Special

MmuINT0108820 @ mm9

Intron Retention

Gene
ENSMUSG00000044220 | Nkx2-3
Description
NK2 transcription factor related, locus 3 (Drosophila) [Source:MGI Symbol;Acc:MGI:97348]
Coordinates
chr19:43686815-43690382:+
Coord C1 exon
chr19:43686815-43687339
Coord A exon
chr19:43687340-43688795
Coord C2 exon
chr19:43688796-43690382
Length
1456 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATGTCTTGCTTCTCCCTTAGAAA
3' ss Score
8.95
Exon sequences
Seq C1 exon
CAAAACCCAGACCCCCAGGTCCCGGCCAATGGAGGGGATTTAGACTGGACCGCGTCTGTCAAAAGCTCGACTCCGCACCACCGCGGAGTCCAGAAGAAGAGCTGGAGCCACCGCACTCCCTCCCCGCCCCCGCCGGGATTTATTGAGTATTTGGACTGGACAATTAAGTGGCCCTGATGATGTTACCAAGCCCGGTCACCTCCACCCCTTTCTCAGTCAAAGACATTTTGAATCTGGAGCAGCAGCGGCACTTCCACGGAGCTCACTTGCAGGCGGAATTGGAGCAGCACTTCCACTCGGCACCCTGCATGCTGGCCACGGCTGAAGGGACGCAGTTTTCCGATGCAGGGGAGGAGGACGAGGAAGAAGAGGGAGAGAAACTGTCCTATTTGAACTCACTAGCTGCTGCCGAGGGCCATGGAGATTCGGGTCTCTGTCCTCAGAGCTATGTCCATACAGTTCTCCGAGACGCTTGCAGCGGGCCCAAGGAACAAGAAGAGGAGGTTGTGAGCGAACGGAGCCAAA
Seq A exon
GTGAGTAGAGGGGGAAGGAAACGCGTCCGCACACCTGGGGCAATGGCTCAGCGCCTATAAACCCACAAACCGTGCCTGCATGGCCACCCGCCCCTTTCACATTCGGCTAGGGTCATGCCTATGCCAGGTTCAAGGACAGCTCTGCAAAGCACAGGTACCTGAGATGGTGCTGGGGCGGGGATAAAAGAGAAAGAGAGAACAGCTCTTGCCCGGAGCAGGGACCCGGAGCAGTCCCCGAGGGAAGGAAAAGTGATTATTGCAATCCTGGTTCCTTGAGTAATGAGTGACGGGGGCCCAGAGCCTGGGTCGTAACTTGTCCGTTGTGTGTGTGTTCTCTCGCACACCCATCTTCTCAAAAAAAAAGGGGGGGGTCAGTTTTCTGCCATTTTTCTGTCTTTCTTCTAACGTGAGGTGAATTCAGCGAGGCCAGGGCAGTCACCCCGGCTGTCCCGAAAAGGCAGTGCAAGAATGTTGTGTTTGGGCCATCCTTTCGGGCAAGACTTTGAGAGACACCAGCTTACTTCGGAGCTTGCAGTTCTTACGTTCGAACTGCAAGGAGGAGAGGTGGTGGCCAATGTGTGGGAGCTCGATCCATATCAGATGACGGCAGCAAGTCACACCCAGGAGGTGAAGGCCTCTGAAAAAAAATATCGTAATGCTCGCTTTGTTTCTTATACTGCAGGCGGAGTGGAATGGTTAAAGTTCCTGAATTAGTTCTGAGTGGGATTCTGGCCATTCAGCAGATCAGAGGTGGGGCAGGCAGGAGAATCAGATAATTGAATAAGCCCATAAGGAAATGTCTGAAAGGGAAACAGGATCAAATAATCTCTTCTCCGAGTGGAGATTTGATCTGGCTGAGACCAAAATCTTTTCTCTAACAATTCTCCAGGCCTAACACAGACATGAAACTGTCTAAATCGGTCCATCCAACTGTTTTTCCTCTGTAAGGTAACATACAGATACTGTCACAGACGCGTTCTCAGTAGTTTTGAAAATTAAAAAAAAAATCAATTCTTGAGCTGCACATACGCCTTTCACTTAGATATTTCCAAAGAGAAACAATTTTTGCAATCAACCCATGCATCCAGGCCTCCAGTCCCCAATACCAACTCGTTCCACACCTTCAGGGGAGTGGAAGGCAAACGAGTTTGCAGATACGGGGTCCTGTTCCGCGGTCGCCTGAAAATTGTTATTAGCCCCTGGACCGGCACATTTAATCTATTTTCTCGCTGATGCTCAAATTTAATAAATGCGAGCTAATTACTCTCACCGAATACGCCTTCTCCCGGTGGAGGTGCTCCGCCTGACGCGGGGGGGATGGGGGGGGCGGAATTGGGCTCCAGAAACTATGAACTTTCCCCAAAACTAGCATTTACTACGGGAGTGTTTTGTGCCTCTGGGGCGCAGGGGTGGTATCCTGAGAACTAGAAAGGCTAATGTCTTGCTTCTCCCTTAG
Seq C2 exon
