Special

MmuINT0180454 @ mm9

Intron Retention

Gene
ENSMUSG00000043872 | Zmym1
Description
zinc finger, MYM domain containing 1 [Source:MGI Symbol;Acc:MGI:1915560]
Coordinates
chr4:126731452-126736275:-
Coord C1 exon
chr4:126736037-126736275
Coord A exon
chr4:126731627-126736036
Coord C2 exon
chr4:126731452-126731626
Length
4410 bp
Sequences
Splice sites
5' ss Seq
AAGGTATGG
5' ss Score
9.26
3' ss Seq
CATTTATTGTTTGTTTTTAGAGA
3' ss Score
8.92
Exon sequences
Seq C1 exon
CTCCACAGTTGACGGTCTTCTCTCCTCTCACCTGACTTGAATAAAATGCTTCCTGCAGTTCCAGGCACAGCTGTTCGACTCTCCTGTGCCAAATGTAAAAGAGTTTTTCAGGAGGGACAGACAGCTTTTCAGAGGAAAGGGTCTGCTGAGCTTTTCTGCTCAAGACTATGCATTGATGGGTACCCGTCACCTGCTGTGTCTCCAGCTCCTCTCAAAAGGATGTGCTTAAATTGCTCAAG
Seq A exon
GTATGGAAGTCTAAGCAAGGCCTTTTATTTTGCTGCATAGATCTTTGGTCAGAGTCTTGGTTATCATTTTATATGCTTTGGTCTCCTCTGAAGATGGAAACCATAGGTAAATGAAAGAACTTGCTCCTGCTTTCAGTTCCTTTAAGATCACTCAGAAGTAGTTTTGATTGTTGAAGGGTTTACACAGATTACATGGAAGGGTGGAGAAGCATTGAGACCCTCTTTGTTAGAGTTTTGTTAAATAAATGTGAGACTTGAGAGCATCGAATAGGATGGTTTCTATGCTCAGAACGTGGATAACGTGTGGGTTTTGGTTTGGGGTTGGTTTGTTTGGTTTTGGTTTTTTTGAGTCAGGGACTGACTCAAGATGGTTTTCTCATGTTTACTCCCAGTTCCCTTGGAGGGATTTTTTGTTTTGAGTTAGGGTCTCAAATGTATGTATGTAGCGAGGAGTTCACTGTGGAGAGCAGGTTGGAGTTGAACTCAGAGGTACTCCTGTCTCTGCCTTCCAAGTGCTGAGACTACAGGAGTGTTCACCACACTGGACTACCTACACTTACTAATAGGCTCGCAGACCTTTGCTTCGATCCTTATTTGGCTGGCACTTCCAATGCTGTCTTTTGTTTCAGGTTCTATTTTCTTGATCTCTACCTAACTTTATCTCTTCTTTTGTTTTCTTTTTTGGTTGGTTGGTTGGTTGGTTTTTTGTTTTTTGTTTTTGTTTTTTTTTTTTTCGAGACAGGGTTTTTCTGTGTAGCCCTGGCTGTCCTGAACTCACTTTGTAGACCAGGCTGGCCTCGGACTCAGAAATCCACCTACCTCTACCTCTGCCTCTCGGGTACTAGGATTAAAGGCGTGCACCACCACGCCCTGCTTCTTTTTTTTTTTTTTTTAAGTTTCTTTATATTATTTTATGTATGAGTGTTTTCTCTACTTGTATGTGTGTGTACTACATACATACGCTGTGCCTGCAGAGGGCCTTTGATCCCTTGAAACTGCCATTACAGGTAGTTGTGAGCCACTGTGTGCGTTGCTGGAAATTAAACACAGGTCCTCTGCAAGAGCAGTTGTGAGCACTGTCCCACCTTTCTGGCCCTCTCTCTTGTTTTCTCCAATTCTACAGTACTATACTATGTCCAGCTTTCCTTTTGGCTATAAGTTATAGGGCATTCTCTTCAGTCTACTTTCTCTTTCTGCAGAGTCCTAAACCTGGAAGGGACATTAGAGATCACCCAGTGCAGACCTTTTCTTTTGCTTTTGAAAAAACTGAGGCCCTGAGGAATTAAGGCACTGTGTTGCTATGGTTAGCATATACGCACTACATTTCTTCAGCCCCAGCTTTGCTACATGTCACAGGCGTTGAAAAGACTCATGCAAGAAAGAATTTGCTGTGTAAGTTGTTCTCATATGGAGTAACAATCAGGTATGATGAGCAGAAATAGACAACCTTGGCTTCCTCTGGAATAAATATATATATATATATATATATTGGTTCAAAGGTGATAGTCATCTTAAACTGGGAGAGGCCACCATTTATTCAGAATAACAACATGTTTCTATTGGCACTTTTTAGATCTATTTTATTTTGCATGTATGGGTATTTTGCCTGCATGTTTATATGTGTACCACATGCCTGCCTGGGGAAGTTGGAATAAGACGTTCTATTTTCTGGAGCTGGAGTTATGGATGGTTGTAAACCTCCATGTGGATGCTAGGAACTGGGCCCAGGTCCTCTGGAAGAGTAGCAGTGCTTTGAACCTCTGAGCCATCTCTGCAGCCCCTTCATTGAGACTTTTAAAAAGTTTCACATTCACAACATCTTTTGGTTTTCTCAGACAGGGTTTCTCTGTGTAGTTCTGGCTGTCCTGGGCTTTGCTCTACAGATCAGGCTGGCCTCAAACTCACAGAGATCCTCCTGCCTCTGCCTCTTGAGTGCTGGGATTAAACACATGCACCACTGCCTGGCTGAAGTCCCAAAATTTTAAGTAATTTTTAAGGCTTCTTTTTTTAGCAATGATTTAATATCTTTTTTTTTTCCTGGTACTGGTATTTTATTTCTTTGTGTACATTAGGCCATGAATTTGTATGGAATGGGCTCCAACAGCTCAGGCTCTTTTCCATTAGTCCTCACAAAGTGTGCTTCTCTGGGTGGCGCAGGCTGGCGCTTCAGCTGCACCCAGGTGCCCTTCTCTTTGGCTTCCTTTTTCTTCTGGTCGTTCTCCATCACCCGCTTCAGGAAGCTGTCCCTGCTCTTTGAGTGCTTGATGTGCTCAATCCGCACATTGATCCTCTTGGCCAGAATTTTGCCCTAAACCTGCTTGTTGACAGTGATGCCCACGGCATGCTGGGTGACATTGTAGACTCTTCGGTTTTGCCGTGGTAGCACTTATGGGGCATTCCTATTGATGTCTACAATATCACCCTTCTTGTAGATTCGCATGTATGTGGCCAAAGGAACAATGCCATGTTTCCTAAAAGGCCTAGAGAACATAATACCGGGTGCCTCTCCTCTTTCCCTTTGTGTTCGTCATTTTGGCGAATTACTGGAAGATGGCTGCGGCGGCCGCTGATTTAATATCTTTAACTAATACTTACTGTTTTTGTTTAATGAAGCAAAATGAAGGATAACTTTGAAGATGACATTTAAAATATTAGAAAGGGGAGACTTTTTATTGAAAACTATTAAGATATGTTTAAGAAACATTTCCACACTTTAGTATTGGAATTAAAAAGAAATTCCGAAGACAAATCATTCCGGTCCAAAATAGGCCGGTCCAGTAATGTTTAATTATTTTCAGGCAGCCGGGAGTGATGGCACAGGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGAGGATTTCTGAGTTCGAGGCTAGCCTGATTTACAGAGTGAGTTCCAGGACAGCCAGGGCTATACAGAAAAACCCTGTCTCGAAAAACCAAAAAAAAAAAAGAGAGAGAGAGAGAGAGAATGGAAGCTGTGGAACTTTCCATTGGGTCTTAACACCTTTACTAATTTTTTTTTTTTTTTTGGTTTTTCAAGACAGGGTTTCTCTTATACACTTATCTACCACAGAAAAATTTAAAAATCCATGACAGAGTTAGAACTAGAACGCATTTTAAAAATCAGCCACCAGTCTCATCAGAAAAGCTGTCAAGTGTTAAGAATTGATCAAGCTAGAGATGGCAGATACAGGTTTCCTAAAATTTCTCATTTTTCTTTAATGATTTATTTTTATGTACATTGGTGTTTTGCCTGCATCTTCGTCTGTGCGAAGGCGTGTGAGGGTGTCAGGTTGTGGCGGTTGAACCCAGGCCCTCTGGAAGAGCAGTCAGTGCTCTCAACAGCTGAGCCTTCTCTCCAGCCCCTTCTCACTCTTCCTTAAAAGTTTAGCAGTAAATACTGTGAGTTGTTTCCCTTGAAATGGCAGCCTTTATTTTCCTGAAAATAGCCCCTTCTAAACAATAGTTTAGCATATAGTCTCATAGAAATATAATTCATAAAAAAGATGGCTAAGGTATAACTCAGATTTTCTGTGTAGTCTGTCTAGAGACAGTGGTCCACCACTGATAAACATTTCAGTGCTTTATGCCCTGTCCCCTTTAATCCCTGTGCTGGTTAGTTTTTCTCAGCTTGACACGAAAGGTTCATCAGAAGGAAAGAACCTTGATTGAGAAAATGCCTCCATCATTGTCCTGTAGACAAGGACGTTTTCTTGATCCATGATTGATGTGGGAGGGCCCGCCTCACTGTGAGTGGTACCGCCCTTGGTCTGTGTTACCAAACTATGGTCAGCCAGCCAGGAAGCAGATTCCTCTGTGGTCTCAGTTCCTGCCCTTCCTTCAGTGGTAGATTATGACCTGGGAGTTGTGAGAGAACATAAACCCTTTCCTGGTCACGGTTAGTGGACCCGACCCACAGCAGTAGAAGCAAACTAGGACAGTCACGCAAATATTCAAGTTTATTTATTCTTTTACCTGCTTTTAGTCTGTGTATTAAGGGCATGCATTGCCCTTGGAGTCCAGAAGAGGGCACTGGATCCCCTGGAACAAGAATTACAGACAGTTGTGAGCTGCCATGTGGGTGCTAGAAATTGTCAAGGTTCAAATTAAAATAACTTGAAAATGTTGTTTTATTGACAGCATCCTTAATTTCTGGAACTAAATTGTTTTGTTTTGCAGTAAAAACATGGCAGAAGGATCCCAAGAGCTCACTGCCCAACCAGCATAGCCCATACAGTGATTCTTGCTCCCAATTCAGTGAGAAACTGGGTCAGGACAATACAGAGAGCAAGAGGGAAAAATGCCCAACGCCTTGCTCTGGGCCCCTCATGTGTACACACAGAAACTCATAAGTTACTTTATATATTTATTGTTCTATTAACAAGCATTTATTGTTTGTTTTTAG
Seq C2 exon
AGACATTTTAAGTCTAAAGGATATGAAGAGTGTCCAGTTGGAGGATAGTAGTTGTGACAAAAACTTTTGTAGCCAATCTTGTCTTACATCATATGAAGAAAAAAGAAAACCAGGTGTTACCATATATACTGATAGCAGTTTGCCCAAGTGCAGCATGTGTCAGAAGACATCTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043872-Zmym1:NM_026670:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF064679=zf-FCS=WD(100=63.1),PF060616=Baculo_ME53=PU(80.3=93.8)

							
A:
NA

							
C2:
PF064679=zf-FCS=PD(70.5=52.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000050669





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000050669f4464A, ENSMUSP00000101705, ENSMUSP00000101708, ENSMUSP00000120772
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:35097567-35104294 
ALTERNATIVE
HsaINT0185966
(ZMYM1)
Human
(hg19)
chr1:35563168-35569895 
ALTERNATIVE
HsaINT0185966
(ZMYM1)
Rat
(rn6)
chr5:145114536-145118571 
ALTERNATIVE
RnoINT0169106
(Zmym1)
Cow
(bosTau6)
chr3:111186878-111191756 
ALTERNATIVE
BtaINT0164713
(ZMYM1)
Chicken
(galGal4)
chr23:4316229-4318032 
ALTERNATIVE
GgaINT0137482
([1])
Chicken
(galGal3)
chr23:4685829-4687632 
LOW PSI
GgaINT0137482
([2])
Zebrafish
(danRer10)
chr17:14757030-14760401 
LOW PSI
DreINT0139566
(si:ch211-266o15.1)
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"