGGGGTGTGGCTGGGGAAACGTTGGTGATGGAAAGGCTAAGACTATCCAGCACATCCTCTTGAAGGAAGGATCTGCCCGCAGGATGTGATGTGATATCGCATGCCTGGGCGCTTTCTGCACCATTCCTAGTATCTATCCTCTCACCTGGAGAGAGGCAGCAGAGGGAGACAGTGTGATCTGAGTGTTGATACCAGGCTGACAAGCTGCTGTCCTGTGTTCCCAG
Seq C2 exon
GACCTTTATGTTGCTGAAGCTTTATCTACTCTGGAGTCTTGGAGGAGCCGTTACAACCAGGTTGTGAAGGACAAAGGAGATCTTGAGTTGGAGATTATCGTCCTAAATGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026790:ENSMUST00000046571:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.549 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF115593=ADIP=PU(5.0=16.2),PF0003816=Filament=PU(0.7=2.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109394





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028128, ENSMUSP00000049272, ENSMUSP00000109384, ENSMUSP00000109385, ENSMUSP00000109386, ENSMUSP00000109388, ENSMUSP00000109391, ENSMUSP00000109392, ENSMUSP00000109393, ENSMUSP00000109396, ENSMUSP00000139390
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr9:128484887-128485364 
Human
(hg19)
chr9:131247166-131247643 
ALTERNATIVE
HsaINT0117812
(ODF2)
Rat
(rn6)
chr3:8476520-8476835 
LOW PSI
RnoINT0105046
(Odf2)
Cow
(bosTau6)
chr11:99064508-99065023 
LOW PSI
BtaINT0105350
(ODF2)
Chicken
(galGal4)
chr17:5121231-5121977 
LOW PSI
GgaINT1020331
(ODF2)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr21:13040627-13042466 
ALTERNATIVE
DreINT0108112
(odf2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AACTTAGAGCGCAGTGGGAAC

				
R: 
TTAGGACGATAATCTCCAACTCAAGA

				
Band lengths: 
292-580

			

		

	





	
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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