AAAGCTGTCAGTTGAAGAAGTCTCTGGAAGCGGCGGGAGACTGTAAGACGAGCGAGGACGGCGAGAGGCCGAAGCCGCGGAGCCGCCGGAAGCCCCGGGTGCTCTTCTCGCAAGCTCAGGTCTTTGAGCTGGAGCGCAGGTTCAAGCAGCAGCGGTACCTGTCGGCGCCCGAGCGCGAGCATCTCGCCAGCAGCCTGAAGCTCACGTCCACGCAGGTGAAAATCTGGTTCCAGAATCGCAGGTACAAGTGCAAGAGACAGCGGCAGGATAAGTCCCTGGAGCTGGGGACGCACGCGCCGCCGCCGCCACCCCGCCGCGTGGCAGTGCCGGTGCTCGTGCGGGACGGCAAGCCGTGCGTCACGCCCAGCGCACAAACCTACGGCTCGCCCTACGGCGTGGGCGCCGGCGCCTACTCCTACAACAGCTTCCCCGCCTACGGCTACGGGAACTCGGCCGCCGCAGCCGCTGCAGCCGCCGCAGCCGCAGCAGCAGCGGCGGCTTACAGCGGCAGCTACGGCTGCGCCTATCCGACCGGTGGCGGCGGTGGTGGTGGCGGCACGGCCTCCGCGGCGACCACCGCCATGCAACCCGCCTGCAGCGCCACCGGCGGTGGATCCTTTGTGAACGTGAGCAACCTGGGAGGCTTCGGCAGCGGCGGCGGCGCGCAACCCTTGCATCAAGGTGCTGCAGCCGGGTCCGCGTGCACGCAGGGGACTTTGCAGGGCATCAGGGCTTGGTAAGGCCTGGGCGGGACACGCGGCGGGCGTCCTACTGCACGCTGGGCACCGCGGGAATGAGACACGAGAAAGGACAGACCCAAGGGCCAGGTCCCCTCGTTAAAATAAAAATACAGACGTATCGCTCCTTCCAAGGGGCCATGGTCGCAGCTCACTCCAGGCCTGGGGCATGGAACTCAGCGGAGAAAGGATGCCCTGGTCCAGTCCTCAAGACTGAGACAGAAACACCGGCCAGGCGCCAGGGAAGAGGTGGCCTCCCATCCTGACTCTGCGGAGAGTGCGGGAGGCTGGGACTCCGGCTGTCGCTTGCTCTCCGGAGGAGGAGGAGGGCTTTTCTCTTCCTGCTTTCCCTTGGCCTTCTCCGAGTGTGGTCCGGGAACCGGACCGAACAAGGGGGGAGGGGGGAGAAAGAAAGAAAGAAAGAAAAAGAACAATTTAAAGAAAAAGAAAGGTAGTTGGAGAGAGAACGTGAAGGAGAGGAAAATGGGGTACTAGCTTGAGAAATTCCACCGATCCGCAGCCCCTTTTGCTTGCCCGGAGCGCCACAACGAAGTGGATTTTTCCTTTTCCAACTGTGTCCCTTCCAAGACAGACTCCGCCCGGATCCCTAGATTGTCAGGGGACTGTTCTTGGAGACCACCACCGCAGTGAGATCGAAAGTTGGGGGAAGGGAGGCAGCTGAGCAAATCCAAGACCTGTCCGCCCAACCTAGGTTGTCGCCAGGTTGGTTTCCTTTCTGTTTTGTATTCTGTATTCCGCACATTATCTCTCTATAACTATATCCACACGCCGTGTACACAGCCGCTGTCACACACTACAGGAGTCAATAAAGAAGGTGCAATATTTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000044220-Nkx2-3:NM_008699:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.538 A=NA C2=0.242
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=23.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000126983





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000050933
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:99533490-99534984 
LOW PSI
HsaINT0113817
(NKX2-3)
Human
(hg19)
chr10:101293247-101294741 
LOW PSI
HsaINT0113817
(NKX2-3)
Rat
(rn6)
chr1:263367616-263369097 
ALTERNATIVE
RnoINT0101367
(Nkx2-3)
Cow
(bosTau6)
chr26:20400743-20402224 
ALTERNATIVE
BtaINT0102046
(NKX2-3)
Chicken
(galGal4)
chr22:1163597-1163649 
Chicken
(galGal3)
chr13:9142328-9143014 
LOW PSI
GgaINT0017983
(F1NC42_CHICK)
Zebrafish
(danRer10)
chr13:40284333-40285485 
ALTERNATIVE
DreINT0104767
(nkx2.3)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCATACAGTTCTCCGAGACGC

				
R: 
ACTTATCCTGCCGCTGTCTCT

				
Band lengths: 
347-1803

			

		

	





	
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"