Special

MmuINT0009483 @ mm9

Intron Retention

Gene
ENSMUSG00000030607 | Acan
Description
aggrecan [Source:MGI Symbol;Acc:MGI:99602]
Coordinates
chr7:86227074-86229736:+
Coord C1 exon
chr7:86227074-86227150
Coord A exon
chr7:86227151-86229352
Coord C2 exon
chr7:86229353-86229736
Length
2202 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CTCCCGCCTTTCTTTCACAGACC
3' ss Score
12.06
Exon sequences
Seq C1 exon
CTGAACTATGACCACTTTACTCTTGGTCTTTGTGACTCTGAGGGTCATCGCTGCAGTGATCTCAGAAGAAGTTCCAG
Seq A exon
GTGAGAACAGTTCTATGCATGACTCCTTTATTCAGTGGGTACTGGGTTCCGAATACAGGGTACAAGTTCGTTTTGGGATACTGTCCCTGCTGCCCCTTCTTTTGGCCTTTTCTTGGCCCTTTCTAGATGTAGTAGGAACACACACACACACACACACACACACACACACACACACACACACACACACTGAATGCCCTCAGCAAGGAGAGTTGCTCAGCCTCCTTCACAGAACCCTTGGGGAATCTCATGCAGAACTACTCCACAGTGAATGGGGTAGAGAGAAGACATGGGGAGCCAGAGGGGGGCATGGATGGGACCACCAAAGGGGAGACGAGAACCTGAGGAACAACGTTGAAAAGACTGGTTTCAACGTTCTAGAAGTGAGGGCACAGCCCTGGTGTGAGCTCCCCAACCCTGACTTAAGGGACATGTGAAGGACTTGGCACACAGTGTGGGGATCTGGAACTCAAGGGCTGAACAGTCTGTGAGACCTCCCAAACAGTGGGAGGGGAGGGGATAAGAGAAGGCTTGCTCATGGTGGCAGGGACAAGAGGAGGCTTGGGCACCCTCCCTCCCCACAACCCACTGTATGCCAATGCAAAACTCCAGGACTTCAGGGTCATGGAAAAAAAAACTTTCCGTGGTGAAATGGAAAGACACTCAGTATTTTATTCACTCACATACTGGCCTGATTCACAGCTTTTGAATATGTAGATGTGGTTATCTGGACCTCCAATGATGCTCAGAGATCTATGAATACCCAGACCCTAGCCATCACCTTGGGAGATGTGTCCATATTAGCAAAACAGTCCACTAGGGTTGGCTGAGAGCTTTGACAACCACCAAGTTGGATTCAACAGTGGTCTCTGGCTATCCCCTGAGGACCACTATTACAGAGCCAGGCTGTGGACACCGGCGTCAGGGCTGGGCAGCAGATGGAGGTGTTTGTGGAGAGATGGTGGAATCTGTCCAGACATCAAAAGGTCCAGGCTGGACTCCAGACATTCCTGGCCCCCCTATCCTTACCCTGCTATGTCTCTACCACCCACAACTATTCTAAACATTTTTATTTCAACCTGTAGCATCCCTTGAAAGGGAGGGTTCTAAAATTTTAAGACCTGCCATGAAAGGTGCTGTATAGAAGACTGTTTCTCTCTCTCCCTTTCCAACAGAATTTAGGAAACACTATGTCTTCTCTATTGACACACTCCATAATTTTTATGTCGTCTAATCCTACCCAACCCCATATTTCTGACTCTACAGGCCAAAAAATAAATGCCTGACCTCCTATTCTCCCCAGTCTTCTCGTCCTTGACTTTAAAAGTCTTGCCCTTCTACAAGTTCCAGTTAAAGCCCAAAGCAGACCTCCCAGAATGGGATATATCTATCTTGAAGTCCTATGTCTCAAGTTTAAAGGCTGTGGAGAATTTTGTAATTCTAATAATTATTATGCCCAATGTGTAGGACAGTATCTGTCTCTATGAGAAAAATATCTCAGGAAAACAGCTTGTCTGTGGCAAGGCAGAAATGTCATGCCTGAAGGTACAGTGGAGGGGAGAGGTTCACCTCACAGTAGCCTGGAAACAGATGTGGGTGGGGGAGAGAAAGAGAGAGAGGGAGAGAGAGAAACAGACAAACACAGACAGACAGACAGACAGACAGACAGACAGAGATAAAGAGGCAGAAAGACACAGAGAGACAGAGACAGAATGACAGAGACAGGGAGTCAGGGAGACTGGGGGCGGGGCTGCGAACAAGATATCCCTTCCAAAGTTGCATCTGCATTGATTTATCTCCCCCCATGAGGCAGCACATCCCCATCCAGTCACCTCTCCTAACACAGCCATACCTTCCACACACGAACCTTTTATGGAGAACTCATGATATCCAAAATAAATACTTCAATATATTTTTCTAAAATCTGTGAATCAAGCATATCACTACTCTAAGAATAAGGGTCCTGTGTATCTAGGGGTTGGCATCCCCTCTGGGTGTCTAAGGTTTGAGGTCTCTCTCATGCTCTTCTGGAAGTCTTTGTTTGGCTCCGGATTTTTGTCTTAGGGTGGGGAGACACCTGGAGAATCCCCAGGTTCCCACATGGTAGGCTGGATAAGGGCCTCTTGGGTGGCTGCATTTCCACGCCTGGAAGGAGGGTCTCTATGATTCCTAACACATGTCTGTCCTCCCGCCTTTCTTTCACAG
Seq C2 exon
ACCATGACAACTCACTGAGCGTGAGCATCCCTCAACCATCCCCATTGAAGGTCCTCCTAGGGTCTTCCCTCACCATCCCCTGCTACTTCATCGACCCCATGCATCCTGTGACCACTGCCCCCTCCACTGCCCCCCTCACCCCAAGAATCAAGTGGAGCCGTGTTTCCAAGGAAAAGGAGGTGGTACTGCTGGTGGCCACTGAAGGACAGGTTCGAGTCAACAGCATCTACCAAGACAAGGTGTCGCTCCCCAACTATCCAGCCATCCCCAGCGATGCTACCTTGGAGATCCAGAACCTTCGCTCCAATGACTCTGGGATCTACCGCTGTGAAGTGATGCACGGCATCGAGGACAGCGAAGCCACCCTGGAGGTCATAGTGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030607-Acan:NM_007424:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.023
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0768612=V-set=WD(100=94.6),PF0019312=Xlink=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000032835f2751A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000032835
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr15:88836277-88838662 
LOW PSI
HsaINT0002220
(ACAN)
Human
(hg19)
chr15:89379508-89381893 
LOW PSI
HsaINT0002220
(ACAN)
Rat
(rn6)
chr1:140792119-140794426 
LOW PSI
RnoINT0011752
(Acan)
Cow
(bosTau6)
chr21:20829181-20831450 
BtaINT0012514
(ACAN)
Chicken
(galGal4)
chr10:12564829-12565391 
LOW PSI
GgaINT0028817
(ACAN)
Chicken
(galGal3)
chr10:14759390-14759952 
LOW PSI
GgaINT0028817
(ACAN)
Zebrafish
(danRer10)
chr25:19122132-19122206 
LOW PSI
DreINT0024954
(acanb)
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"