Special

MmuINT0125909 @ mm9

Intron Retention

Gene
ENSMUSG00000051977 | Prdm9
Description
PR domain containing 9 [Source:MGI Symbol;Acc:MGI:2384854]
Coordinates
chr17:15694265-15696036:-
Coord C1 exon
chr17:15695987-15696036
Coord A exon
chr17:15694422-15695986
Coord C2 exon
chr17:15694265-15694421
Length
1565 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
ATATGTGACTCTAATTAAAGGAA
3' ss Score
3.98
Exon sequences
Seq C1 exon
TCAGTCCTCCTTGGGTGCCTTTCCGGGTGAAGCACAGTAAACAGCAGAAG
Seq A exon
GTAAGTGCTTTCCAAATCCTACAGACAAGGAAACCTTCCTCATAGATCCAAACACAGGTAAGGAAAGGAGAAGGCTTAGAGTACCCTGGGAATTGCTACCTTCCCGGTCTCATCTACACAGTGTCTCTCAGCCTCCCGGTCATTTGAATTAATAAGAACATCACTCACTTGAGTGTTCCTACCTCAGTTTTTTTCTGCTATGTGAAAGTGAGAAATTCACTAATGTACTCTAAGGATAGTTTACAAATACAGAGGATTTTACTTTGAATGGCACACATAAAGGAGATATGATCCTCTCCTTCATAAAGACTCACTCTGATAAGAAACAGCAACTCTCGTCACTTAGAAGATTCAAGTTTAATAGCAAGGGATCCACAAATGAGACATGACTTAATCAGGCATGGTAGTGCTTGCCTGTAATTACATGAGAAGCAGAGTCCCAAGGAATACTGTGAGTTTGAGGCCAGCCTAGTCTACTTAAGGAGTTCCAGGTCTACCACAGGTATACAATGATATAATGAGTTTTGGAATGGGAAAAAGAAAAGGATGTAAGCGTTCATATAGGCAAATAATTTCCATAGAAATATCATCTGTCGGAAAGACTGAGAGAAGCTAGTAATCTCACACTAGTATTATATTCAGTTGTGGGTATTCTAAATAGAATTATTATGTCTGGGTGGTTGGAGAGAGGGCTCAGTGGTTAATAGCATTTCTTGTTCTTCCAAAGGTCCTGAGCTGTACAGTTCAAAACTACCCTTTAACTCCAACTCCAAGAGATTGAATGCCCTTGTCTTACTCTGACAGAACCTGTGCACCACCCCCTCACACACACAAATAGAAATGAAAATAAATCTTTTAAAAATGAACAATTAGCATGTATACAAACTTATGAGTGAAAAAATTATTGAATTTTTCTGGAAAATTAGTACAAGAATTAATCTAATTCCAGAGTCATCCTAAGCATTATGCTCAGATCTGTAGTTTGAGCACTTGAAAGGCTGAGGTAGGAGGAATCCTGTGAGTTTGAGGCCAGCCTCTATCATGAGACCCCCATCTCAAACAAGCAACCTAATTCTAGAATCAACTATTTCCAGAATGCCAATTTACAATTTTATCATTACTTCGTTAGTTGTAGAGGTACATTTCTGCCGCCATCTCTTCATTTTCTTCCCAGAGACACTGCTCTGCTCTCACTTCCCTTTACAGATGTGTTTTATCAACTTTGTTTTCTACATTTCTCATCTGATCAATATTTCCTACTTTACGGATATACCCTCTTTCTCTCTGTAAGCCCTATCTTCTTCATTGCAAACTTTGTTGACCTTCCAGCTAGCCTTCCCAAGTATCTACCTTCCTCAAGCCTGAAAGAAGCCTGAAGGGAGAAAGCCTAGCAGATGGCCTCTTGCCCTGGATTCATTTAAGTTCTTCCTTGTCTCTTCCTTATTCAGATACTCTACACATTAACTAAAGTCACAGGTGAAGTTTTATAAAAAGCCTTAAAGAACTACTTGAAATGCCTGTTTTTTTTTTTTTTTGTTTTTTTTAATATGTGACTCTAATTAAAG
Seq C2 exon
GAATCATCTAGAATGCCATTTAGTGGTGAATCTAATGTGAAGGAAGGGTCTGGAATAGAAAATTTGCTGAATACAAGTGGCTCAGAACACGTCCAGAAACCAGTGTCCTCCCTTGAAGAAGGAAATACCTCTGGACAGCACTCTGGGAAAAAACTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000051977-Prdm9:NM_144809:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.494 A=NA C2=0.970
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF095145=SSXRD=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000131871





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000131871f4794A
          









    
Other Skipping Isoforms:
ENSMUSP00000040727, ENSMUSP00000118454, ENSMUSP00000125785, ENSMUSP00000130976
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr5:23517931-23521022 
HsaINT0131493
(PRDM9)
Human
(hg19)
chr16:90132565-90132761 
HsaINT0131493
(PRDM9)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr1:45027173-45027738 
BtaINT0117276
(PRDM9)
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: 
AGTCCTCCTTGGGTGCCTTTC

				
R: 
TTTCCCAGAGTGCTGTCCAGA

				
Band lengths: 
198-1763

			

		

	





	
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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