Special

MmuINT0007041 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr6:47912524-47915298:+
Coord C1 exon
chr6:47912524-47912631
Coord A exon
chr6:47912632-47913320
Coord C2 exon
chr6:47913321-47915298
Length
689 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TTTGTGTCTCATCCCACCAGAAA
3' ss Score
9.41
Exon sequences
Seq C1 exon
AAACAGGCCAGCTGGAATCTGCCCCGAGTGTTCTTCCCTGGATCAAGCAAGAGGAAGAGGTATGTGAGAAGAGCCTGCAGGAGACAGCCAGTGCATCCCTGTGCTCAG
Seq A exon
GTGAGGCCCAGGGCGGGCTGCATTTCTGGGTCTCTGAACAATATGAAGCCTTCTGTATGAGTGTCTGGAAGTGGCATCGAGCAGGTTTCCTGTGGTGTCCTGTGGTCCCTGTGTGTGTTTGCTGTGGTCATCTTCCCACAGAGTTGCATGAAATTGTCATTTTGTCCCCAGTCTCCTGTCTTTGCTTTATGACCTATAGTTTGCATGGTACTAGGGCACTGTAAGGACTGACTGCATGGGACACAATCCCCCATCCCCAGGAGGGCTTTTCAGTTAGGAGAAAGATTACCAGAAATTAGCACTACAACATAAGAACAAGAAGCTATGTCTGAGCCAGAGAGCCCTTTGAGAATGGTAAAAATTGTGGACAGCATACACAGAAGACACATATACTCTGTGTTTACACTTCTGTAATCAGGTTGTTAGAGGCAGCCTATCTATCTCATTCATAGTCTTGATGGCACAGATCAGTGCTTGTCAGAGAGCAGCATCTGATAGTATAAATGAGAAGAAGCCTTAAGCGAGGCACATGGCTTAGCTTAAAGGACATCTGGGTGTCATGTAGATGACTCAGAGTGGGCCTCTGGCAGAAGACAGATGGGAGATAGGTTAGTGCAGAGCGAGCGTCAGTAACAGGCTCGAGTGAGCCTGTGGCCGAGATGACTCATGTTTGTGTCTCATCCCACCAG
Seq C2 exon
AAACATGGCTGGCTAACAAGAAAAGGACCCTGGAGGGGATGTCCATGGCACCAGAGCCATCCTGGGCAACTGAAGGAGGACCTGGCAAGGAAGATTTCGAGCAGGGAAGCTGTGTCGATCTGCTCCCTGTTTGCAGAGAGAGAGAGGCAGCTCCCCTCCCTCGAGGCTCTCAGAGTCAGCCTGTGCCAGCTGCTGAGGCCACTGAGGATGACCAGAACTTCAGTGTCAGAGAGCTCAGCACACAGCCTGAGTACTCCCACCATGGATCTCAGCCCTTTGCCAGTCTCCAGTGTCCCCAAAGTGCTACACAGCAGGTCACTCTCACCAGGAATCGCCGTGCACCCACAGCCCAGCGTGCCTACACCTGTGTCCAATGTGGCAAGAGCTTTGTCCACCAGTCAACACTTACCACACACTACCGCACACACACCGGGGAAAAGCCTTACAAATGTGCCGAGTGTGAGAAGCGGTTTGGCCGTCTGTCCACGTTGCTGGAGCATCAGCGTACCCACACTGGAGAGCGACCCTTCCCATGTGCACAGTGTGGTCGTCGTTTTGGGCGCCTGTCTACTCTAGTGGAACATAGGCGCACACACACGGGTGAGAAGCCATTTCCATGTACCCAGTGTGACAAACGTTTCACACGCCTGGCCAACCTGACAGTGCACCAGAGTGTGCACTCTGGCGAGCACGCCTTCCAGTGCACCCAGTGTGGCTCATGCTTCACGCACAAGCCCAGTTTCCTGCGACATCTGCGCAGCCACTCTCAGGAGAAGCGCTTTAGCTGTGGCCAGTGTGGCAAGAGCTTCACCTGTCGCTCCTGGCTGGTACGCCATCAGAGCAGTCATGCACACTTGGCATCCTCTGCTTATGTGGCCTGTGAGAGGAGCTCACCAAGTCATGTGTCACCTACAGGTCTGTTTAAAGGCGCAGCCAGGGGAAAGTTCTCCAGTGACCCTCCTGTCTCACCCATATCCAAGGACACTGTGGTCAGTCAGGACCACAAGGCATATGGTGGAGGTCAGCAGCTCAGCGACCATGGTCAGGAAAGTCTAGTGGGGTCTCTGCATAGTTGTCTGTCTGTAAAGATGGAGAATGCAGGGTAGCACCCAGGGAGCTCCATAACGAGGCCACTAGGACACGGGCCTCCTGGGTCCCCTCAAATCCAAGCCATCTGCTAGGCTTCCCAGGGCTAGGTTCTCCCATGGACTGCTGGTGCTAAGTGCCCCTGGGATTCCTGCTGCAGGGAAGTTTCATGAACACAGAAAAGGTGGCAGAAACAAGCAGTTCAACAGTCCCCTGAGATCTTGGTGGCTCCCATCACTGTCTTAGCAATGTAGGCAGCAACAAAAGGCCGGCTAGGAAGGTTGCAATTTTGAAGTTGTTCAGCTTCTGGTTGAGCAGCTCAAAACTCAAACTAGTTTCCAAGATTTCTCTAGGGCAGAGCTGGGGATGTGACTCAATAGAGTGTTTATCGAGCATGTGTGGATGGAGCCATGGTTAGATCCCCAGCATTAGATTAAACCGGCCTTGGTGGTACGTGTCTGTAATCCTTGTATTTGTGTAGAGGCAGGAGGTGCAGAAGTGTAAGGACATGCTTGGCTATATGAGCCCCTGTTTCAAGGAACCAAAACTTAGGAGTTCAAAGTCGGAGTTGTCAGATTGTCTCTCTCACCAGTGGCCACATGCTTATATAACAGCTTGTGTGTTTCCAGGGAGCCCCACTGGAGGGGATGGGACTGTTAGTGTCATTGTCACCACTTTGGAGGAATGTGGGAAAACAGGCCTGTGCTGTTTGCATCTGGGGCTGGGGTTACTGAAGGTCTGATTTCCCTTACTTTGTTGTTGTTCTTTTAAGACAGGGCTGCCCTGGAACTTGCTCTGTAGGCTGACCTTGAATTCACTGAAATCCACCCGCCTCTGCCCCATACTCACTTTAAAAACCTGTGAAAATAAAGGTATTTGTGAAGACGTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
-AI894139:NM_178898:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
NA

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000098989





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000050200, ENSMUSP00000098989f4544A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr7:148991108-148991470 
ALTERNATIVE
HsaINT0093515
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
chr2:495308-495385 
Chicken
(galGal3)
chr14:13135087-13135496 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AAACAGGCCAGCTGGAATCTG

				
R: 
GTGTGCTGAGCTCTCTGACAC

				
Band lengths: 
351-1040

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • 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"