Special

MmuINT0050107 @ mm9

Intron Retention

Gene
ENSMUSG00000041911 | Dlx1
Description
distal-less homeobox 1 [Source:MGI Symbol;Acc:MGI:94901]
Coordinates
chr2:71369014-71372037:+
Coord C1 exon
chr2:71369014-71369213
Coord A exon
chr2:71369214-71370320
Coord C2 exon
chr2:71370321-71372037
Length
1107 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCT
5' ss Score
8.16
3' ss Seq
GTTGTCGCCCGATCCTGCAGGTC
3' ss Score
8.89
Exon sequences
Seq C1 exon
GGGCGGACTCCGAGAAGAGTACGGTGGTGGAAGGCGGCGAGGTGCGCTTTAACGGCAAAGGGAAAAAGATCCGTAAACCCAGGACAATTTATTCCAGTTTGCAGTTGCAGGCTTTGAACCGGAGGTTCCAACAAACTCAGTACTTAGCTCTGCCTGAGAGGGCGGAGCTGGCGGCCTCCTTGGGACTCACACAGACGCAG
Seq A exon
GTACCTGGCCGCTCTGCCAAACAAGCCTCGGGAGCTGGGCTCCAGCCCCAGGCTTCACATTTTTTGTTCGCTGGGCCTCTGGTTCTAGGTGTCACAGTCCGCCCCCCAACCCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATCCACCTCTGACTTTCAGCGTCTCCTCTTCCTCCCTCAAACTGTTTGCCCTAGCTCGGACCCTACTCTCTGACCTGCAGGCTACCTGGTCTTCTGACCAGGCAGGGAACTGGAAGGATTTCCCCAGACGTTTTGTTTGGAGGTTCTGAGGTCACACGTGCCTGAACAACTGGAACAATAGAAGGGGGATTTAATCTTCCTTAGCCTTTAAAGTGTGCCACTAATCACTCAGGTCCTGGGCCTAAGCCTGCTTCCCCCACCTCCTTCTTCTTGCGAGGTGGCAGAGGCAGATCCTTCCCTCTGGCCCTTCACTTCCCAAGTTCCAGATCCTTAAGAAGAAGGGGGAAAAAAAAAGTGAGATTTTTCTTTTTTCTTCCTGCACTTCTCTAAGACCCTGGGCAGTTCCTAGGCATTCGAACGAGGGCCAGTCTGTCTCTAGATTTAGGTTGGAGCTGGGGAAAGCAAATACACCGTTGGGGGTGGGGGGGAGAATTGGTTTGAGTCTAAAGAGTTTAACAAAGACGCTGTAGCCTCTTCCAATAGTCCTACGAGGAAAGGAGATCTAATTTTAACAAATGCCCCCGCCCCCCACCCCGTTCCTATCTAGGTTTTAAATTTTCTTTATTGTTATTGCATTGTGCTGCATGAGGTCTTCCATAAACGTCGCCCAGGTGGCATCGTCTCATTTGCAAGCCAAGGCCTGGCTCTCCCCTGTTCTCTTATTCCCGGCTCTGATAGCTGCTCTAAAAGTTGCCAACAGCGGCTGGACCTGGGGCTCAATTTTCTGGCCTTTGGCCCTCATGGGGTGTGGGGAGGCGGTGGTCTCTGCCCCTCTGTCCTGGAGCTGTCAGCTTTCCCAAAGCAAGGAGGGCGGGTATTGTTGTCCACCCGTCCCTTTTCTCCTTGGACCTGGGTAGGCTCAATGGTCATAGTCCAGTCACGTTGTCGCCCGATCCTGCAG
Seq C2 exon
GTCAAGATATGGTTCCAGAACAAACGCTCCAAGTTCAAGAAGCTGATGAAGCAAGGCGGGGCAGCTCTGGAGGGCAGCGCGCTGGCGAACGGCAGAGCCTTGTCTGCCGGCTCCCCACCGGTACCACCCGGCTGGAATCCGAACTCCTCATCTGGGAAGGGCTCCGGCAGCAGCGCTGGCTCCTACGTCCCCAGCTATACATCATGGTATCCCTCAGCGCACCAAGAAGCTATGCAGCAGCCTCAACTGATGTGAGGTTATCAGTTCGCACTCACCCGCTTCCTGCCCGTCTCCCTTGGCCCGGCCCCTCCCGCCTCCAGGTTCATCCACCTTTTCGCACGCCCTGGGCCAGGAGGAGAAGAGCCCACGAGCGGGAGCAGGGGTGGGGGTGGGGAGCTAAAAATAAAAGAAAAAGGAACAGTGAAGGCAGAGGGCTTGCTGCTTCTCGGAGCCCCTAAAAGTCTGACTCAGCGACCTTTCAGCCCGAATCTGGTTTGGGCCACGGTGAACAGCAGAGTGGCCTCAAAGCGCAGGCACAGCCACTGGAGACAGCCAGTGCCACAAGATAACCCGCTGGACCGGACCAGACTCTCATCTTTGTGAGACTATCAGGAAAAACAAATACGTAGGAGGGGGAAATACGCTCTTTTTTGATTCTGTCCGTCTTTGTCTCCTTTTTGCACTGTCTGTGCGCCGAAGTCAAGGTCCTCGTGTGTCTGCTGTCCTCATTCTACGACCTCTCCAAAAAGTCACCAGGTCTGAGCCACACCGGTCTGCCGGCAGCCCATCCACCGAGTCCTGGACCACTTTTTCCTGAATGGTCTTCTTCCGGGCCCTGCTTGACCATCTATGTAGCTTGTTTGGGAAATGGGGGAAATCAGAGGGAGGGGGGTTAATTTATTGAAAAACAGACTTCATCTGACGCTGAGTGTTGGCCAATTCCAAATTCTCTGGGACATGGAGTGGGCGCTGTCCAAACATACTATTTACCTTAAACACACCAGAAGAGGGAACAAGGACAGGAAAGTGACTTTTAAGGTGCACAGTAACTTTTGTACTTGGCTGAAATGCAGAAAGGGAAAACAGGATGCCGTGCATTTTACATGCTCCAAATTATTAAAAATAACAACAAAAGAAAGACCGAAGTAAGGAAGTAAGATATGTAAAACCAATAGGATGTTGTCAAAAACGTTTGGACAAGAACACCTGGCCAAGAAGAAAAATCATACTTTGGGCAGCAAGAGAGAGGACCAATGAGCCTTGGAGAGAAAATAATTTGTCCTTTATGTAAAAGCACCCCAATTCCAGGTCGCTTTAAAGTAAGACACAAGCAGCGGCTCGACCACAGAACACAAGTCATCACCCTGAATGCACGGGCTCTGGTGCAAGATCTAATTGCTGTACATATTATTGTTGTTATTATTATTAATTATTATTATTATTGTTCTGTAAACATGTTGCACAAGCTTAGCCTCTTTCCGTTCTGTTGTGTGTGGCTGTAAACCCGATGCTTTGTGAAATGAGAATCTTGACATTTTACTTGTGAAATTTGGAAAATGTGACCGATTGAAATCCACCGTGTTTTGTGTTCTCTATGTCAAAGTTTAGTTTTATATTGAGAATGTTAACTTATTGCTTTGTATCTTGGGGGGGGGGCGAACTTTGTAAATAAGTTATAAAGTTTCTTTGAGACAGTAAAATTATGGTTTCAAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000041911-Dlx1:NM_010053:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.358 A=NA C2=0.512
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF043607=Serglycin=FE(39.8=100),PF0004624=Homeobox=PU(73.7=62.7)

							
A:
NA

							
C2:
PF043607=Serglycin=PD(44.6=87.1),PF0004624=Homeobox=PD(22.8=15.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000042413





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000134335, ENSMUSP00000134713
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr2:172086854-172088002 
ALTERNATIVE
HsaINT1011204
(DLX1)
Human
(hg19)
chr2:172951582-172952730 
HsaINT0048736
(DLX1)
Rat
(rn6)
chr3:58166647-58167826 
ALTERNATIVE
RnoINT0048269
(Dlx1)
Cow
(bosTau6)
chr2:24504179-24505345 
ALTERNATIVE
BtaINT0049782
(DLX1)
Chicken
(galGal4)
chr7:17338218-17338505 
LOW PSI
GgaINT0050664
(DLX1)
Chicken
(galGal3)
chr2:24408213-24409557 
ALTERNATIVE
GgaINT0099740
(F1NCZ0_CHICK)
Zebrafish
(danRer10)
chr9:3426913-3427978 
LOW PSI
DreINT0057758
(dlx2a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCCGAGAAGAGTACGGTGGT

				
R: 
GCCCTTCCCAGATGAGGAGTT

				
Band lengths: 
355-1462

			

		

	





	
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






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