Special

MmuINT0163689 @ mm9

Intron Retention

Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34848379-34850142:+
Coord C1 exon
chr17:34848379-34848702
Coord A exon
chr17:34848703-34849854
Coord C2 exon
chr17:34849855-34850142
Length
1152 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TCTCATATACTCTCTTGCAGCCT
3' ss Score
9.3
Exon sequences
Seq C1 exon
CTGCAGTGGAAGAGCCCCCCAGCCCCACAGAGCCCAGCATAGAGGCCCCAGAGCCCACTGAGGAGCCACTCCTGGGAGAGCTGACAGTGACAGGATCGTCCCCAGACTCTCTGAGCCTCTCCTGGACCGTTCCCCAGGGAGACTTTGATTCCTTCACTGTCCAGTACAAGGACAGTGATGGGCGGCCCCAGGTGATGCGTGTCGGGGGCCAGGAGAGGGAGGTCATCGTGAGAGACCTGGATCCTGGGCGCAAGTACAAGATGAACCTGTATGGGCTCCATGAGGGGCGTCGTGTGGGTCCCGTGTCGACTGTGGGTGTGACTG
Seq A exon
GTGAGTGAAAACTGAGACCTGCTTCTTCTCAAGACCCTATCTTTCCTCCTTCCTGTCTGCCCTGTCCTTCCCTCTCCCTTTCTTCCAAGCTGTCCCTCTGGTGTCAGACACTAAGCTTCTGATCCCCTCACCTAGAATATGGGTCGGTGTGGCTGCCCTCAGAGCTGTTCTTGTCCCCTGTCCTTCCCCATACAGCCTTCCTCCCTCACTCCAGAGCACCACTAAGTCCCACATTCCTTCATTCCTAGCTGTCTCTCTGGGTATCTGGTGACTCGTCAAATGCTCTGCATTTGGGTCCTGGTCTGCCTCCAACTGGACTATGTGGGGTTTTATAAAGCTTTTCGCATGTCGTGTCTGCTCCTGCAGCAGAGGGACATTCATGGTGACACCTGCTAAACCAGTGATTCTCAACCTTCCTAATGGGGTGACCCTTAAAACTTCTTTAAGAACTTATTTATTTAATGCATGCAAGTGCTCTATTTGCATGTATGCCTGCATGCCAGAAGAGGGCATCAGACCCCATTACAGATGGTTGTGGTCCACCATATGGTTGCTCAGAATTGAACTCAGGACCTCTGGAAGAGCAGCTTGTGCTCTGAACCACTGAGCCCTCTTTGTGACCCTTTAATATAGTTCTTCATGTCATGGTGACCCCAACTACTGTTTTTGTTTTGTTTTGTTTTTGCTTGCTTGTTTTGTTTGTTTGTTTGTTTTTGAGACAAGGTTTTCTGTATAACTTTAGCTGTCCTGGCACTCTTTCTCTTTGTAGACCAGGCTAGCCTCGATCTCACAGAGATCTTCTTCCTGCCTCTGCCTCCTGAGTGTTGGGATTAAAGGCATGTGCCACCACCACGTGGCTAACCTCGCTATTGTCATGAATCATAATGCAAATATTTTTGGAGGTTTGTTATTTTAAAGGCAAAGATGCTTTGGAGGTATAATATTTTAGTTTTTCAAGGGGTCTTGACCCACAGGCTGAGAACTCTGTGCTAAACACACTTGGGAGATTCTCCTAAGTGTGAGCCGCCTGCAGCAGTTGCGGGGCGTCCATGGCTGGGGTTGGGTAGAGAGTTAGAAGAGGCCCTGAGAAGCTGCTTTGCAGCCTAGGGACTGCCTGGTCCCCATTCCTCAGTCTCATATACTCTCTTGCAG
Seq C2 exon
CCTCTCTGACCACAGAGCCCCCCATAGAGCCCCGCCTGGGAGAGCTGGCTGCAGTAGAAGTGACTTCCAGTACAGTGCACCTGTCCTGGACTGTGGCCCAGGGCCCCTTCGACTCCTTCCTGGTCCAGTACAAGGACACACAGGGGCAGCCCCAGATGGTGCCTGTGAGTGGAGACCTGGGTGAGGTCACCGTCTCAGGTTTGGAGCCAGCCCGAAAGTACAAGTTTCTACTCTTTGGACTCAAGGATGGGAAGCGCCATGGCCCTGTCTCCACAGAAGCAAAGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.647 A=NA C2=0.330
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=WD(100=74.3)

							
A:
NA

							
C2:
PF0004116=fn3=WD(100=83.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084661





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000127487
  



Associated events






Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:32016428-32017046 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:27093058-27093665 
LOW PSI
BtaINT0151339
(TNXB)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr16:26311-26979 
ALTERNATIVE
GgaINT0123654
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCTCTGAGCCTCTCCTGGAC

				
R: 
TGGACCAGGAAGGAGTCGAAG

				
Band lengths: 
345-1497

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"