Special

MmuINT0011520 @ mm9

Intron Retention

Gene
ENSMUSG00000036040 | Adamtsl2
Description
ADAMTS-like 2 [Source:MGI Symbol;Acc:MGI:1925044]
Coordinates
chr2:26950923-26954223:+
Coord C1 exon
chr2:26950923-26951292
Coord A exon
chr2:26951293-26954125
Coord C2 exon
chr2:26954126-26954223
Length
2833 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TCTGTTTGACCGTGTTTCAGGAC
3' ss Score
9.14
Exon sequences
Seq C1 exon
ACCACAATGCCACTGGGAGAGCTTTCTCCGCGGACAAGGATGACCGGGAGATCAGTGCCCATTTCACCTCCCACGAGCTTCTCTCAGCCAACACCATCTCCGACCAGCTCTTGGGCACAGGCTCTGAATCAGAAGAGTTCTCACTCAATGAGACCATGAATAGCATCTTTGCCCAGGGTGCTCCCAGAAGCTCCCCAGCTGAGAGCCTCTATGTGGATTATGAGGAGAATGAGGGGCCTGCTGCCTACTTGATCAATGGGTCTTACCTGGAGCTGAGCAGTGACAGGATCAACACCTCCTCTGAGGCCCCATTCCCCAACACCAGTGCCAGCCCCCCCAACTTGGCTGGGAACAGGACTCACAAGGCAAG
Seq A exon
GTAAGAGGCACTTCTCCTTGCCCTATCTTACTGCCCTATGGAGTAGGAGTCATTGTAGAGGGATCTAGCTAGAAGGGCCAGGAGCCTGGAGATAAGTGGGAAAGCACGGGTAAGTGAATCTGACATGAGGTTGTGAGTCTGGATTGTTACGTATCTTTCTAAAAGGTTGACAGTCCAAATGTCCCCAGATCTAAATGTCCTAAATGGGAACCATGTTGCTAACAGACTTCTGATGCTGGGATGGACTCAACGTTTTTTATGCATAGAGCAGGGAGTGCTCACAACTACCATGAGTGTTAGGCTCTTGGGAAGGAGCTGAGAAGGGACTAGCAGCCACATAGTCCAGAATCCCTAAGCCACATTCCAAAGCGTCCATCTGTTCTTTCCCTTGCCCCCTTAGCCCTGTGGGACAGACTGGATTCCTAGAGTCAAGTCATTAAAACAGGTTGTCAGCACTCAGAAAAGTGCAGCTCAGTGAGATGCCCAACCGACTGCCATCAAAGGATGCTGCTGGTGGGGACCAAAGATGGTCTGGGGAGATAATGGGCTGAGGGAGGCCATGGGGGAAACTACCAAGCCGAAATAGCCACATCTCCGAGTGTTGTCCAAACATAGGAAGTCAAGTCTGCTCCGGGAGCCGGTGAAATCAAAGGGACAGCCTAGAAAGGAAGGGCTATTTTCATCTTCTAGAGAGGCTTCAAACAATCCCGGGAGGGGCTGTCACCAGACACTTTGGGATCAGGCGTCTGGGATGCAAAGGCACACTCTGAAGCCTGGAGGGTGGTAGGAAGAGAATTTCTGGTTCATTTATAAACAAACAGTCATTTCAGAGCTCTGCTCTCTGGGGATTTCAGGAGCCTGTGTCCCGCCAGGCACTGGGCAAGAACCCAGAAAAGTGGCCACCGGTGTCTCAGAAACCATCACCGCTGAGGAAAGGGCTCTTCCATATTGGGGTGGTGATGGTTTCCAGGGTGTGGCACTTTTGGTGCACCTTCCAGCAAGAAAACCTGATAGGTACGCACTGTGATCTAAGCAGCACCCAGCACCCCACACGTGCCGGAGAGTGGGTGTAGACAGCCCCTCCAGAAATACCTTTAGAGCTTAAAATCCAAAGGGTTATTTTGAACCTGGCGGCTAGCTCTTGAGTCAGGGATGAGTCATGCAGGCTGTGGCTGAGAAGTGTGTAATTATATAAAGATGGAGGCTTCCACACCAAGCACATCTTCTCTCTTTTTGTTTTTTTGGGAGGAATTTAAGGCTGCTCAAGGCAGTGTCAGGGGCCCAGGCAGCTCCAGTGTTATCTGGGTCGAGCCTTAAAGGATAAACTCTTCTCCCCAGTTTTCTCCCCCTGAGGGGTTTGGCCCACCCTCAGTTGGTGCTGTGAGTGGGTCCCACTGGGAGCTCAGGGCTAGGATCTTTTGCTTTGAGACGCCCTTCCCCTCCCCTCAGTGTTGAAGCTTTGTTTATAAGCAGAGAAGAAGGCAGAGCTTTCCCTGCACAGAGCCTGGCTTAAGGACCAGTTTGAGGCCCAGGAGAGGTGGCCCAGGCCCTAGCCTCCCTCCTTTCCTGCCCCCACCCTCCCCTTGAGAATTCATGGAGTCACATCAGTAAACTCATGACTGAGGCTCCTGTGGGTAGATCATTTCCTGGGTTCTCAGAGCGTGACGTGCTATCAGGACAGCAGGGTAGTGTTCGTCTCCAGAGCACTCTCTCGGGAGACAAGAGCCAATCTGAGCCAAATGCAGGCGCAATTCTTACCCACTTGACTAACAGTCCTTACAGATGTCTCTACCATAGATTCACACTGAATGGCTTTTAGAATGTAATGGCCTATAACATCCACAGTTCTCGAGTGACTGTGGTCCCCAGGAAAGAGTCTGGTCCATTTAAGTCCTGTGAAAGGTGGTACTGCACCGCCCTTAGGTAGCCCCTTTTAGTTCCAAAGAAAGAAGAGCTGGGCTATGCAGCCCAAGGGAGCTGTGGTGATGGTGATGGTGATGGTGATAGTGATGGGCTGCCTCCTCAACTGCTCTTCTTGGCTCCCAGGGGTTATGAGACTCAGAGACTGTGTTCTTATTTGAGTGGCCAGGTCTTGAAGCAGATAACCTGGGTGGAGATAACAGTGCAGCAGCGGCTTCCTCCCCCTGCAGAGTCCCGCATAGCCTGCACAGAGGGTGTTGAGGCTGGTTCAAAGAAGCTAACAGTCCTAACAATACTTGGCTTCTGGCCAAGAACCAGAGCTGTTAGCTGGCCAGCCCCCAGCGTGCCTCTTCCCGTCAGCTGGCCTGTGCAGCCATCGTGGACCTGAGCTGCAATGCAGTGTGGGGACGAGGCCACTCTCCCTCCTGCAGCTGGGCTTTGTGAGTTTGAAATTTGGAAGCTGAGTGGCTGGTGTCCCCATTCATCAGAAACCCAACTGAGGGAGGCAGCTGGGGAAAATTCTGGAAGCGCTCAGGCCCTAAGGGCTTTCTGAGATTCCTTCTGGGGTGGGAAGAAGGAATCTGCTAGCGTGTGCGAGAAGACGGAGTGAGAAGCTGGTGGATGTTGAAAGAGCAGTTAGAACACTGGTGAGTTCCCCATTGCTCAGCGTTCCTCTGAAAGAACAGGGTGCCTCAATGCAGAGTCTCTAGTACCTGAAATGAGAAGTACCCACGTCTGCTCATGGCCAACATGTATGTCTCCTTTTCTGTTCCAAAGGGTGGAGCCCTGGTTTACATGGAGGGTACTTGCTGGAGCCCAGGAAAATGTGTCTTTAAGGGGAGTGTGTCTTAGAGGCAGACTAAGCCTATAAGCACCCAGCTTTCTCACCACGCTCTGTTTGACCGTGTTTCAG
Seq C2 exon
GACCAGACCCAAGGCACGCAAGCAAGGTGTGAGCCCAGCTGACATGTACCGGTGGAAGCTCTCATCCCATGAGCCCTGCAGTGCCACATGCACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036040-Adamtsl2:NM_029981:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.742 A=NA C2=0.265
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000088774





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:133555931-133561197 
LOW PSI
HsaINT1002809
(ADAMTSL2)
Human
(hg19)
chr9:136421053-136426319 
Rat
(rn6)
chr3:5641041-5644671 
ALTERNATIVE
RnoINT0013622
(Adamtsl2)
Cow
(bosTau6)
chr11:104491154-104495778 
LOW PSI
BtaINT0014340
(ADAMTSL2)
Chicken
(galGal4)
chr17:6980363-6984228 
ALTERNATIVE
GgaINT0126468
(ADAMTSL2)
Chicken
(galGal3)
chr17:7653457-7657321 
ALTERNATIVE
GgaINT0126468
([1])
Zebrafish
(danRer10)
chr5:65221925-65225391 
DreINT0026408
(adamtsl2)
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"