Special

MmuINT0107879 @ mm9

Intron Retention

Gene
ENSMUSG00000039103 | Nexn
Description
nexilin [Source:MGI Symbol;Acc:MGI:1916060]
Coordinates
chr3:151912624-151915920:-
Coord C1 exon
chr3:151915772-151915920
Coord A exon
chr3:151912666-151915771
Coord C2 exon
chr3:151912624-151912665
Length
3106 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
ATGAAATTCTCATTCAATAGATT
3' ss Score
5.21
Exon sequences
Seq C1 exon
GGACAGTTAAAGGTAAATTCGATGAAATGGAGAAACACAGACAGGAAGAACAAAGAAAGAGAACAGAAGAAGAAAGAAAACGCAGAATTGAGCAGGATCTGTTAGAAAAGAGGAAAATACAGCGCGAATTAGCAAAAAGAGCGGAGCAG
Seq A exon
GTAGGTGCTAAATGCTACACTGGGGGTTATTTCTGTAACTAACAGAACAAACGAGAACTAATCAGGATGTTGCTGAATTAAAATACTTAGTACAGTATAAACTTATTAATAGTGGCTAGCCTAAAAATATTATCTGAAAGGAAAATATTCACGTCCGTTGCCCAGTAGTATGGGCAGAATGGGCCTATCTTAGGAGTGATATTTTATTCTGTATAATCTTACTAATTATTTCTACATTCCTTAAACTGACTATACTCCCAACTTTTCTTGGTATCTTTGAGAGTTTTATAAAGCTTTAGGACATTTTCACACATAAATTATAATTACAAAGCACAATTATGGCTTTTCAATAGCAGCATTTCTAAGTGCTGCCCTATATGCTCGTGTGCCATGGGCATGCAGTGTCCACAGAGGTCAGAAAGCATTGAATCCCTTGGGCTTGGAGTTACAGACAGTTCTGAGTCATCATGTATGTGCTAGGAACCAAAGCCAGGTCCTGAGAACACAGAGATGCAGAGGTGTCTTAACCACTGAGCAGCCTCTCTACTCCTTTAAGTTGATGTGCTATGCTCCATTCATCTTTATTGTTTTCTAAAGAGAAAAGTGATAATGCAAATAAGGCATTATTGCATGCCCGAAAAATCCATTAACTTCAATTTTGCAAATAACCTCTGCTGGGACACAGCAGCTCCTTGTTTGCTGGTGAATGATGTATGCTGCATTAACCTTAAGAAGACTGAGAATTTCCTACACTTTGCTTTATAGCCTTATCTGAAGAACGCCATGGACTTCAGGGTTGCCTCTAGGTTGTAGTGATTAAAGGTGAACATTCATTTTGTAGTGAAACTTTATAAGGAAGTCAAATTATAAAATGAGAATTATTAAATGTTTATATTATATTTAACTCAAAATTTTAAGCATGTAGATATAGGAGTTAAGATTATAGTTATATCAAGATTATAAACAATCCTGAAGTATATAAATTGTGACATCTAATACAGTATACCATGTATATATATAAAATATCTTTCAGTCTTCTATACTTTCAGTGAGCCTGACTATAATAAAGACTGGATGTTCAAAAGTAAATTAAAAACACACATACACACACACACACACACACACACACACACACGTATATTCATGAAAAAAAAAAGTCAGTGTGTTTACAGCAAACACTTGCTGTATGTAGGGTGCCATAGAACCCTGGCTAATAATATTTTAGCCCTAAGAAATTAAGAGTACCACAGCAATGTAGTAATAGTAACTTCTTCTTATAAATATGGAAAGTCTAATTCTGAAATAGAAGTACCTTTTCCACTCAAATTTAACATGACTTCATGGAGTATGGTGTAATGTTTGTTTACAGTTTACCAATACAACCCACCGTGCTGAGAGGTGTTCCTGAGCTCAGAAAGGTTAAAGTGATCACCAAGATAATTGCCAATTCTAAGATTGCAGGATCTTACAAAGACTTTAAAAGGAATATACCTTGTATATTAGATATTAGAATAAAAAAATTTCATTGGAAAACCCTGTAGGTGAATTATCTGGTTAACTCTGAAGATACCTGATGGACAAAATTAAGTCCATCCTTTTGACACAGAGATGGTCTTGGTGGGAGATGGGATCTTGAGAAGAGGCAGGGAAAGAAATCTGAGGAAGAAACAAATTTGCTTTACATAAAGAAAAAAAAAGTTTAGAAACAGTTATGTAATGTTAACTTGTGAAAGTCAGCAATAACTGAATGTGAACGTCTGTTCTTGACTACACTAGTAGCATAGCACCCCTCAAATAAATGTATCATTTTCCATGTTTGTTGAAAAAAACACACGACTGTATCTTTTGTTGCCTTGTGGTGGTTTAAAGTGAACAAAAGTAAAAGAAAGCAACAGCAACAGAAATGTAAGCTTCAAAAAATTAAAGGCCCACAGACCAGGGCCTAGAAAAGCTGTAGGAGATAAGAAACTTAGATTTAAAGAGCTCTTTCTCTTTCCTGTATTCTCACTGTCTGGCTTCTCAGAGTTCCTGGGTCTTTTTTTATTGAATTACTTGACTGTTCATTAGAAAACAGTTTATTTTGTAATGAACTGTTGTACTTTAAACTTTACTGTTCTATTTTTGAGACATGGTGACACGATGTAGCCCTGGCTGGCCTGGAGCTTGACATATAGGTGAGGCTGAGTTTAGACTTGCAGAAGTTATCCTGTCCAACTTTAACTTCATAAAAGTTCTTACTTGTCTGTTGCTTCTGTTTCCTTTTCCTGAGAGTTCAGACACTGCATTGTTAGAATCACCTATCTTCTCTCAGCATTTTGCTCAGGTACCAGCCTGCCCATGAAGCTAACCCAATGTTTCTTCAGCTTCAAAGAAGTGTGCTTCAAATGATGGCCTTTCCCTAATTCAGTATGAGAACATATTATAAGTACCAGAACTATCCTCCTTGTAAAATCTACCTGATATTTCTACCATACTTTATTATTGTATCAGTTACATTCTTGCCGGATATCTTTGATAAGAAATAGGGTCACAGGCTGGGTGTGGTTGTACATGCCTTTAATCCCAGCATTCAAGAGGTAGAGGCAGGCAGATCTCTGTAAATTTGAGGTTAGCCTGGTCTACAAGGAGAGTTCTAGGACAGCCAGGGCTACACAGAGAAATACTCTTTCAATAAAAGATTAGAAAGAAAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAGAGGAAGAAAGAAAGAGAGAGGAAGAAAGAAAAGAGAGAAAGAAAGAAAAGAAAAGAAAAGAAAAGAAAAGAAAGAAAAGAAGAGAAAAGGAAAGAAAAGAGAAAAAAGAAAAGAAAGAGGGTCACCACTATTTGATTGCTTGGGATGAATCTTCCTTCTACTATCTCAGGGGCAAGAGGATGGAGGGCACCTTTTTATATCTCACTTTAAATTGCTACTAAGTTAAAATTCATTCCTTGTAAGCTCACAGTCAAGTTGAAGTTTTACCACAAGCCATGGATAAATTACTTTTCAGATGTATGTTTAAAAGCATCAAGCAGAGATTCAACGTAATGTAACGATATGAAATTCTCATTCAATAG
Seq C2 exon
ATTGAGGACATAAACAATACGGGAACCGAGTCCGCATCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039103-Nexn:NM_199465:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.940 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000037120f3923A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000037120
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:77918274-77925187 
ALTERNATIVE
HsaINT0112847
(NEXN)
Human
(hg19)
chr1:78383959-78390872 
ALTERNATIVE
HsaINT0112847
(NEXN)
Rat
(rn6)
chr2:257467344-257472128 
ALTERNATIVE
RnoINT0100569
(Nexn)
Cow
(bosTau6)
chr3:67022883-67029090 
LOW PSI
BtaINT0101222
(NEXN)
Chicken
(galGal4)
chr8:17830368-17831883 
ALTERNATIVE
GgaINT0037484
(NEXN)
Chicken
(galGal3)
chr8:19630599-19632114 
ALTERNATIVE
GgaINT0037484
(NEXN)
Zebrafish
(danRer10)
chr8:18491288-18496268 
LOW PSI
DreINT0103974
(nexn)
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"