Special

MmuINT0086108 @ mm9

Intron Retention

Gene
ENSMUSG00000054611 | Kdm2a
Description
lysine (K)-specific demethylase 2A [Source:MGI Symbol;Acc:MGI:1354736]
Coordinates
chr19:4345518-4348761:-
Coord C1 exon
chr19:4348646-4348761
Coord A exon
chr19:4345645-4348645
Coord C2 exon
chr19:4345518-4345644
Length
3001 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGC
5' ss Score
9.14
3' ss Seq
ATTATTCTTTTTCTGTGTAGGTT
3' ss Score
9.5
Exon sequences
Seq C1 exon
GTTGGATTCATGCTGTGTATACTCCTACAGACACATTAGTGTTTGGAGGCAATTTTTTGCATAGCTTCAACATCCCCATGCAATTAAAGATATACAGCATTGAAGATCGAACACGG
Seq A exon
GTAAGCAATGTAACAATTATATGTGTAGATGTTTCCCCATTTAAGGCAGATGTTAGATGAACATGGTTACACTTGCCTCTCATCTTTGAAGCACTCAGGAACAGGAAGATTGTGAGTTTAAGGGAAGCCTGGCCTATGTAGCAAGACCGTGTCTTAAAGAAAAAGATGGGTTTAATAAAGAGATTGATGGGATGAGATGGCTTAGCAGGTAAAGATACTGATGCTATTTGATAACAAAGTTCAGAATGAACGTGGTGTAAGGATAGAATTGACACTTGCTGGTTACCTTCTAATCTTCATATTCATGCATCTAGTGCTATCCTCCATCCCCAACAAATGACTTAAATGAATCAGATAGGGATTCGTGGATAATTTGTCACAATTTCAGATTGATTTTTTTTTTCATTAAAATGTTTTCACATATTGAGAATATAATAAAAAAATTTACTGGATGCTTGAGTCTTGTTTTGGGGGACTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTGGGTTTTTTTGAGACAGGGTTTCTTTGTGTAGCCCTGGTTGTCTTGGAACTCACTTTGTAGACCAAGCTGGCCTTGAACTCAGAAATCCGCCTGCCTCTGCCTCCCCGAGTGCTGGGATTAAAAGCGTGCGCCACCACACCCGGCTTGGGGGACTTTTAAGTCTGTGAAGCTGTTATCCCAATGTTTGTATAATCCCTTGAAACATGTTTTTCATTTTTATCCTGATGAATAATTTGTGGAATGGGAATGATCACTTCAAATTTCACACCTTTGAGGTTTTTTTTGTCTTTATTTTGATTACCAGTTCTCCCCTTCTTCACTTTCCCATTGTAAAAATACAAACATCTTTTTAAAACTAAATTTTATTTATTTTGTGCATGTATTTTGGGTTGCTATGCCAAGGCATATGAACAGAGCTTAGAAGACAACTTGCACAAGTCAGATTCTCTATTTTCACCATGTCCTAGAAATGTCATTGAGGCCATCCAGCTTGACAGCATGTGTCTTTAGCCATTGGTAACGGCCATCTTGTTGGGGCCTTCCCTCCCCATCATAAGTGTCAGTATTAATCAGCTCTCATAAAAATTGAGGTTTTTTTTAATATAATTTATACTTGACCTGAACTCAAGAACTGTCCCAAAAAGTATTAATATACTTCAAAGGCTAATCAAGAAGTGTGGTATATTGTACTTAGTTTAAGGAGGCCCAATATCTGTTAGTTCTTAGCTCTCTACTCTTTTGCCAGAAAGAAATTGGGTTTTAAATGAGAAAGAAGAAACTTCTGGTTAAAGCCATAATCATATAAGAGATCCAGATCTGGGTCTGGCCATATGCTTCATTGGTTGTATGCTTCTTGTCTAATGATAAAGTGATTTTGTCACTTCATAATAATACCCTGTGATCTGGTGAACGGTTTTGAAAAGGGACCCCCTTTCATTTTAAATTCATGAAGACAGATGGACATCATAGGGGGTGCTATTTGGCCTTAATAAGTAGCCATTCTAAAAGGAGGGTAATAGAAAGGAAGGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAGAGAAACAAAGAATTAATTCAATTCTTTTGTTTTTCAAGACAGGGTTTCTCTTGTATACAACAGCCCTGGCTGTCAGTGGCCGGTACTGGTCCTGTGCCGTTAATTCCAAAGGCAGATGCAGGCACATCTCTGAGTTTGAAGCTAGCTTGGTCTACTAGGACAGCCAAGGCTACGTGAAGCCTTGTTTGGAAAAAACTAAAACCAAAATAAACAAAAATAACCCTGTCTGGTCTTAAACTCACAGAGATCCACCTTCCTCTGGGTCCCTGGTGCTGGGATTAAAGGCATGAACCACACCTAGTTTAATTTTATTTTTTAAGACAGGGCTTATCTATGTAATTCTGGCTGCTCTGGAACTTAACAATGTAGATTAGACTGGCCTCAAACTCACAGAAATCTGTTTGTCTCTGCTCCCTGAGTGCTAGGAGTAAAGATAGTATCCAGAGGGCAGCAGATAATAGTTTAGAATGGCATCTGGCACTCATCTTCCTTGTTCATTGATATATGGTTTTGTTTTGTTTTTTTTAATTTATCTTATCCTTGGCAATGGTATATCTAAGGGGCATTCTTTATATTTCTGAAATAATTTTTAAGATGCTCTGAATTGAAAAGAGCGCTTATGCTACAAAGATAGTGACAGATAAAGCCACACAGACTAGTCTGGTTGGTGGGTATACTACAGAGGACAAGCCAGGGAAACTGAAGGTAGACGTTGGACAAAGGCTCAGTGTTGTAAACAGATGCAGCTTGAGAATGAGTTTAAAGTTATACTTTCATATAGAGATACAGTGATAGACTTACTGTAAGTGTAGCTCTATGTCCTGTCTGTCATTCATTAGATTCTTTGTCCTATGTTCTAAGATTCAGAAAAAAAACAAAGCCAAGGGTGGGATGCCTTCATACTTACTCTAAAGCAATATTTTTTCCCTTTTTGAGACAGGGTCTCTATGTAGTGCAAGCCTTGCCTTGACCTTGCTTCTTGTCTCAGCCTCTTTTTTTTTTTTTTTTTTTTTAAAGATTTATTTATTGATTATGTGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCTGGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCTCCAGCCCTTGTCTCAGCCTCTTGAGTGTTGGGATTGCAGTTACAAGCTACCATTCCTGTCTCTCAAAATTGACAGATTGACTTTTGAGTTCTTGCCTCAGATGCCAGCTTGAATTTATAGATTGACTAACAAAGAATTTTCCCTGGGTTAATCATTGCAGTTATAAATTGTCTTTCATATCTCTTCCCTTGAAAATTGTCATTGCCTCGTTTTCTCATTATTCTTTTTCTGTGTAG
Seq C2 exon
GTTCCAAATAAATTCCGTTACCCATTTTACTATGAAATGTGTTGGTATGTGTTGGAGCGCTATGTATACTGCATAACCAACCGATCCCACCTAACTAAGGATTTTCAGAAAGAATCCCTTAGCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054611-Kdm2a:NM_001001984:10
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
PF0237317=JmjC=PD(17.8=46.2)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047683





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000047683f4920A, ENSMUSP00000076698, ENSMUSP00000132929
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr11:67219404-67228036 
LOW PSI
HsaINT0084993
(KDM2A)
Human
(hg19)
chr11:66986875-66995507 
LOW PSI
HsaINT0084993
(KDM2A)
Rat
(rn6)
chr1:219594961-219597441 
ALTERNATIVE
RnoINT0078334
(Kdm2a)
Cow
(bosTau6)
chr29:45798857-45800536 
BtaINT0080145
(KDM2A)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chrUn_random:27626873-27627697 
ALTERNATIVE
GgaINT0002797
(KDM2A)
Zebrafish
(danRer10)
chr14:21465697-21465780 
LOW PSI
DreINT0085304
(kdm2ab)
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"