Special

MmuINT0107218 @ mm10

Intron Retention

Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52150967-52151456:-
Coord C1 exon
chr2:52151364-52151456
Coord A exon
chr2:52151060-52151363
Coord C2 exon
chr2:52150967-52151059
Length
304 bp
Sequences
Splice sites
5' ss Seq
TCGGTATTG
5' ss Score
3.83
3' ss Seq
TCCGCCTTTGTTTCTAACAGGTG
3' ss Score
11.61
Exon sequences
Seq C1 exon
GTTTTGTACAAAGAAAATGTGGGGAAAGCCACCCCAACCCCTGTCACTCCAGAGATGCAGAGAGTCAAACGCAATCAAGAAAACATTAGCTCG
Seq A exon
GTATTGTCTTGAGAAATGAAAAGTGCTTCTGATTTTACAAAGTAACTCTTGCAGTTTGGCCTGCTCTTAATCCCATCCTAGGTGAAAAGCAAATAAAATGCCAGCTGTGCTCTTATCTCCTCTAAGCACCCCACAACACTCACCATTGCCATTAACCACTCTTGCCTTTTTTCTTGAGCGCTAGTTTCACTAGTAGCAGTAGGTTACACCTAACATTTCCCTCTCCCACCCAACTGTATATATGTTTAATAGTGAATATTGCCTCCTCGTGAGTGACTTGTAGGTCCGCCTTTGTTTCTAACAG
Seq C2 exon
GTGCTATACAAAGAGAACATGGGGAAAGCAACCCCCACACCCTTCACTCCTGAGATGGAAAGAGTCAAACGCAATCAAGAAAACTTTAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950:ENSMUST00000075301:144
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.936 A=NA C2=0.968
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0088013=Nebulin=PD(35.7=32.3),PF0088013=Nebulin=PU(57.1=51.6)

							
A:
NA

							
C2:
PF0088013=Nebulin=PD(35.7=32.3),PF0088013=Nebulin=PU(55.2=51.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047763





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000074773
  



Associated events







Other assemblies


mm9




Conservation


Human
(hg38)
chr2:151493868-151494160 
Human
(hg19)
chr2:152350382-152350674 
HsaINT0112146
(NEB)
Rat
(rn6)
chr3:37667328-37667637 
LOW PSI
RnoINT0099859
(Neb)
Cow
(bosTau6)
chr2:44745859-44746152 
Chicken
(galGal4)
chr7:34681167-34682591 
Chicken
(galGal3)
chr7:36806549-36807007 
GgaINT0049822
(Q9DEH4_CHICK)
Zebrafish
(danRer10)
chr9:23001504-23007253 
ALTERNATIVE
DreINT0103408
(neb)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGTACAAAGAAAATGTGGGGAAAGC

				
R: 
CGAGCTAAAGTTTTCTTGATTGCGT

				
Band lengths: 
182-486

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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