Special

MmuINT0125893 @ mm9

Intron Retention

Gene
ENSMUSG00000029913 | Prdm5
Description
PR domain containing 5 [Source:MGI Symbol;Acc:MGI:1918029]
Coordinates
chr6:65809351-65812988:+
Coord C1 exon
chr6:65809351-65809472
Coord A exon
chr6:65809473-65812908
Coord C2 exon
chr6:65812909-65812988
Length
3436 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
GTCTTTCATCCCTGTCCTAGGTG
3' ss Score
10.17
Exon sequences
Seq C1 exon
TTTTGAGCAGCACCGGAAGGCTTGCCGAGGGGAGGCCAGGTTTGTGTGCAAAGCCGACAGCTGCGGGAAGAGGCTGAAAAGCAAGGATGCCCTGCGAAGGCACCAGGAAAATGTCCACACCG
Seq A exon
GTGAGGAGACACTGCACAGTCCTTCCAAACTCGCCCCGTTCCCTAGGCCATGGGATCTGCTTCGAATTCTCTTTTGTGAGGAGGGGGCTGGCTTCCGTTGTGCGCCACACAGACACACATCTTACCCGTTTCCTAGTTGATTTCAGCAGCATTTATCATTTTCCCCATGTCTGAATTAATCATTACTGTAAACCAGGCTCACACTTAACTGTTCTTGCCTCTCAGGTATACTTTTCAATCATTTCACTGTTTTAGTCTATAAACTTGATATTTCACACACTGTTGAAATTGATCATTTGTAGGTATCCTTTGAAACTAGGAAGTGATGTACTTCTGCCTTCATATTTTTACAAGAATGTTCAGTGCCTTAAGTGCTTACATTTCTTCTGTACTGGAGAAAATTCCTAATTATCTTTTGCCTTGGAGTTGAAAATATTTGAAATTTGAGCAGATCATTTCCTTAAGCCCTTGTAATCCCTAGCTAAAGAATAAAGCAAATAAAAGATTTGCTTGTCACCTAGGATTTTTTTCCTTAATTCTTTCTTGCCTACCAATAAATATATTCTGGGTTGTGGTACCTTTTGCTCTGTGGGGCCTTTTCTCTTCTTTGCTGTCTGTTTGGTTAGAGAGTGTGAGACCTAAAGAAACTCTCCTGTCCTTCTGCACATGTCTTTTCTCATGAGTTTGCTTTTACTCTCCGCTTCTGGGAAGTGAACAGAAATGTGTCTTTGCATAGATAGGCAGGACACTCTTTTCTTCCGTCTTGGTTCATTCTCACAATTAGGTGAAGAGAGTGACTGATACCTGGCATCAGGACCTCTGTGGCCTGAAAATAACTGACTTCAGTAACACAGTGAGAGGTTACTTACCATGAGTGTGACTGCAGGCCTCCCTTCCTCACTGCCTGAGCCTGCACACTGTGAGCCATCCACAGTGCTCTGGGGGCACAAGGTGAAGCTTTTAAGCTAACCTTCAGGGGGTGCCAATCATCAAGACTTCCCAGCATTGTTTTGTGGCTTTCTTTGTGAAGAACATATGGCTGGTATATGGAAAATGACTTCCCCTGCTGAATTTAAAATATACTGGTGCCTTTCATATGATGGCAGAAGCAGGCATAACTTTTTGATAGATTTGCTTTCGTAGGTTTTTATTTTTTTTTAAATGCTGTTTTGGCTAAAATGCTGTTCTTAATTTTCTCCTTCTTTGTCTGCAACGTATTTTAATCAAACTTTTATGTCAGTTTTAAAGTCAACTTTGCTGAACTAAGTAAAAAGCCAGATGGATGCTACAACTCTGGAAACTTTTCCGTCCGCATCACTAGGCATATGGTCCTCCTGCTGTGCTTATAGTGTAGTTTTTGAGTCTTCTGGTAATTGGCCTTGGGTTGCTTACTGTTGCAGCTCTGGGGCATTCATGGTGATTTTGCAGGAAACAAGTCATACATGAAGAGTTTGTTTCATCATCATTATCCCATGTTGCAGGTTGGGATAAGATGTGAACGTTGCTGTATTTTAGCAAAGGTCTCTGTACACACCTCTCAGTTGGTTTGGCACGTGGTATCATTTTCTAATCCTTAGCCTGCTTATACTTCTTTTTTTTCTCCTTAAAGTAGGGATGATGGGGAGAATACTTCCTGTTAGAGCCAGGAGAGCACCACTAAGGTATGGCTGAGGACTCTCTGTATAGAACACAAGGTGTTTAAGGAGCTAGGAAACCAAGTTCCTTTTGTATTGATTGATGAGGAAGCATGTCCTGTTAGATGATATGACCAGTAGCAGGTAAAAGAAGGGAAGCTGAATATTTAAACTCAGGTCAGACATTTTTATGTAGATACAATAGGGGATGATGGATAGGTTTGTAGGTGAGTAGAGTTGTATGGCTTCCTTGACCGTTGCTTGCTTCTGTAACTGTTAGTATAATATTTTTGCTGTTGTTTGATTTGTTTTTCTGATCCTGATGATTTAACCCAGGGCCTCAAACCACCCCTGAACTTTATCAGAGTACTCCCAACTCCTGAGAGTTAAACACCATGCAAACCTGAGTATAGGAAGCCAAAATTCTATGGATTCTGTGGCTGCTAAGAAAAAGGTTGTGTTTATGAGAAATAACATTTCATAAGCTCTTTCTATATTGCTCTGCGTAAATCTAGTTTTCCAATTGTAAGATGAAAGAGATGTGAAGAAGAGATGGTAGGGATGGGAGATTGGTACTGAAGCAGAATCAGCAGTGAAATGAATGGTTGGAGATGTCAACTTCTTTCTCTCTTCTCCCATCCTTATGGGAAAACCAGGGGCTGGTCTCAACAGAGAACTATGCCAATCACAAATAATTGGAGTTAGAAAAATGGAATGTTGTTTTTCTCGGTGGTCTTTCTAGAGTTCATGTATAGACTGATGAACAAGTCCATGCAAGATGATGTCCATTTTGTTGTGTGAAGATGTTTCTCTTTTGAATCCCTAGTGTCACCACCAAACATATTTTCATGGCTGTGTAGTCGGTAGAGTGCTTTAAACAATTAAATGTACCTGCTCTTGCTGTGACTATCTTAGGATCTTGAAAACCAGAATGAAAATTCCTACCTTTCTTCTCCTAAATGTTTGTTTCCCTTTTATAAACATAGCTCTGCATCATGATCACACAACACTGCAGTATTACTTCTGCTTGTCAGGGTTTCCTTGTTGTTGAGGTTAGAGCAAGGATGGGCATGGGTTTCACCTAGTTTGGGGGAAGTGATGGGCACAGGGTGCTACATTATGTTAATATTTACTTTAGGAGCTTTCAAATATTTTTTAATTATAAAATATCATTTTGAGGAAATTTGTGCTGGTACAGATAATGCAGTTATGGCATCACATTTTGAAATTATTTTGAGTGTCTAATTACTGTGAAGTTTGAAATATGATATGAGTTTCTATTGTTACTGTAAAAGAAGATGAATTTTAGTTCTGGTTGGGTTTTCTAACAGTGTAGGTTGCCAGTATAATACATTATTGTGGTTGATTTTATGATTTTACATTATACTATGCATTAACAGTTATTTAGTAAGGTATGGGCTCAAATTCTACAGGAATTTAGTTCTGGAGGAATAGTCTGACTAACGATAGCAAGAAATCACTTGATGAAAGGTCAAGGAAATAGGGTAATCAAGTTATGAGTTAACATGGTCATTCTTTTCCCTATAAAAAGAACATTTGATTTACTTAAATTTTGTTCTGACTTTTTGTGGAAACTTTCTCTCTAGAGACTATTTTAACAGATGGAATAGAGAAAAGTTTATTTGATATATGTGGAAACTGATGAGCTGGGAACTCTCAAGTTTGAAAAGAAAGACTTGAATATAACCTCGTAGAATTCTCAATTACTACCATGAAATGGTGTGGAAGGGATCCTGGGTCAACCTCAGTTAATTTGTGATGGTCTTTCATCCCTGTCCTAG
Seq C2 exon
GTGATCCTAAGAGAAAACTCATATGCTCGGTGTGCAATAGAAAATGTACCTCAGTGTCAAGCCTGCAGGAGCACAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029913-Prdm5:NM_027547:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.214 A=NA C2=0.018
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF089965=zf-DNA_Pol=FE(41.4=100),PF097235=Zn-ribbon_8=PD(39.4=31.0),PF0009621=zf-C2H2=WD(100=61.9)

							
A:
NA

							
C2:
PF128742=zf-met=PU(87.0=74.1),PF144711=DUF4428=PU(38.0=70.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031976





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000031976f2652A
          









    
Other Skipping Isoforms:
ENSMUSP00000031976f2653A, ENSMUSP00000031976f2654A, ENSMUSP00000133423
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr4:120811450-120816452 
ALTERNATIVE
HsaINT0131465
(PRDM5)
Human
(hg19)
chr4:121732605-121737607 
ALTERNATIVE
HsaINT0131465
(PRDM5)
Rat
(rn6)
chr4:96736503-96739877 
ALTERNATIVE
RnoINT0117093
(Prdm5)
Cow
(bosTau6)
chr6:4608087-4613366 
LOW PSI
BtaINT0117257
(PRDM5)
Chicken
(galGal4)
chr4:53677708-53681448 
ALTERNATIVE
GgaINT0068811
(PRDM5)
Chicken
(galGal3)
chr4:55804013-55807753 
LOW PSI
GgaINT0068811
(PRDM5)
Zebrafish
(danRer10)
chr23:2007977-2010911 
ALTERNATIVE
DreINT0119313
(prdm5)
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






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