Special

MmuINT0112725 @ mm9

Intron Retention

Gene
ENSMUSG00000028256 | Odf2l
Description
outer dense fiber of sperm tails 2-like [Source:MGI Symbol;Acc:MGI:1098600]
Coordinates
chr3:144813924-144816879:+
Coord C1 exon
chr3:144813924-144814049
Coord A exon
chr3:144814050-144816347
Coord C2 exon
chr3:144816348-144816879
Length
2298 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TCTGTCTCTCTCTTCATTAGAAA
3' ss Score
8.78
Exon sequences
Seq C1 exon
GTTTCAGAAGAAGTAGAGAAAATGTCATCTAGAGAGAGGGCTTTACAAATTAAAATATTAGATCTGGAAGCTGAGCTTAGAAAGAAAAATGAAGAACAAAACCAACTTGTTGACAAGATGAACACT
Seq A exon
GTAAGTATTCGTGTGGTTTGTTATGAAAGTGAGCACTTATCATGCATTCCATGTACCTTAGTTACATCTGTAACGTACAGGTGGGGGCCGGTTAGGACTTTCATTTTACTGTGAATATTAGGAATGACAAATAATCAAAATGCAAAACAGAGTTTTCATCACCCTGCTCTGTGCAGCTTCAGTCACACAGCCTCCCAGCCTCACCGGGAGGATCCCTGCACAGTGTGTCTGTGGACAGCTGCGCAGTGAAGGCTCCACATAGAAGCTACTTAAGTTTTATTTATACTTTATTTACTTGAATTTTCATCTTTTAAAGATACATGCAAGCTTAGAAAGATATGATTTTAATATTCACCATTGTCCAGTCTGCGTGAGCGATGGATGCTTTGATTCATTCAGCTGTGAAATGAGAATACCAAGTTTAATTAGTCTCTTATATTTTTTCCTGAATATTCATGAAATAGTCTGTTGGCATAAGATACTCTTAAAGCTGGCATTAGTTGTGCTTAAATTACTTAATAACTCTCTACTTGATAATTACATAGAGAATGCTGGTATTTTCCTTTTCCACAAGTTAGAGACTCTGTTAAAACTCCTTTTTCATTTCCAGGTTGTAAATCTAAAGGGTTCAAAAATTAAATTATTTTGATGTATACTGTTTACTCTTATTGTCTAATAAGTTTGCTGGCTTTCTACATGAAAGCAAACAAACTCCTCCCCATCAGGATTCTAAAATGTGTGATGTTCTTTGTGCAGTTGAAGCCCCTGAAAAAATAAGCTGACATGAGATGGATTTCTCTGTTCTGTGTTTAGTACTTTGTGAAAACTGCTAATAAATAGGTTAAGATCTGATGTTAAACCTGATAATTGTTGTGCTAGTAAACCATCTAGAATTCTGAGCCTAATTTAGAGATAGCTAGAAATAAACGAATGTCTTGGGTGCCATCCAGGCACAGACAGTTCAGTGAGTAATTAGCATCCGCGTGCACATACATTAGCCAGACCGAGTTGTGAGTGCTCAGACAGCCTGAACCTAACCCTGGCCACATGACTATCTTCACAGTACATGGTGTACCCTGCAGGCTGTGAGGTGGGGGGGATGCACACTTTGAAGGGTGACCTCACAGCTTCACAATCGTGGCAACCCTACTGAAGTCACAGTGTCTTTCAGACCTTACTGTCCCGAAGCTCATTTGCGTTTACATTCTGCCCTGCAGTGAGTAATTGTGTAGCTACTGTTCTCTCCAAACGGATGCGCCATAAAGCCCAGCTCCATTCAGTCTAATATGTGAGCAGTCCAGTCTAGGGCTTTGCCACGCAATTCCCTGCATCTCCTGCTGGGCACTGCTCAGTTTTGGGTGCTGGTGTCTATAATACCTGCTATGAGAAACACAAAAGGAGTTCTTGGAGTGTGTGGGTTTTAGCTGGAAACCAGTCTTACCTAAAACATTTGCAGTAAGCAGCCTACCTAGAAATCTGTATACAACCAAAGGTCAAAATTTGTATGAGTTTACTAAATCTTCTCCCTCAATGGACATGAATTAAGTTCTTTTTAGTTTTTAAAATAGTTTAGGAGAAAATGTTCATGTTATCAAAGTTGAAATTCTAGCCGGGCGTGGTGGTGCACGCCTTAATCCCAGCACTCGGAAGGCGGAGGCACTCGGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACACAGGGAAACCCTGTCTCGAAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAACAAAAGAGCTGAAATTGCTGAAATTCTGTCAGTTCTTAAAACACTTTCCTTTCAAAACGTGTATTCTAATGGTAACAGATTATTAAACTTTGGGTCTAGTTAATTTTGGTGTTTGCTGTTTTTTATTTGCAAGGTTTTTTTTATAGTAGTGTTTATAAAATAAAGTTTAAGACAGTGAAGGTCTTATGGGATAAAACATGATATTTTGGCAGAAAAAAATGGCAAAAAAAGAGTAAGAAAAGATGTCATGATAACATAATAGGAACTAATCATGATACTCTAAATATCACATTATACCTAATAATTTAGGGCAAAGTTACAGTATGCAGTAAATTGTCAAAGTAGAATGATTAATCACATATTATTCAATCACTAAAGATACTGTTTTAAGGAAGATGATATGTAAAATTTCTTTGGGCAAAACTGATATGTCCAGCTATTGTGTATATACTTACAAATCTTCACCTTGCATACGAATGCCATATTGATTCTCTGTCTCTCTCTTCATTAG
Seq C2 exon
AAAACCCAGCACCAGGCTATCTGCTTGAAGGAAATACAGCACAGCCTTGAGAAGTCGGAGACTCGGAATGAGAGCATTAAGAATTACTTGCAGTTTCTTCAAATTTCCTATGTAACGATGTTTAGATAAATTGTTGATTTTCTCTGATTGTTATGCTTTGTAATTTATAGGTTAGCAGTATTAGAATTTCTATGTGAAGATACTTGAAACATAATTTATTATCTAATTGAACTTTAAGGAATAGTAGCTCTTACTATTCTTTTGTGGTAGATAATTTGCATTGAAGTCTAGTTTAATTCTTTTTAAAAATATATTAATTTTTAAAATATTTTTCACCATATATGCAAAAATCAGAATTATTCTTATGAACCATTGAAGTAAATTTGTAACAAATCTAGACCGATTATGAGCCAAATACATAGATTTAAATAATGTATTTACTTTAAATAATGTATTTACTTGTTTTATATTATAATGCTATACCAATAAAATATTCAGAAATTTAATTTTAATAACAGTATAAGTTTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028256-Odf2l:NM_001162538:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.381 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF059116=DUF869=PD(12.4=68.8)

							
A:
NA

							
C2:
PF059116=DUF869=PD(13.3=76.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096140





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000029920, ENSMUSP00000096140f2303A, ENSMUSP00000096141, ENSMUSP00000101798
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:86352209-86352858 
ALTERNATIVE
HsaINT0117841
(ODF2L)
Human
(hg19)
chr1:86814562-86818541 
ALTERNATIVE
HsaINT0117841
(ODF2L)
Rat
(rn6)
chr2:251030226-251032388 
LOW PSI
RnoINT0105065
(Odf2l)
Cow
(bosTau6)
chr3:57854550-57856797 
ALTERNATIVE
BtaINT0105373
(ODF2L)
Chicken
(galGal4)
chr8:14950264-14951320 
LOW PSI
GgaINT0038678
(ODF2L)
Chicken
(galGal3)
chr8:16718675-16719731 
LOW PSI
GgaINT0038678
(ODF2L)
Zebrafish
(danRer10)
No conservation detected
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"