Special

MmuINT0180539 @ mm9

Intron Retention

Gene
ENSMUSG00000040123 | Zmym5
Description
zinc finger, MYM-type 5 [Source:MGI Symbol;Acc:MGI:3041170]
Coordinates
chr14:57422986-57423700:-
Coord C1 exon
chr14:57423252-57423700
Coord A exon
chr14:57423077-57423251
Coord C2 exon
chr14:57422986-57423076
Length
175 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
CCTCATCTTTAACTTCACAGACC
3' ss Score
8.3
Exon sequences
Seq C1 exon
ATTCATCAGTGGGAAGACTAGTTGACTGTACATTGGACTTGGACATGGAAGCTCATCTCGCAGATATGGAATCATCTGGGGGTCCAACTAGTTCTTTAGCCGGTACATCTAGAAACACACATGTGGAAGATGATGATGTTGTATTTATTGAATCAGTACAGCCTCCAATTTGTGCTCCAGCAATACCTAATGAAAGAAACTTTGTATTTGCTTCCTCAAAACATGAAAATCCACCAGGAACTGATTCCACAATTTCCCCTTCTTGGAGAGATTTGACTTCTCAGAAGGGAAATCTATGTGAAACAATTGTAATTGATGATGAAGGGGACACAGACACAAATGGAGGGGAGGAGAAAAATCCTACCGACTTTATTGAATGGGGACCGAATGGAAATAAAAGTAGTACCAAAAATGTGGATTTCCCCATTGCCAGTCTATCAAGAAGCAAG
Seq A exon
GTAAATTCAGCAAGGGTTACTAATAGTATCATCTTTAGAAGCAGGTGTAAGCCCTAAAGGCTGGGTGAGAGAGGAATTTAATGATTGTACATCACCATAGAGTACCAACTTGGGAGATGTCACTAAAGGATTTAGTGCTAATATACAAACATACGCCTCATCTTTAACTTCACAG
Seq C2 exon
ACCAAGACTGCAGTAGGACCTTTTAATCCCGGTAGGATCGATGTCACGGATGCGTTTCAGAATGGAAGATTTGCAGTTCATCACAATCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040123-Zmym5:NM_144842:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.889 A=NA C2=0.871
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000106916





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000043625, ENSMUSP00000134057
  



Associated events






Conservation


Human
(hg38)
chr13:19851449-19851688 
ALTERNATIVE
HsaINT0186053
(ZMYM5)
Human
(hg19)
chr13:20425589-20425828 
ALTERNATIVE
HsaINT0186053
(ZMYM5)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr12:36503147-36503384 
BtaINT0164796
(ZMYM5)
Chicken
(galGal4)
chr1:178343708-178343971 
ALTERNATIVE
GgaINT0106886
([1])
Chicken
(galGal3)
chr1:183400589-183400857 
HIGH PSI
GgaINT0106886
([2])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCCACAATTTCCCCTTCTTGGA

				
R: 
TCCGTGACATCGATCCTACCG

				
Band lengths: 
254-429

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






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