Special

MmuINT0107266 @ mm9

Intron Retention

Gene
ENSMUSG00000026950 | Neb
Description
nebulin [Source:MGI Symbol;Acc:MGI:97292]
Coordinates
chr2:52123214-52125832:-
Coord C1 exon
chr2:52125728-52125832
Coord A exon
chr2:52123322-52125727
Coord C2 exon
chr2:52123214-52123321
Length
2406 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
AGAGTCTCTTTACTTTTCAGAAA
3' ss Score
7.76
Exon sequences
Seq C1 exon
CATTTATACACTATTGACTGGAATAAAGACAAAACCAAGATTCATGTGATGCCGGATACACCAGATATTTTGCAAGCCAAGCAGAATCAAACACTTTACAGTCAG
Seq A exon
GTAAAGAATGCATGCACAGTAATGGCATGTTTTGTCTCAAAACGTACTGTTAAAACCTGATGTAATAGAAAATAACGTCTGTAAATGCTGAAACTCTTTATTTTAGAGGTCTTTTACTATATTGTCAGGAGCATGGGCCTCAGCTGTGTGCCAGGAGTAGGCAGGAGTTGTTCAGGGAACTCAGTGCCCCCTCGCCCCACCCCCATCCCCAGGTCCTCTTTGAAGCAGCCTAGGAGAAAGAGTGGTGGGGGCAAGACTTGGTCTTACAAAACTTCAGGTTGCTCTCTATAACAATGTTTACCTGTGTTGATTCTTTTTTTTTTCCATTTTTTATTAGGTATTTAACTCATTTACATTTCCAATGCTATACCAAAAGTCCCCCATATCCACCCACCCCCACTCCCCTGCCCATCCCCTCCCCCTTTTTGGCCCTGGTGTTCCCCTGTACTGGGGCATATAAAGTTTGCAAGTCCAATGGGCCTCTCTTTCCAGTGATGGCCGACTAGGCCATCTTTTGATATATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATGTTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGCTACTTTCTCTAGCTCCTCCATTGGGAGCCCTATGATCCATCCATTAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGGGTCCTTTCAATAAAATCTTGCTAGTGTATGCAATGGTGTCAGCGTTTGGATGCTGATTATGGGGTGGATCCCTGGATATGGCAGTCTCTACATGGTCCATCCTTTCATCTCTGAAGCCAGAAGTTGCAGGCCTTGAGTGAATTAACACTTGTCAAACAGCAGGGAATTAAGTAAAGGATTAATTGATAGGGCTTCTTTCTCACTTGCTCAGAAACTTTACCTCTCACTTGTCAGTACTGAGGGAGGTTTGGAGCAATAAACTTTTACTGATCCATGCAAAAAGAGTCACCCACTTGCAGAAGGAAAAGCTTTATATAAGCAAACATACATAAACTCACATAGATTTATATACAAATTCGGGTACACATACTCATACACCTTCATGCACTCCTGTTGGGCTCAGCTACTTACTTATCTCACACACACACACACACACACACACACCTGTCCATACTCACATACACATCTAGAGCAAAAGTCCAAGCACCAATGCAGAAGGAACTCACTCATTCTGGATGAAAACTGAGCTCAGGTGTAGACTGGCAGAGTTCTAACTGCAGTTTTCATATCAGAGAGGGCTTTAATAGCAGTCCTAATATAAAGGACTTAATAATTTCTATTGCAATTTTAGGAATTCTTCCTAGAATCATCATTAGGAATTAAGGAATCATCTCCTTGTCTATATAGCATCACTACAAGACAGTACATCTTTGTTGATCTTCAGAAATCTGCCCAATAGGGTGAGCTAACGCCCAGTGTTAATTTTATAAGGACAGGGAAGACATATCAGCTGCAGAAATCATTGCCTAAGATTTTGTCCTTTGAGTCTTGCCTCTCAAAGGCTCTTTCATTGTTGTTCCACAATGAGGCATCTCTGGAAGATCACCTGCTAGCTTTTAGCCTTGGCTAGATGGCTCCTGACACTATACCTGTTCATCTGTACAATCATTGTACTTTGACACAAAGTAGAGTTGCCATAATTATTAAAACGTATAACTATGTCAAACAGACCTGATAGAAGTTTGGCTTTGGCATCTATGAGTTGTTTGATACTGAATGAATCACCTACTCTGAAGTGTGGTTCTTTCACTACTAAAATCAGGACCTGTGTCATTGCTTTGCCATGAGAAACAAATTAAAAACCCCTTAAGATACTGTTGTACTCAGCACATAGAATGTCCTAGATGACTATTTTGCTGTGGTGATTCTAACATACCTCCAACAAATTTGACTAGAACAGCTAGCATATTTATTGCAACTTACAAAAAGTTGTTACTACTATTATCATGTAGGTAGTTGAAATTATCTGATCTGATTGTCTTTTTTTTTTAATTATCTTAATGTCAATGTTTAAAGCAGTGACCCAGGCTGCCGTTAATTATAGGGTGAAAGGTACCTTATAAACATGATAAGACCAGATGGTTGCTAAATAGTGGAAGCTTTGTTCAAAAACGTCATCACCCCGAAATGAAACAAAAAACAAAGCTAGATCACATGATGCTATCTATACCAGTGCTAAGTCTACTCCTATCCTATCAAGCCACCAGCTTGGTTCTGTATATGTTCAGAGTCAGGGTAGAGGATTTTAGGGTTCTGTGTCCACTCTCTAGATATACTTTGGTGTATCTGCAATTTTAATAAAGAATGAATAGTGCTAAAGAGTCTCTTTACTTTTCAG
Seq C2 exon
AAATCCTATAGACTTGGTTGGGAAGAGGCTCTGAAGAAAGGCTATGATCTCCCTGTTGATGCGATTTCTGTCCAGCTGGCCAAGACATCAAGGGACATTGCTAGTGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026950-Neb:NM_010889:51
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.162 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0088013=Nebulin=PD(37.9=31.4),PF0088013=Nebulin=PU(55.2=45.7)

							
A:
NA

							
C2:
PF0088013=Nebulin=PD(37.9=30.6),PF0088013=Nebulin=PU(55.2=44.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047763





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028318, ENSMUSP00000074773
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:151654100-151655269 
LOW PSI
HsaINT1024705
(NEB)
Human
(hg19)
chr2:152510614-152511783 
HsaINT0112191
(NEB)
Rat
(rn6)
chr3:37789473-37791988 
LOW PSI
RnoINT0099868
(Neb)
Cow
(bosTau6)
chr2:44627931-44628019 
LOW PSI
BtaINT0100677
(NEB)
Chicken
(galGal4)
chr7:34761044-34761199 
LOW PSI
GgaINT0049725
([1])
Chicken
(galGal3)
chr7:36887237-36887392 
LOW PSI
GgaINT0049725
(Q9DEH4_CHICK)
Zebrafish
(danRer10)
chr9:23045685-23045890 
LOW PSI
DreINT0103449
(neb)
Zebrafish
(danRer10)
chr9:23042373-23042550 
LOW PSI
DreINT0103454
(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"