Special

MmuINT0112701 @ mm9

Intron Retention

Gene
ENSMUSG00000026790 | Odf2
Description
outer dense fiber of sperm tails 2 [Source:MGI Symbol;Acc:MGI:1098824]
Coordinates
chr2:29770728-29773265:+
Coord C1 exon
chr2:29770728-29770837
Coord A exon
chr2:29770838-29773129
Coord C2 exon
chr2:29773130-29773265
Length
2292 bp
Sequences
Splice sites
5' ss Seq
TGAGTATGT
5' ss Score
4.43
3' ss Seq
CCTGTCTGCTGACCTTCCAGCCG
3' ss Score
7.65
Exon sequences
Seq C1 exon
GACCTTTATGTTGCTGAAGCTTTATCTACTCTGGAGTCTTGGAGGAGCCGTTACAACCAGGTTGTGAAGGACAAAGGAGATCTTGAGTTGGAGATTATCGTCCTAAATGA
Seq A exon
GTATGTCTTTGTGTTCAGAGAGAAGACTGAGTGAGGGGAGGGCTTGAGGGGTGTGGTACCCTGAGGAGGTCCCAATGCTCAGGAGGGCCTTGTGCTCTCCTTAGGTTGGAGTTGTAAACTGGGCTAAGGTGTAGGTGGCCCTGGCCCTTCCTCTGGGCTTCTACTTCATTTGCCTAGCATGTGAGAGGCCCTGGTCTCCATCCCCTAAACTGCAAACAACCATAAGGACGCTCAAGGGGAGAAGCTTCTCCACCACAGAGGCCCAAGGCTGGCCATGGCACACAGTTGTTATGCTTGTCCCAGTGCACTCTGCATTGCCTGCCCAGAGGCTTCCTGCCAACAGGTCAAAGTGAAGGCAGGCAGGCCGAGGCAGCCAGGGCTTCCAGGGTTGGGTGACTGACCTTGACCACTTTGCCACTGGTGAATGTCACTGACCACCTGCTGTCCTCAGCCACGGCTGTTTGTTCCTTCACTGTGAGAGTGTACATGGAACAACTCTCATCTGCCAGCCTGGGTGCCAGCTCTGGGATGCAGCTGGAGGAAGACAGGTGTATTACCCGTCCCGAGCTCCATGCCAGCTCTGGGGGCTACAGGATGCATGGGCTTCTTTCTTTGGCCAAGGAGATAGGCTACCAGGGAGCTTGCAAGCCTCCTTCCCGCTTAAGGAAAACTTCCCTGGAGGAAGTGTTCATGTTACATGCAAACCAGTTCACCATGCACAGCCTGAAAACCTGCCCTGTACTGGGTGCTGTTCTCAAGGGAGTGCTTAGTGGGCAAAGAGAGGAGAGGGAAGGGGTAGGAGGGTGCATGGAACAGATGAGGGTTAAGAAGTAACATCCTCACTCAGGAGGGCAGTCTGTACAGAGGCTCTCTATAAGCATCACCTGTCAACAAGAAAGCCTATGTCCAATGAGCTGAGGCAGCAAATAGGGCGTGGGACACTGGTAAGAAGAGAGGACTCTGGGAAATAGTGAGAGGCGCAAGAGATTCACCTGGAGATGGACATAAGCCAGCAGGTACCTGAAGTTAGGAGAGAATAAAGAGGAGATTCACCCTGGACTTGAGACATGAAGCTGAGGAGAGGTTACTAATGATGTAGAAGATAGAGACTGGTTTGAATATGTTAACTAAGTTAAGAGCTAGTCGGGGAGTGAGCCAGAGCTTATGGCCTAGGCATTTATTAATAAAGAGTGTCAGAGACATCATTTTCGGGGAGGGGTAGGAAAGAGGAGAAACTCATTTATATTTTACAGGAGTCTGAGAGGGCTTTAAAGGGTGGGTAACGTCGCCAGGTGAGGTGCTGCACACCGGCTCCGCCCAGTCAGTGCTTCACTCTGGGTTTGCTGAATCCTGAGTGAACCCTCTGAGAACACAGCTGGGGTCACAGCTCAGTGGAACACTTGGCTAGAATGTAGAAGCTCTGCTTTGTATCCCCTGAGCTGCAAAACCCCAAGTGATTATAATAATTTTAAAGCCTCCAAGCAGCCCAGCAATGGTGGCTTAACCTTAACTCTCAGCACTAGAGAGGCAGAGGCAGGTGGAGCTCTGAGTTTGAGGCCAGCTTGGTCTACCTAGCAAGTTTCAGGTCAGCAAGGACTACACAGAGAAACCTTGTCTCAAAAACAAAGAATAACACTCCCCCCAAACAAACCAAACCAAACCTAAAACCTAACTCAGCAAGCAAACAAAGCCCTCCTAGAGCACAGAGCGTGCACAGGTTGTGGTGGTGGTGGTTGAGGTGGAAGAGCACCTGAGCCTTGGAACTCCAGAGAGACCATGCACGGTGCATTGACCTCACTGGCAACCCTGCTGAGCGGCAGCAAGGAAGCGGGAGTGGGCAGGAAGCAGTTCCCCTTGGCTCCCTCATGTCACGTGAGCATAGTCGCTGATCAGATGTGCACACATAGGAACATGGCTGTGGGGACAAAAGCCACACGTGCCCAGTGCCTTGGGGTGAGGACTACCTGAGCAGCCCTTACTGAATGTATCCTAACACTGAGAGGGTGGGAGGCATGTCAGGTGGTGCTGAAGGCTGGGAGGGTGATGAGAATGGGCTCACTCTAGTCAGCCTGGCTAAATGGTAGACAGCGTCCAGAGAAGGTGTCAACTGGATCACTTTTTAAGAGACGTTACATGGAAATGGGCCACTGGTGTGGGACGGTGGCATGGCTTCGTGGTGAGGAGACTGGGGAACAGCTAGGCAGCATGCCCTGAGGTGAAAATGGCCTTTGGTGGGGTGGACTTCGTCCCTTAGCAAGATCCAGGAACTGATCCTGTCTGCTGACCTTCCAG
Seq C2 exon
CCGGGTGACAGATCTTGTAAACCAACAACAAAGCTTGGAGGAGAAGATGCGGGAAGACCGGGACAGCTTGGTAGAGAGGCTGCACCGGCAGACGGCTGAGTACTCTGCATTCAAGCTAGAGAACGAGAGGCTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026790-Odf2:NM_001113213:13
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=0.413
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF115593=ADIP=PU(13.0=45.9),PF0003816=Filament=PU(2.8=10.8)

							
A:
NA

							
C2:
PF115593=ADIP=FE(34.4=100),PF0003816=Filament=PU(30.2=91.3),PF121283=DUF3584=PU(12.3=41.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109394





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028128, ENSMUSP00000049272, ENSMUSP00000109384, ENSMUSP00000109385, ENSMUSP00000109386, ENSMUSP00000109387, ENSMUSP00000109388, ENSMUSP00000109388f6171A, ENSMUSP00000109391, ENSMUSP00000109392, ENSMUSP00000109393, ENSMUSP00000109395, ENSMUSP00000109396
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:131247754-131250168 
LOW PSI
HsaINT0117813
(ODF2)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:99065134-99066505 
LOW PSI
BtaINT0105351
(ODF2)
Chicken
(galGal4)
chr17:5122088-5122762 
ALTERNATIVE
GgaINT1020332
(ODF2)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr21:13042577-13043031 
ALTERNATIVE
DreINT0108113
(odf2a)
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"