Special

MmuINT0107222 @ mm9

Intron Retention

Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52004614-52005217:-
Coord C1 exon
chr2:52005110-52005217
Coord A exon
chr2:52004798-52005109
Coord C2 exon
chr2:52004614-52004797
Length
312 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGT
5' ss Score
9.49
3' ss Seq
GAAGTAAATTCCTATTTCAGGTG
3' ss Score
7.21
Exon sequences
Seq C1 exon
GTTCTTTACTCCGATAGCTTCCGGAAACAAATACAAGGGAAAGCTGCCTATGTGCTAGATACACCAGAGATGAGGCGGGTTAGGGAAACCCAACGGCACATCTCAACA
Seq A exon
GTAAGTCGAAGACTCTTGTTTAAATATGTATACATTGATATGTATGTGTGCAATGTGTGTGCAGTGCTCACAGAGGCCAGAAGAAGGGTATCAAATCTCTTGGACTGGAGTTACATACGTTTATGAACTACCTCATGTGAACTGGGAACTCAACACAGATCCTCTGTAAGAACTTGTGCTCTGACCCACTGAGCTGTTTTTCCAGCCACAGAATCCTTTATGATTGGCTGACCAGCCTGCTGGAATATATTCAAACAGAGATGGTCACACTACTATACTACTGTGTCTTCAAGAAGTAAATTCCTATTTCAG
Seq C2 exon
GTGAAATATCATGAAGACTTTGAGAAACACAAAGGCTGCTTTACACCAGTGGTGACAGACCCTATCACTGAACGAGTAAAGAAAAACACACAGGACTTCAGTGACATTAACTACCGAGGTATTCAGAGAAAAGTGGTGGAAATGGAACAAAAGCGGAATGACCAGGATCAAGATACCATTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950-Neb:NM_010889:152
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.624 A=NA C2=0.629
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0088013=Nebulin=PD(37.9=30.6),PF0088013=Nebulin=PU(55.2=44.4)

							
A:
NA

							
C2:
PF0088013=Nebulin=PD(37.9=17.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047763





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028320, ENSMUSP00000070747, ENSMUSP00000074773, ENSMUSP00000118735
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151492282-151492386 
ALTERNATIVE
HsaINT0112149
(NEB)
Human
(hg19)
chr2:152348796-152348900 
ALTERNATIVE
HsaINT0112149
(NEB)
Rat
(rn6)
chr3:37665556-37665885 
LOW PSI
RnoINT0099862
(Neb)
Cow
(bosTau6)
chr2:44747613-44747717 
Chicken
(galGal4)
chr7:34677655-34677853 
ALTERNATIVE
GgaINT0049826
([1])
Chicken
(galGal3)
chr7:36804204-36804402 
ALTERNATIVE
GgaINT0049826
(Q9DEH4_CHICK)
Zebrafish
(danRer10)
chr9:22998830-23000930 
LOW PSI
DreINT0103411
(neb)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTTCTTTACTCCGATAGCTTCCGG

				
R: 
TGGTATCTTGATCCTGGTCATTCC

				
Band lengths: 
286-598

			

		

	





	
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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