Special

MmuINT0107215 @ mm9

Intron Retention

Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52012811-52013444:-
Coord C1 exon
chr2:52013352-52013444
Coord A exon
chr2:52012904-52013351
Coord C2 exon
chr2:52012811-52012903
Length
448 bp
Sequences
Splice sites
5' ss Seq
TCGGTATTT
5' ss Score
4.52
3' ss Seq
TACTTTCTTGTATCTCACAGGTT
3' ss Score
9.78
Exon sequences
Seq C1 exon
GTTATGTACAAAGAAAACCCGGGAACAGGCATCCCGACCACTGTCACTCCAGAGATTGAGAGAGTCAAACGCAACCAAGAGAACTTTAGCTCG
Seq A exon
GTATTTACAGATACATGAAATAAGACATTCTGTCCCATAAAAAAACTACCAGAATAACCTCCCGTTCTACTTTTCAAAGTAACAGCTTAACGACTCAGTGTGTGTTTTGTGTATCATCCTCTGATGAAAACCACCTGACCTGATGCAGAATTGGCCACTCTTCGCTCTTTAACAGTTTCAGCAACTGACTGGTGTGAGCTAGATCTGAAACACTGTTAGCAGCATTAACAAGCTTCCTTGGGGTGCTTGAACCCTGGAACCCAGTGCTTCCTGCTGTACCTAAGACATAGCAGTGTAAAGTGCATCTGTAAAGTTGTCACTTTCAGAACATTACCCTGACTAAATACTGCTCTCTAAAATCGCCCTCCTCACCCACACCCCAACCTACCCCCTTCCTCCGTCTCTGCTTGTTTTGAATGTTTTCTGGGTACTTTCTTGTATCTCACAG
Seq C2 exon
GTTTTGTACAAAGAAAGTTTGGGAAAAGGAACCCCTACAGCTATCACTCCAGAGATGGAGAGAGTCAAACGCAATCAAGAGAACTTTAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950-Neb:NM_010889:146
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.855 A=NA C2=0.879
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0088013=Nebulin=PD(25.0=19.4),PF0088013=Nebulin=PU(57.1=51.6)

							
A:
NA

							
C2:
PF0088013=Nebulin=PD(35.7=32.3),PF0088013=Nebulin=PU(57.1=51.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047763





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028320, ENSMUSP00000070747, ENSMUSP00000074773
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151502886-151503348 
ALTERNATIVE
HsaINT0112137
(NEB)
Human
(hg19)
chr2:152359400-152359862 
ALTERNATIVE
HsaINT0112137
(NEB)
Rat
(rn6)
chr3:37674723-37675165 
ALTERNATIVE
RnoINT0099857
(Neb)
Cow
(bosTau6)
chr2:44739174-44739648 
Chicken
(galGal4)
chr7:34686955-34689565 
Chicken
(galGal3)
chr7:36816057-36816541 
LOW PSI
GgaINT0049820
(Q9DEH4_CHICK)
Zebrafish
(danRer10)
chr9:23001504-23007253 
ALTERNATIVE
DreINT0103408
(neb)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGTACAAAGAAAACCCGGGAACA

				
R: 
CGAGCTAAAGTTCTCTTGATTGCG

				
Band lengths: 
182-630

			

		

	





	
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






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