Special

MmuINT0071351 @ mm9

Intron Retention

Gene
NA
Description
NA
Coordinates
chr9:105780880-105784409:-
Coord C1 exon
chr9:105783753-105784409
Coord A exon
chr9:105780971-105783752
Coord C2 exon
chr9:105780880-105780970
Length
2782 bp
Sequences
Splice sites
5' ss Seq
GACGTAAGT
5' ss Score
10.93
3' ss Seq
TAACTTTGTTCCCTCCGTAGGCG
3' ss Score
10.45
Exon sequences
Seq C1 exon
ACAAGTGTTTTCCAAACACCTGTGCAGAAGAGCCTTTCTTTCCTGAGAATTCCTACATGGATGTTGCATTCCTCTTAGACAATTCCAAAAACATCGCCAGCGATGACTTCCAAGCCGTGAAAGCGCTGGTGAGCTCAGTGATTGACAGCTTCCACATCACTTCAAACCCTTCAGCCTCAGAGTCTGGTGACAGGGTTGCTTTGCTGAGCTATTCTCCCTCAGAGAGCTCCAGAAGGAAGGGCAGGGTGAAGACAGAGTTTGCCTTTACAACCTACGACAACCAATCAATCATGAAGAACTACATCTACACTTCCCTTCAACAGCTCAATGGAGATGCTACTATTGGCCTTGCCCTACAGTGGGCCATGGAAGGTCTCTTCCTGGGAACCCCCAATCCAAGAAAACACAAGGTCATCATTGTGATTTCAGCTGGAGAAAACCATGAGGAGAAGGAATTTGTGAAGACGGTGGCTTTGAGGGCCAAATGTCAAGGCTATGTCGTATTTGTGATATCTCTGGGCTCCACACAAAGAGATGAGATGGAAGAATTAGCCAGCTACCCACTCGATCACCATCTGATACAGCTTGGGAGAATGTACAAGCCAGATCTGAATTATATTGTGAAATTTCTGAAGCCCTTTATATACTCGGTCAGAC
Seq A exon
GTAAGTCATTATTTGGTTATTTTCCTTTGGTAATAATATTGATGATCTAAGATCAATATCATGAGATCTATAACTAATCCAAATATACAAATTGGGTACTGACTTGGGGCAAAGGTGGGTGCATATCCTGAGTGCATCCTGCTTCTGCCTTGGGTATAGGATGGTGAGACTGTGCTATGGTAGAACATCTCTTGCCCAAATCTATGGAGTAAAAACATCAAAGTGGCTGGTGGTCTCCTGAACTGTGTTTTATCACCCAAAAGAAGTCCTAGCAGCTCTTAGAAAGTATGATGTAAGCATTTAAATGAGTTCATTTCCCAATCTTGTGGAGAGCTATGTGAGGGTGTGGTGTTGACCAATCATGTCTCATAGGGATGCTAAAAACCTGGAGGCAGCTCCTGTCCAGAAGGGCTTGGGTGGAGCCTGAGACCATTGGTCATAGGCGCCTGAGTAATGCCAGTGTTGTGGTTCACAGACCACACTTTAAGCGCCCTGGCTCCAGTCCAGCATGCTGTCACGTGTTACCCTTGGGATACAGGCCAGCCCACAAAGTGATCAGTGAGGTGCTAAGTTCAAAGACTGAGAGTAAGCACACTAGGAAGTTTTTGAAGAACTTGACAATGGTTGCTGGAGCATAAGAGTGCAGGGTCAGTGAACTCTGTGTCATCGGAAATGATAAAGGGTAACAGTGTTAGCCTGCTAAGGTTTAGAAATAGCACTGTGTCCTGTCCAGAAATGCCTGGAACAGTTTTCTGATTCTTACTACTTACAAGTGCTGTTAATGTCAAGTAGGTAAACCTAGGGACGCTATAATCACTCTACTGTTCACAGGATGGACATCCAGCCCTCTGAACAAAAAATAACCTAAGCCTGAAACGCCAAGAAGTTTGTTGAGGAACTGGTGTGTTATTCTGCCTAATACAGAATTAAATACCCAAGGCAATTATCTTATAAAAGGGAAAGGTTTATTTTTGGTCATGGTTGTGGAGTTTACTGTCCAGAGTCAGGAAGCCTGTGCTTTGAGCCTTTGGCATATCATGGCCAGAGTGTGAGGGAAAACACATTTGCTTCCTTCAGAAGCCAGGAAACAAGGCAGATGAGAAGGGGAGGGGACCCAAGGCTCTTCTAAGGGGCTACCCTGATGACCTAGGAACCTCACTTTAGGTCCTACCTCCTAAAGAGTAGGGAATCTCTCAGTAACCCTGCCCATGAGTTCAGGTCTAAACTCTTGGACTTCTGGGGGACATTTATCCAAACCATAGCACTGTCTTCTGGAAGATTCCAGAAAATGGAGCTGAGCCTGTTCTTTCTGGAATTCTTGCAGGTTTAGAATGAGGTTCAGCCCCCTGCTTCCCTAGTGTTGAAGGAATGTCCCCCACCCCATAGCAGGAAAGTGTCTCCCGTAATTCATACTCACTCGTTGAAGCCATTACCTGGGAATGTTAGATTATTGCCTTTAAACCTAACATGGACTCATTTGGATGCCATAAAAAGGAATTTAAATAAGTGCTTTCAAATACATTTTGATGCCAACTTTTCAGCTGGATTAGAGCATTTTATTTTATTTTATAGTAATTCTTTCAGGTGTACACCACCATGTTACTCTGGTGCATACATATGAAGAACAGATGTGTGGTAGACTTCCAGGCTATCCCCCAGACAACTTCTCATCTGAAAGAGACTCTTCCAAATGCTCAAAATTTAGAATGTTGATTTTTTGCCCCAGAGGCAGGGCTGTCTGTTGTTCCCCACACAGTATTGTCTTTTGTGCTCTCTAGATGGCTAACAATGTTGAAAGTTTTAAGAGACTCAGAATAACTCAGGTCTGCAGGGCTGGGGAAGTGGCTTTGCAATTGAGCAAAGCTGACGGACTTGGACCCCCCAACTGTCCCTGACTTCCTGAAGGAACGCACTTCATCTGTTGGAGTTAAATGACTGCTCTTGCATTTTCTGGTCCTTTGAGAACCTTTTCCCAAAGTGCAGGCTCCAGTTCTGGCATTTTTGTTTTTTCTGTTTAAAGCTGTGACATGATTCCTCCTTCTACCCATAGCCACTGTCAAAGGAACTAATCAGAGACACTCTCATTTTAGACAAATAGAAAATAAAAGTGTATCCTAGAACCAGAGAAATGAAACTGCAGAGATTCTTTGAGATGCTTTTGCGCTTGAGTCTTAGATCTTCACTAACCAAGGCCCAAGTTTTCATCAAAATTTGTTTTCCTGCATGAGAGGAAAATTACAGTCCATGGTACACTATGCAGCTTATAGACTGCATAGAAAGAGCGTAAAGAGATGTATTGTGTTGGCAGTAAGTTAAGATCCTCTCTGCGGCCCATTTTCTCATAGGAAATCAGTGCTCATTGGTGCAGAAGCAAAGAAATAATATCATGTCATAAGACACCATCTTTCCTATGTTTGAGCTGGTAGTTTAAGTCTGGGAGAAAAAGCCAATGAGAATCAGAATAGATTGTCTTTCAGATTATGTTAGCCTGGGCATGTAGTACTCATGTGTTCCTGCATTACAATGAGCTCATCCCTGAAGGGTTAACCTTGAGCCTATTCCCATGACCCTTGTCACTCTCTGGCCCTCTGAATTCTCTGAACTTGAAGTTGTGAATGCCGTTTCTAGTTATCAGTATTTTCCATTTTCACCGTGGCCAAACACTCTTGAAATGTGTTACTAATGTTTTATTGCCTTGAGAGGATTCCTGTCGGGCTTCTCTTTGCCTAGGAAACCCAATTTCTGGTTTGGAAATCAAACTATAACTTTGTTCCCTCCGTAG
Seq C2 exon
GCGGATTTAATCAATACCCACCACCCACGCTGAAGGACGACTGCAGACTTGTTGAGTTAGAGAGGGGAGACACACTGCCCCATGGCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
-Gm7455:NM_001167923:35
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





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:
ENSMUSP00000131146





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr3:130440826-130443475 
LOW PSI
HsaINT0039569
(COL6A5)
Human
(hg19)
chr3:130159670-130162319 
LOW PSI
HsaINT0039569
Rat
(rn6)
chr8:114545486-114548326 
LOW PSI
RnoINT0040251
(Col6a5)
Cow
(bosTau6)
chr1:153585497-153589180 
Chicken
(galGal4)
chr2:42174878-42174883 
GgaINT0094998
([1])
Chicken
(galGal3)
chr2:41594782-41595653 
LOW PSI
GgaINT0094998
([2])
Zebrafish
(danRer10)
chr16:36755805-36757810 
LOW PSI
DreINT0050263
(col6a6)
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
  • 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"