Special

MmuINT0107883 @ mm9

Intron Retention

Gene
ENSMUSG00000039103 | Nexn
Description
nexilin [Source:MGI Symbol;Acc:MGI:1916060]
Coordinates
chr3:151906790-151910238:-
Coord C1 exon
chr3:151910050-151910238
Coord A exon
chr3:151906988-151910049
Coord C2 exon
chr3:151906790-151906987
Length
3062 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
AAAATATTTATTTTAAATAGGTA
3' ss Score
7.06
Exon sequences
Seq C1 exon
GTAAATGAGGAGGATGAAAACCAAGATAGAGAAACAGTTTTTAAAGAGTACCGCCCAGGAAAACTCAAACTCAGTTTTGAGGAAATAGAAAGGCAAAGGAGAGAAGACGAAAAACGAAAAGCAGAGGAGGAGGCCCGAAGGAGAATAGAGGAAGAGAAGGCGGCATTTGCTGAAGCAAGGAGAAGCATG
Seq A exon
GTAAGACAAAAGCTAACTCAACAGTGGTTTGGAATTCAGCATGTGTGTATGGTATGTGTACTTGCCCAAGCTAGGAGAAGCCAGACAACCTTGGATGCCATTCTCTGACAGGACTGGCTAGCAGTCTGAGGAATCCGCTTGTCTCTGCCTCCCCTGTGCTGAGATTACAGGTGTGCACCTGGTTTTACTTGGGCTCTGGGGACTCAACTCAGATCCTCATGTTTCCAAGACAAGGACTTTACTTAATAAGCTCTCAAGTCTAGCCCAAGGATTCTGTCTGTAGAGCATGTAAATGAAGTGACTAGACTCTGAGGAGGAACAGCCACCCTATCATCTCTGCAGTCTGTAGAAGAGGATGAGTGCAAATAGCAGGTACTTGTCAGCATTTGCTTCAGTTGGTGTTGAAAAGACATGATTACTAATGCCATGCTAGCTTACAAGGCTGGAAACTGCCATCCCTCTCTGGAAAGATACATTTCTTTAGGCCAGATCTCAGTGTCAAGAACAAAAAAGGGGTGGGGTGGAGAGATGGTTTAGCTGTTAAGAGCACTGACTGCTCTTCCAGAGGTCCTGAGTTCAAAACCCAGCAACCACATGGTGGCTCACAACCATCTGTAATGGGATCCGGTGCCCTCTTCTAGTGTGTCTGAAGAGAGCATATATACATAAAATAAATAACTTTGAAAAAGACTCAGGAAAAAAAAAAAGAACAAAACGGAATTTCCCCTATCATTTCCCTGCTTTCTGCTCCTTCTCTCATTTCATTCTCTTCTCTGCTGTCCTTTTCTCCTTCATCCTTGCCATTTTAATCCCATTCAATCTATATTAGATGATCAATTCACAATTATCTAACTTCAAAATACCCAACTTTTTTTTTTAAAGATTTATTTTATTTATATGAGTGCATTGTAGCTGTTTTCAGACACACCAGAAGAGGGCATCAGATCTCTTTACAGATGGTTGTGAGCCACCATGTGGTTGCTGGAAATTGAACTCATGACCTTTGGAAGAACAGTCAGTGCTTTTATCCACTGTGCCATCTCTCCAGCCCCCTAACATACTTTCTTGCATATTGATATCTAATTTGTCAAAAAGTTAAAACTTTCCACATTATGTTAATGTTTGTAAAATAGTTATCCGAAGAATCAATTTAAAGCACTTTAACATAAAAAAGATTTATTTATTATATGTAAGTACACTGTAGTAGTCTTCAGACACTCCAGAAGAGGGCGTCAGATCTCGTTAAGGATGGTTGTGAGCCACTATGTGGTTGCTGGAACTCGGGACCTTCAGAAGAGCAGTCAGTGCTCTTAACTCTGAGCCATCTCTCCAGCCCCCAAAGAATTGTTTAATGTTTATGAGCACACTGTAGCTCTCTTCAGACACCAGAAGAGGGCACCGGATCCCATTACAGGTGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTGCATCCCCTTTTTGCATTTTAATTGCCTTCTGATAAAATAGCCTAGCATTTGTTCCTGCCTGTTCTGGGCATTCTACCAAGTACGTTGTTTAATCACTCAAATCAGAAACTCAGAACCCTGAAACACATGCCTTCAGCTTTTCACTCAGCCCAACTGGCTCCCTGATTTACTCTCACTTCACTACTGTAATCCATATCACTGTTGCTATTCCTTGGCTGGGACCAAGTCCTAACTTGCTTGCTTTTTTGCCTGTGAGCCCATGTCTGCAGGCCACAGTTCAGATCTCAACAAAGTGTTTTTATCTCCAGGACACAGAAAAACAGAATTAAATTGTTCTTCGTGGTAAAATATATCAGCTGTCAATAGCTTACAAGCAAAGGTTCTAGTTTTAATTTTGAGACTGCCTGTATTCAGGTGATCATATAATAAAACTGTTATTGGAGACTGGGAAGATGGCCCAGGTAGATAAAGATACCACTAAGCCTGGTGACCTACTGTAAGTCCACTCATGGTAGGAAGGAAGAACTGACTCCTGAAAAATTTCTTCTGACACCTGCATGCCCCCCCCCCAATAAATAAGACAGATAAACAATTTTTTAAAAAGTTAAAACCCGGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAGGTAGGCAGATTTCTGAGTTCAAGGCCAGCCTGGTCTACAGAGTAAGTTCCAGGACAGTCAGGGCTACACAGAGAAATCCTGTCTCGAAAAACCAAAAAAAAGAAAAAAAAAAAAAGTTAAAACCCTACAGTTGAGAGCCTACCTCAGTGTACTTAGTATTTCCAAGCTTCACTTAATCCCGAGAGAGAACCAGAATAAAATTGCCACAGGGAGGCTCAAGAGAGGTAAGTAGCTTGCCCATGGTCACAATCAAATTTATTCATATAAAGTTACAAAATTACAAAAAAGCAGTCTGTTAATTATTCACATTTCAAATGTCTTGTAGCATATAAAGTGAAGGATTTCACTCTGGCACTTTCACACATGTGGAACATTATAATCTTACTGGAAATATCCTGAAGCTGGACTTGTGGCTTTGGATAGGTTACTTTTCTGTCACTCCCTCTGGTTCCTCCTGTGCAAACCACGGATAGTAATCCTATGCTATTTTATAAAGTTAGTGGGTTAAATATATGTATTTATAACTGGACTGGCAGTTGTAGGAATATATGAACTATTATGTCTTTAAAACATCTTGGCAGCAAAACTGCACAATTAAATGGCATCATGGCACTGCTTTTTTCTGATAAAAGCTTATGACGATACAGATGTAACTCAGTAAGACTATGATTTTGGAGATTCACTTCAATCCAACAAAAATATTTTTAATATGATTAAAGAACATCAATTTCTGATTCAAATGATTCAATGTATAAAAATGGAGCATGTTTTGTTCATTTCAATGGAGAACTGATGTACATGGTTATCCTCCATATCACAGATACCCCAGTCTAGAAGGAATAACTTTTTAGTATGCACAATTCTGAAAAAAATATTTATTTTAAATAG
Seq C2 exon
GTATTAGATGATGATTCCCCAGAGATTTATAAAACAGTGTCTCAAGAATCTCTTACTCCTGGAAAACTAGAAATTAATTTTGAACAATTATTAAGACAAAAAATGGAAGAAGAAAGACGACGAACAGAGGAAGAACGCAGGCATAAACTAGAAATGGAGAAACAGGAATTTGAACAACTGAGACAAGAAATGGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000039103-Nexn:NM_199465:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.714 A=NA C2=0.864
 
                        

				
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






Conservation


Human
(hg38)
chr1:77929505-77933281 
ALTERNATIVE
HsaINT0112851
(NEXN)
Human
(hg19)
chr1:78395190-78398966 
LOW PSI
HsaINT0112851
(NEXN)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:67011324-67019328 
LOW PSI
BtaINT0101226
(NEXN)
Chicken
(galGal4)
chr8:17822087-17826094 
ALTERNATIVE
GgaINT0037488
(NEXN)
Chicken
(galGal3)
chr8:19622318-19626325 
ALTERNATIVE
GgaINT0037488
(NEXN)
Zebrafish
(danRer10)
chr8:18487561-18488262 
LOW PSI
DreINT0103977
(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
  • 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"