Special

MmuINT0011569 @ mm9

Intron Retention

Gene
ENSMUSG00000015850 | Adamtsl4
Description
ADAMTS-like 4 [Source:MGI Symbol;Acc:MGI:2389008]
Coordinates
chr3:95483511-95484118:-
Coord C1 exon
chr3:95483914-95484118
Coord A exon
chr3:95483688-95483913
Coord C2 exon
chr3:95483511-95483687
Length
226 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TCGGGTCTCTCATCCTTCAGTGC
3' ss Score
7.77
Exon sequences
Seq C1 exon
CTGGGAGGCTGGCGAGTGGACATCCTGCAGCCGATCCTGTGGCCCTGGCACCCAGCACCGCCAGCTACTCTGCAGACAGGAATTCGGAGGTGGTGGCTCCTCGGTACCTCCAGAGCGCTGTGGACATCTCCCCCGGCCCAACATCACCCAGCCTTGTCAGCTGCACCTCTGTGGCCACTGGGAGATTAGCTCCCCCTGGAGCCAG
Seq A exon
GTGAGGAGGACCCTTGAGAAGTAGGCTCCAAAGAATTTCCACCTTTTCTTCTTTGTCATCAGAAACTTTCCAAACAAGACCTCTATGGAACCTAGTATCAGACAGACACAACAGGATTGGCAGCCTGGAGGCCCTTGCTCAGCTCCCCCAGTCTGTGAAACCCTAGTTCTGTAGAAGCAAGGCTGGAAGATGGCTGACGCCCAGCCTCGGGTCTCTCATCCTTCAG
Seq C2 exon
TGCTCTGTGCGCTGTGGTCGTGGTCAGAGGAGCCGGCAAGTTCGGTGTGTTGGCAGTAATGGTGATGAGGTGGACAAGCAGGAGTGTGCTTCAGGGCCCCCGCCGCCCCCCAGCAGAGAGGCCTGTGACATGGGCCCCTGCACCACAGCCTGGTTCTACAGTGACTGGAGTTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015850-Adamtsl4:NM_144899:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.058 A=NA C2=0.198
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009014=TSP_1=WD(100=81.2),PF0009014=TSP_1=PU(12.7=10.1)

							
A:
NA

							
C2:
PF0009014=TSP_1=PD(83.6=78.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000015994





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000015994f480A, ENSMUSP00000113424
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:150558150-150558472 
ALTERNATIVE
HsaINT1002817
(ADAMTSL4)
Human
(hg19)
chr1:150530626-150530948 
Rat
(rn6)
chr2:197806834-197807062 
ALTERNATIVE
RnoINT0013671
(Adamtsl4)
Cow
(bosTau6)
chr3:20189422-20189729 
ALTERNATIVE
BtaINT0014388
(ADAMTSL4)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr16:1287409-1289325 
LOW PSI
DreINT0000461
(ADAMTSL4)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAGACAGGAATTCGGAGGTG

				
R: 
CCAGTCACTGTAGAACCAGGC

				
Band lengths: 
302-528

			

		

	





	
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






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