Special

MmuEX0036985 @ mm9

Exon Skipping

Gene
ENSMUSG00000029913 | Prdm5
Description
PR domain containing 5 [Source:MGI Symbol;Acc:MGI:1918029]
Coordinates
chr6:65781243-65819259:+
Coord C1 exon
chr6:65781243-65781365
Coord A exon
chr6:65809351-65809472
Coord C2 exon
chr6:65819175-65819259
Length
122 bp
Sequences
Splice sites
3' ss Seq
CCTTGCTGCTTGTCTTATAGTTT
3' ss Score
8.36
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
Exon sequences
Seq C1 exon
GTACGTGGGAGCAAGGGAGAAGTTCTGTATATTTTGGATGCTACCAACCCAAGACACTCCAACTGGCTTCGCTTTGTTCACGAGGCACCATCTCAGGAGCGGAAGAACCTGGCTGCCATTCAA
Seq A exon
TTTTGAGCAGCACCGGAAGGCTTGCCGAGGGGAGGCCAGGTTTGTGTGCAAAGCCGACAGCTGCGGGAAGAGGCTGAAAAGCAAGGATGCCCTGCGAAGGCACCAGGAAAATGTCCACACCG
Seq C2 exon
ATTCATGAGATATTTGATTGTCAAGAATGTATGAAAAAGTTTATTTCTGCTAATCAGCTGAAGCGTCACATGATTACCCACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029913_MULTIEX1-3/11=C1-5
Average complexity
C3
Mappability confidence:
100%=100=100%
Protein Impact





	

	
ORF disruption upon sequence exclusion





Show structural model

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.191 A=0.214 C2=0.023
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF156161=TerY-C=PU(20.3=36.6),PF042167=FdhE=PU(30.4=51.2),PF134651=zf-H2C2_2=PU(4.8=2.4),PF102764=zf-CHCC=PU(5.0=2.4),PF132481=zf-ribbon_3=PU(0.1=0.0)

							
A:
PF089965=zf-DNA_Pol=FE(41.4=100),PF097235=Zn-ribbon_8=PD(39.4=31.0),PF0009621=zf-C2H2=WD(100=61.9)

							
C2:
PF128742=zf-met=PD(4.3=3.4),PF144711=DUF4428=FE(56.0=100),PF134651=zf-H2C2_2=PU(38.5=34.5)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000031976





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031973





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000031976f2652A, ENSMUSP00000031976f2653A, ENSMUSP00000031976f2654A, ENSMUSP00000133423
          









    
Other Skipping Isoforms:
NA
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr4:120816453-120816574 
ALTERNATIVE
HsaEX0049961
(PRDM5)
Human
(hg19)
chr4:121737608-121737729 
ALTERNATIVE
HsaEX0049961
(PRDM5)
Rat
(rn6)
chr4:96736381-96736502 
ALTERNATIVE
RnoEX0069364
(Prdm5)
Cow
(bosTau6)
chr6:4607965-4608086 
HIGH PSI
BtaEX6029852
(PRDM5)
Chicken
(galGal4)
chr4:53677586-53677707 
HIGH PSI
GgaEX1045919
(PRDM5)
Chicken
(galGal3)
chr4:55803891-55804012 
HIGH PSI
GgaEX1045919
(PRDM5)
Zebrafish
(danRer10)
chr23:2010912-2011033 
HIGH PSI
DreEX6078716
(prdm5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGGGAGCAAGGGAGAAGTTCT

				
R: 
TGAGTGGGTAATCATGTGACGC

				
Band lengths: 
202-324

			

		

	





	
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
  • Neural differentiation time course
  • 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"