Special

MmuINT1035870 @ mm10

Intron Retention

Gene
ENSMUSG00000042446 | Zmym4
Description
zinc finger, MYM-type 4 [Source:MGI Symbol;Acc:MGI:1915035]
Coordinates
chr4:126865497-126868965:-
Coord C1 exon
chr4:126868717-126868965
Coord A exon
chr4:126865627-126868716
Coord C2 exon
chr4:126865497-126865626
Length
3090 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
TTTTTTTTTCCTACCTCAAGATA
3' ss Score
7.43
Exon sequences
Seq C1 exon
GTTACATGTTCTCCCGCATTGAAGAAGAGCATCTGTGGGAGTGCAAACAGCTGGGCGCTTACTCGCCCATTGTCCTGTTAAACACCCTCCTTTTTTTCAATACCAAATACTTCCAACTAAGGAATGTTACTGAGCACTTGAAGCTGTCCTTTGCCCACGTGATGCGCCGGACCAGGACTCTGAAGTACAGCACCAAGATGACGTACCTGAGGTTCTTCCCGCCTTTACAGAAGCCGGAGTCAGAGCCAG
Seq A exon
GTGTGCTGTTGGTAGATGAGGTTTCTGTTTGAAGTGCAAAGATGGTTATCACTGAAGGTCATGGAGGGCACACTGAAACTTCTTTAACGTTTTAATATTTTTCTGTTTCTGAGTATGTTACAAGCTCTCAAAATAGGAGACTTTTTGGTTCATTTTAATTTTATTAACTTAAGTTAGAAATGCTGACTTAATTGTATAGTGCCGGGATGGCGAGATGGTTCAGAGGTTCAGAGCACTGTCTGCTCTTCCAGAGGTCCTGAGTTCAAATCCCAACAACCACATGGTAGCTCACAACCATCTGTAATGAGATCTGGTACCCTCTTATGGTGTGTAGGCATACGTGCAGACAGAACATTGTATATATAATAAATAAATAAAAATTTTTAAAAATATTGTGTAGTGTTTCCCCCTCCCCACCCCCCGATTTAGTTGGGTAGATTCCCAAATAATCTACATTTAAAACTTACCAGAGTATTTAAATCTGTAACCATGGTGATAAGCTCACTATTTCCAGCTATCAGTCAACAATTAACAGTTAAAAGAAACATGCTTAGCTTTAATCTATTGGACTTTTTGTTTTTTACAGGAGCATCTTGATTTGGTTAGCATCTTTTAGTCAGTTCTAAAATTCTGAAATAACTCAGAAGCCGACCTAAAGTAGGCCGTTATTAGTACTGTAGACCTGGGTCAGTAGTAGCAGCTTCAGTAAGTGGATTATGGTCATGTATTTCAGAAAGAGACTAAATGACTCCATGTCTTCAGTATCTGAAAAATCCTGCTATTCTAGAACTAAAAATTAAACTTTTGGTTTATGTTTGGTTTTGTTTGTTTGTTTGTTTGTTTTGTTTTTTTCCAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCGCCTGCTTCCCAAGTGCTGGGATTAAAGGCGTGCGCCACCACCACCCAGCGGTTTTGGTTTTTTTAAAACCTTACTATATAGTAGCTCAGGCTATCCTTGACCTCAGTCCTCTTAAGTCAGCCTTTCTGAGAGTTGCAGTCACAGCTCTATGCCATCATGCTCATATGGCATATATACACACAAAGACGCTCTTAATTTACATCAATATTAAGTTCTCCCAATCGTTATTACTTTTAAGAATAAATTACATAGTGGAAATGTGAGGACTTAAATTTTCTAAATCTAAACTCTGAATAGTTGGTATGTGTGCACCATACATATTAGCTTGTTTTCACTTGCTCCTTTAGCTTTAGAAATACTACCATCATCTTGCCCTTTCCCCTGGTGTCTGTCTCTGGCCATAGCGTGGTACTTATGTGATCCACTTCATAGTTTTGTTTTGGTTCTTGCTTTTTGAGACAGCTCACTCTGTATCCCAGGCTGCCCTAGAATTCAGTTGTATTTCCCAAACTAGCCTCAGTCATGAAGCCACACATCCTCCTTGGCTTTCTGAGGGCCGGGGTTGCAGACCTGGTTCTCCCCCTGAAGGTTTGCTTTATCCTCTTAGATAATATTAGCAAAGGAGTGAGAGGCAGTCAGTTATTTCCACATTTGATTGAGTACTTGACAATGTTGATAAAAAGTTCAACTTGTTTTTAAGTAACTTGTAAGGCATTTCTATATAGGAAACTGGAGTTATTTTAAAGCAATAATACTAATAGCTGGAGAAAAAGAGTCCTAAACCATTTGTTTAAGAGTGACTTTAACAATGGGCTTTGGAGGTACCTGGCAGGCTCAGTGTTTTAGAGGACCTCTATTCCCAGCACCCATATGCAGCTTAACAGCTGCTTGGAACTCTGCTTCCAGTGGGATCTGATGCCTTCTTCTGGCCTCTCTGGCACTGCATGAAGTGGTGCACAGACATACATCAAGGAAAACACCCACAGGCATAAAATAAAAACAAAGACTTCATTTTAAAAAATGGAATGAGGCTATGGCTCAGTGGATGACAGTGCTTAAAATGCTTGCAGCCTAGATCAAGATCCCCAGCTCCATCTGGCAGTGGTGGGGCACACCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTTGAGGCCAGCCTGGTCTACAGAGTGAGTTCCAGGACTACACCTGTCTCAAAAAAACAAAAAACAAACAAACAAACAAAAAAAGCGGGGGGTGGGGGTGGGAAGAAAAGATCCCTAGCTCCCTTGTAGCAGTGATAATGTATATCTCCTACCTCAGTACTGAGGGGCTGAGACGGGTGGATCCCTGAAGCTTGCAGGCCAACCAGTGCTAGGGTATGACTAAACTTCAGGTCAGTGAGAGAACCTGTCTCAAGAATAAAATGGCTCAGCAGGTAACAGTGATTGTTTCTTAACCCTGTAACCTAAATTTGATCTCTGGAACCCGTGTAAAACTCGGAAGGAAAGGGTTGGTGCTACAGAGTTGTTTCCTGACACGGCGTTGTGAATGAATGAGTGTGCATGTGTGCGCACACACACACACACACACACACACACACACACACACACGCATGCACAAACACAAGTGGCTTGGGCTCTTATGTCTACATACAGAGTTCTGTTTAGTTTGCTGAATGGGCAGATGAGACACAGCAGCCTCCTTCCTGTGCCTGCACCATGCACTGTCTAACAGCCCAGCCCCATAGAGTCCTGTCCTATCAAATGATAACTCAGATGCTGTTCCTTAGAATACGTAAGTACAGGGAACTTGAGCAAGAACTCAGTCTGTATTAGTACCCCAGAGGAGAGACGCATCCGTATAAATGCTTCGATTCATGAGCCCTATACCTAATCCATTCTACTGAGAAAGCCAACTCCAGATGAGGACATATCAGTGACAAATGGTCACTTTTGTCACACGACTCCTCGTTGCTTAACAGGAACATACATGTTACAGGACAAGCCTAGTGTTTAGCGTATAAACAAAACTCCTGGCACATAGTTGCTTAACAAATATTGTTGAATATTTGAAAGAGCAGGAGTTAGAGTCTGGCTGGGAAGCAGAGCTCATTAGGTAGGTTGACACTTATACAAATCTTTGATTTTTTTTTTCCTACCTCAAG
Seq C2 exon
ATAAGGTAACTATTGGCAAGAGGAAACGAAATGAAGACGACGAGGCCCCAGTGGGAGTGGAGATGGCAGAGAACACTGACAACCCGCTGAGGTGCCCGGTTCGGCTTTATGAGTTTTACCTGTCAAAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042446:ENSMUST00000106108:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.018 A=NA C2=0.534
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF120123=DUF3504=PU(47.7=98.8)

							
A:
NA

							
C2:
PF120123=DUF3504=FE(24.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000101714





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000120813
  



Associated events






Conservation


Human
(hg38)
chr1:35415715-35418442 
LOW PSI
HsaINT0186042
(ZMYM4)
Human
(hg19)
chr1:35881316-35884043 
LOW PSI
HsaINT0186042
(ZMYM4)
Rat
(rn6)
chr5:144881661-144884363 
LOW PSI
RnoINT0169176
(Zmym4)
Cow
(bosTau6)
chr3:110914123-110924684 
LOW PSI
BtaINT0164785
(ZMYM4)
Chicken
(galGal4)
chr23:4301634-4301956 
ALTERNATIVE
GgaINT0137504
([1])
Chicken
(galGal3)
chr23:4671234-4671556 
ALTERNATIVE
GgaINT0137504
([2])
Zebrafish
(danRer10)
chr19:40523630-40523709 
ALTERNATIVE
DreINT0181043
(zmym4)
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
  • Ribosome-engaged transcriptomes of neuronal types
  • 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"