Special

MmuINT0050111 @ mm9

Intron Retention

Gene
ENSMUSG00000001510 | Dlx3
Description
distal-less homeobox 3 [Source:MGI Symbol;Acc:MGI:94903]
Coordinates
chr11:94983022-94986605:+
Coord C1 exon
chr11:94983022-94983212
Coord A exon
chr11:94983213-94984722
Coord C2 exon
chr11:94984723-94986605
Length
1510 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
TCCTTTCTTCTTCTGTCCAGGTG
3' ss Score
10.55
Exon sequences
Seq C1 exon
TGTCGGTGAAAGAGGAGCCGGAAGCCGAGGTTCGCATGGTGAACGGCAAGCCCAAAAAGGTCCGAAAGCCGCGAACGATCTACTCCAGCTATCAGCTGGCTGCCCTGCAGCGCCGTTTCCAGAAAGCCCAGTATCTGGCCTTGCCTGAGCGCGCCGAGCTAGCTGCACAGCTGGGCCTCACACAAACACAG
Seq A exon
GTTGGTACTGAACGCTCCAGGGTCTCAGGAGGGATCTGGGATTCCCTAGGTACCCCTGAGCCTGGCTGGCCCATGAAGCACCCCTTTGCCCTGCCCCTGCCCGGCAGCTCGCTGCAGGAACTCTTGCCTGCCCTTCCAGTGACTTGAGTCTCAGCTTTCAGAGAAAGGGTTACAGTAGGGAGCATAGAAGGGTGCAGTGTGCATCTTTGTGAACTTTTGCAACTGTGTATGGCGTGTCACAGAGAGATGCCCTCCCCTGTACCCCAGAACTCCCAGCTCCCAAGACCCTTAGCAACGTTTAGGACATAGGAGATCCTGTTGTCTCTCTCCCAGACTAAGTATGTACGTGTGGGGCATGCATGTGACATTCCAGGGAATATTCACATAAGGAATGAGGTCCTTTAAGGGTCATTTTGCAAACAGAAGGCCAGTATCTGTGATGAGACACTAGACAACGCACGCGTGTGTGAACACACACACAAAGTATGCTTGTATAGAAACATCATGATCCTGCTTCCCACCCAAATGCCTTTGCCAGTAGCCAAGTGGATAGGTTCTCCACTAAAAGGATGTAGAAATCAGAAAGTGGGAGTCCATCTCCACCCTCTTACCTGTCCCTAAACCCCAAGCAGCCTTGCTGCTCTTGGGGAGGAATGTCGGGTGCTGAGCTCCCTACAGGTGTTGACAGGCTGGCTTTGGTTGTGGCTGGGCTGTGTGGGGCCTGGTCCATCGGGAATCTGGGTCACCTGGTGAGGCGCTGAATCATTGTTTGTACCAGTCATGGAGTGGAGAGAAGCAGGGGAGGGGGAGATACCCCACGGGAAATTTAGGGACTCTGGAATTGTGGTTCACCTGCCCCTGAGTTCCTAGGTCACCCTTCATACCCAGCCAGAGTCTAGGAGCCCCTCCATGCCTGAGTGTTTATGTCGTGGGTGTTTATCTGGGTGTTATCTGCATGCGTTTATAGCTTTACTGTCTGGCGGCTGTGTGAGGCTGAGTGGGTATGTTGCCGAGGAAAGAGATACCTGTGTGGGTGTGTGTTTATCCCAGTGTATCGGTGAACTTTGGCTAAGGGCCTCTAACGTGGGCAAAATATCACAAACTGCCCGGTTCCCACTTAGGACGCCTTTGATTGAGCGCTTGCTGTATAACAGACCGTTTAAGTTGTCTTGTGTCTTAACTTTCTTGAGCCCAATATTGACCCTTTGAGACAAATGATGGTGTTAGCATGGCCTTCATTTTGCAGTGAGAGGAAGGTGAGGCCAGAGAGGTTAAGTAACCGGCGTAAGGTCGCACTTCAGCAGTGGCAGTAGAATATTCTAAGCCACAGAGTTTTTTCCCAACTGGAAAGAAAGATGCTAGCTTGGGTGTGAGGGCCCTGGGGTTTTGCCTCGTTTTTCCCCTCAGGAGGCTGGGTAATGCTTTGCCTTGTCCAGGCTGGGCTCCCCATGGGGTCTCCTTTAGGCATGCTGAGAGGCTGACGGGGCTGCTCCTTTCTTCTTCTGTCCAG
Seq C2 exon
GTGAAAATCTGGTTCCAGAACCGCCGCTCCAAGTTCAAAAAGCTCTATAAGAATGGGGAGGTGCCGCTGGAACACAGCCCCAACAACAGTGACTCCATGGCCTGCAACTCACCGCCGTCACCAGCACTCTGGGACACATCTTCCCATTCCACGCCAGCCCCTGCCCGCAATCCGCTGCCCCCACCGCTCCCATACAGTGCCTCCCCCAACTACCTGGACGACCCCACCAACTCCTGGTACCACACACAGAACCTCAGTGGACCCCACTTACAGCAGCAGCCTCCTCAGCCGGCTACCCTGCACCATGCCTCCCCTGGGCCCCCGCCTAACCCTGGGGCTGTGTACTGAGTACCCACCTGGCCTGCGCCCCTCCACGAAGGACCCCCTCCAGGACCAGGCAGAAGGTGCCCTGTCCTAGCGACACTCAGGAATCATTGAGGGGCACAGGGGGAAAGACTCCCTTCCCTCTCCCTTGTCCCTTCTTCCAGGGACCCAACAACCTCCAGATGACAAATGCATGGACCGAGGATGCCCCCCAATCTCCCTCCCCTTGCTTAGACTGGGGTGCCCTCCAGACGGCGAGGAGTTCTACCCCAGTGGGGACAGCACATGCTCTCTGCTCCAGGAACCCGGATTGCCTCTAGATGGCTCATCGCTTTCCAGCTTTTCAAACACAGTAGAGACCTCCAAAATGGGAGCCAGAGTGTTTGCAGGTCCACCTGTGCTGGGGCACCAGGCGCCACGGATTCCAGCACAGCCAGACCTAAAGCACCAAGGGGCAACTATACATTCTTGAGCCACTCTTTAAAAGACATTGGACATTACATCATGGCTGATCCTCAAGATGGGGGGGGGCTGACCTAGTCCCCACTGTTCTCCAGCCCTCATTAGGATTTGAGGGTCCAAACCAAAGAAAACTCCCCCAAATGAGGGAACCTTTGATATCCAGGGCTTCCAAGGGAAGACTTAAAGGAGCCATCCCTCCGCCCCTTCCCTGGGGAAAAGGATTGCCCATGTCCTTTTCCAAGGACCTGTTTCTCCTTCCATGTACAGGACTTTGCACAAGTCTGGTTTTAAAAGCTGTTGAAACCTAGGACGACAATGGGCATTGTTAACAGTTAGGACCAAATCCACTCCTCTCTGGGCGGGCAGCTCTGCTCTGCCCTGACCCTGCTCACCCCTTCGTTTTGTTTTGTTTTGTTTTTCTCCCAGTAAGTTTGCAGTCTTGGGGGACGGGCTCAAACCCCAACTCTCTACAGAGATAGACCAGGCAAGACACCCCCCACTCAGACACCCCCTTCGTGGCAGCTTTGGAAACAGGTTGTCCGTTCTGCTGCAGGATTCAAGTGAGGATCCAGGAGACAAGAGGAGGCCTAGAACTCAGTGCCTTAGGGGTAAGGCTGTCAGCTTGGACGGCTGGTACCAGTGCCTCTCCCTGGCCCAGGCATCCCCCAAAGCTAACTTTCTTCTGCCCCCTGATGTGGTAAAACATCGAAGAAAGGAGAGGTGACAGACTGTAGTTATATATATATAGTATGGTTTTTTTTTGTTGTTGTTGTTTCTTTTTTTTTTTTTTTTTTAAGAGCAACCAAGAGAAGCAGGTCCCCTCCCTTGTGGTTTCCTATTTATGTGACCCTGTTCCTCCTGGACCAATCTCCCTGTGTTGCAAGTCGAAAGAGGGATGTGGGCTCCTGCTGGATTTGGGTTTCGTGGGAAGTGAAGGAGTAAGAAGAGACAGACGTGGTGGGTCTCCGAGTCCCACCCCAAAGGGACAGGACTGAAGCCAGCTCCCACCCCTCCCCAGCCTTCTCATTTCTGCTTTCTTACTGGACCAGTCTTTATATATAATGTTAATAAAAATTAAAAAAAAAGAAGAAGAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001510-Dlx3:NM_010055:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.328 A=NA C2=0.878
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004624=Homeobox=PU(73.7=65.6)

							
A:
NA

							
C2:
PF0004624=Homeobox=PD(22.8=11.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000090443





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr17:49991865-49993399 
ALTERNATIVE
HsaINT0048740
(DLX3)
Human
(hg19)
chr17:48069229-48070763 
ALTERNATIVE
HsaINT0048740
(DLX3)
Rat
(rn6)
chr10:82939716-82941425 
LOW PSI
RnoINT0048273
(Dlx3)
Cow
(bosTau6)
chr19:37296729-37298307 
ALTERNATIVE
BtaINT0049786
(DLX3)
Chicken
(galGal4)
chr27:2990826-2992673 
LOW PSI
GgaINT1011409
(DLX3)
Chicken
(galGal3)
chr2:24416274-24416408 
LOW PSI
GgaINT0091523
(DLX5_CHICK)
Zebrafish
(danRer10)
chr12:5674826-5676039 
LOW PSI
DreINT0057762
(dlx3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGCCCAAAAAGGTCCGAAAGC

				
R: 
GTAGTTGGGGGAGGCACTGTA

				
Band lengths: 
356-1866

			

		

	





	
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"