Special

MmuINT0107881 @ mm10

Intron Retention

Gene
ENSMUSG00000039103 | Nexn
Description
nexilin [Source:MGI Symbol;Acc:MGI:1916060]
Coordinates
chr3:152247933-152248368:-
Coord C1 exon
chr3:152248180-152248368
Coord A exon
chr3:152248104-152248179
Coord C2 exon
chr3:152247933-152248103
Length
76 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATT
5' ss Score
6.49
3' ss Seq
TAACAAGTTTGTTTGCATAGGAT
3' ss Score
4.65
Exon sequences
Seq C1 exon
GAAGGAGATGACTCACTACTTATAACAGTGGTACCTGCCAAATCATACAAAACACCTGGAAAAACAAAGGATCCTGAGGACCTGGACAGAGAAGAAGGAAATGGGAGAACCAACCATGAAGAAGATAAAATGAGATATGAAGAAGAGTGCCGAGTTCTCAAAGAAGCAAAATGTCTTTCATTAGTCATG
Seq A exon
GTAATTTTTTTTTACAAGAATAAATCAAAAGTTTAGTTTAACAATTGCCCTTTGGGTAACAAGTTTGTTTGCATAG
Seq C2 exon
GATGATGAAACAGAGGCCAAAAAAGAATCACATTTTCCTGGAAAATTGAAATCAACTTTTGAAGAACTGGAACGACAAAGACAAGAAAATCGCAAGAAGCAAGCGGAAGAGGAAGCGAGACGACGCTTAGAAGAAGAGAGACGTTCCTTTGAGGAGGCGAGAAGGCACATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039103:ENSMUST00000046045:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.781 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000142936





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037120, ENSMUSP00000142559, ENSMUSP00000142569, ENSMUSP00000142574, ENSMUSP00000143180, ENSMUSP00000143294, ENSMUSP00000143436, ENSMUSP00000143573
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr1:77926612-77926715 
ALTERNATIVE
HsaINT0112849
(NEXN)
Human
(hg19)
chr1:78392297-78392400 
ALTERNATIVE
HsaINT0112849
(NEXN)
Rat
(rn6)
chr2:257467079-257467154 
ALTERNATIVE
RnoINT0100570
(Nexn)
Cow
(bosTau6)
chr3:67021366-67021458 
LOW PSI
BtaINT0101224
(NEXN)
Chicken
(galGal4)
chr8:17828920-17829009 
HIGH PSI
GgaINT0037486
(NEXN)
Chicken
(galGal3)
chr8:19629163-19629240 
ALTERNATIVE
GgaINT0037486
(NEXN)
Zebrafish
(danRer10)
chr8:18488452-18490794 
LOW PSI
DreINT0103976
(nexn)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGCCGAGTTCTCAAAGAAGCA

				
R: 
CGTCGTCTCGCTTCCTCTTC

				
Band lengths: 
167-243

			

		

	





	
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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