Special

MmuINT0107242 @ mm9

Intron Retention

Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52186329-52190030:-
Coord C1 exon
chr2:52189966-52190030
Coord A exon
chr2:52186371-52189965
Coord C2 exon
chr2:52186329-52186370
Length
3595 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
CTCTTGTGCTCTGTTTACAGTAC
3' ss Score
8.47
Exon sequences
Seq C1 exon
TTTGTAGGTGCCACTACTACTCTGGAAAAATGGCGGATGAGGAAGAGTATGAGGAGGTGATAGAG
Seq A exon
GTAAGAAGAGAGCCCCTCCGGCAGCAAAACACTCTGTGTATTGACAGCTGAAGCCAGGGGGTGAATCAGTCATTTGAAAAAACACATCATCTATTATAACATCCCAAAGAGTCACCAACAAAGTACAAAGAAGGCATGTTTCATGTTCCGTTTCACCTGGAAGTGAAAGGGGGCATCACTACTTCCCAGTTTTACTTTTTCTTAACTGCTCCAAAAACAAACAACACAACAAACAAAAGCCGGGCTGTAGGTGCAGATAGGTTTTACTTTACCTTTTAAAAGGATTGCTTTCCCACATCCCAGCCCCAGCGATCAAAGGGCCCTAGGCACGTTTCCCAGCACCTGCACCAAGAGAGAAGGAATCTGCTTCAATTAGCTGAATTGCATAGGGGAGGTGTTACACACAGGAGGAGCCATCTATGAGCCGCTTGTGTGTGTGTACACGTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTACTCCCATGATTTCACTGATACACATGTGAGCCCATGAAGGTCAGAGAGACAGCTGGAGCCACTTTCCCACCAACTCCATCATACTTAAGTAAACAAGATGAGCTTTTGAATCTTGACTGAGAACTAAGACTACAGCAGCTATCTTGAAAACGTCCTCCCAAGTCATTGGTGGCCTCCTGGACGTTTTGCAGAATTAATGTGTACTTCCTGTTAGTGTCACATTGTTGTAATCTCAGTGTTTCCTTTCCTTAGCAGCTCTTGCCTTTATCTTCTAGAACAGAAACCCAAAGGCTTGAGGCTAATCTGTGTTAATATATTGCTATGAAATTGAAAGTGCCTAAAAAGTTCCAATTAACAATGATCTAAACAGATGAAAATCTGTTGATTTTTTTTTTTTTTTAATGATTGAAATTAACTAGAAGAGCTGTCCCAAACAAAACTCTGGATAAAGGTGCTAGAATTTATACTTGCTAATCAATCTCTATTTAGGCAAAGAAAATTTTTTATTCTATAAATAAAATTACCGTTATTACTGAAGTATATAAAAACCAAGCTGTATCTGACAGAGGTAGTGAGTACCTCTCTACTCCTATGTCGGTGGCTGCAGCTTCTCATGAATTGCACCATCACTAATGAGCATATTAAAGTAAGTTTGGAGAAGTCAGAACTATCCCTATTAAATAAGCACACTATAAATTAGTAATCATGAATAATTTCTTTCCTGTTATGATAATCAGAGGAACATTTTCAAGTCTCCAGTCAGACTACCTTAGCCTTTAAGTGTTTGTGTAAAGTGTTTAAGGGCATTGTGTTAGCCTTGATTGAGCCAGCTCGTCACGACAGTGGAAGGGGCTATTTTAGGCATTCCAACCTCGCTCTCTTGTTCCCATTCCTGCTTGTGGTCTGACTAGCACATACTAACTAATAGATCGCCTGTCAGGGAGTGTTGAACTCTAGTCTCTTTGGTCTCAGAAAAGATCACAAGCATTGGGTGGTTGCAGATCCAAGAGGATTGGCTCAAAAAGAGTAGCCAGTCTCAAATCCATGGCTCTTGGATATCTGAAATAAAATATTGCTGGCACTGTCTATATGGACTGAAATGAAGAAGGAGAAAGGAGCAGTAACGCACTGCCTGATTAGCAGAATAACTCTAAAAGCATGAGGTTTGGCATTCAAGTTCATACCAAGCACTTGGATGATGTTGTAGTTTTTGTGAGCTTACTTCCAAGACAGATTTCCCCATTGTGAGATCCCAGAAAAGGTGAAACCACATTGCTCACAAAAGCTGCTTTTACTGGGATGTTAAGAAAATCTAAAATCGATGGGAATCATCCATTGTAGTTAAATATTTCTTTGCAGGCTACTCAGGCTCTGTGTGACCAATGGAATAGCTCCATTTGACCTCAGTGCTAAACAGTAGTACTACTTAAAGTGGCTAAATGGCCTTTGTCCTGCGCTGAAGTCACAGGGGTAAAGAGCTCTCCTCTGTCCTGAGAGCACATGGCGCCTATTACTATATATAAAGATGCGTGCACACAAAAATTAAATTTTAAATGGAAAATAAGTACAAATGTAAGGAACATTAAGTGAGCTTTATATAGTTAATGACCACGGTGAATAGCTCAGCAGGCCTGGGGCAAGGAGAGCTTACTGAACCAAGGGCAGGAGAAAGTAGGGCGCTGAGGAGAATTTTGCTTCAGTGTCTCTGCCCCACCAGCCCCCGTCTCAAAAGCTTCCCTGACAGAAATAAAAGAACATCAGCATAAAATTCCATCCTTGTTTTTTTTTTTTTTTTTTTTTTTGGATTGAGAAAATGAGCCAAGTACTTCCTTTCCATCCCTTGGTTGAGTTCGTTGACCCACAGAAGCCATGCCTGCCGTTTGCCCAGCAGCACTGGATGAAGCTGGGGCAGGATTCCACTCTCCTTAGGCACCAGAGACAAAATGTCAGCCAGTTCCTCTCTGCATCTATTTATTCCTCATGATGTCAGAGAACAAACCTGGAGTGGGTTTCAGATCCAGGCTGCAGGCCCAGTGGCAAACTGCAGCCTCACTTTCCACAGTCCCATGAGGTGCCTTTCCCTCCCCTTTCTTCCTATGACCTACACCAACTGAACCTCAGCAACTCCCCTTTCCCCACAGATATTCTACCCCAGTTAAGCTAGTGAAGTCACCTGCTGCTTCAGCGGAGGCAAGTGCTGAGTGGGATGTAGGCTATACTGTATTGAAAAAGAGGCAGCCATCACTCCAGAAGACACTCGTAGTAATCCAGGGGAGATGGGAACAACAGATGTGAATATTAGTAGACATTTGCTCACAGTAGGTTTGTGTTTTGTTTTATAATCGGTATCGGTGAGTCCTGTAGTAGCTTCCCTTTGTATGCCCACCACACCCTGAGTCCTCTCCCAAGCAGATTCTCTTAGATATGGTGCTGGTTAGTTTTTGTCCACCTGAGAAGAGGGAACCTCAGCTGAGGAATTGCCTCTATCAGATTGGTCAGTACGCAAGCCTGTGGGGCATTTTTGATTAATGATTGCCGTGGAAGGACCTAGCCCACTGTGGACAGGGCCATTCCTGGGCAGGTGGTCCTCACTTGTAAAAGCAAGCAGTCTGGGGGGCATCAGTGAGAGCAACCAATAAGCAGTGTTGTTCTTCCATGGCTCCTGCCTCTGCTCCGGATTGAGTTCCTGCCCCGACTTCCCTGGATGGAACTGTCATGTGACGTGTAAGCCAAGTAAATCCTTTCTGTCCTAAATTGCTTTTAGTGGTGGCGTTTTCTCACGGCAACAGGAAGCAGACTGGGACAGAAATTCTAAGGGGCAAGTGTTTCTTGCCCCAGGAAAATAGCTTCCAGTGACTAAGAGGCACCTCAGACCCCTCATCTTGCTGGACGGTGTGCAACTTCTTGCTAGATCTGATGTGTGCATTTTTAGCTTTACTCAAACTTCCTAAGTGAAAATAGATCCCAGAATAGGAACAGGACGTTACCTCCTTCCTCCCTGCAGATATTCCACATCCAGTCAGCCAGGGAGCAACCTCACAGGTTCAGTGGCAGCAGGGGAGGGCTGGCTGCTGGCTGTTCTACTTGTCTCATAGACACTCTTGTGCTCTGTTTACAG
Seq C2 exon
TACTACACAGAGGAGACAGTTTACGAAGAGGTGCCAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950-Neb:NM_010889:3
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=0.750 A=NA C2=0.643
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047763





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000074773
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151729657-151733120 
LOW PSI
HsaINT0112167
(NEB)
Human
(hg19)
chr2:152586171-152589634 
LOW PSI
HsaINT0112167
(NEB)
Rat
(rn6)
chr3:37850927-37854525 
Cow
(bosTau6)
chr2:44547376-44550622 
LOW PSI
BtaINT0100644
(NEB)
Chicken
(galGal4)
chr7:34783992-34789958 
ALTERNATIVE
GgaINT0049689
([1])
Chicken
(galGal3)
chr7:36912192-36916151 
LOW PSI
GgaINT0049689
(Q9DEH4_CHICK)
Zebrafish
(danRer10)
chr9:23074230-23080587 
LOW PSI
DreINT0103433
(neb)
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"