Special

MmuINT0163673 @ mm9

Intron Retention

Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34825545-34826592:+
Coord C1 exon
chr17:34825545-34825877
Coord A exon
chr17:34825878-34826268
Coord C2 exon
chr17:34826269-34826592
Length
391 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CCTCTCTGTCTCCTTCTCAGCTG
3' ss Score
9.52
Exon sequences
Seq C1 exon
CCCCACCAGATGTTGTAGACCAGCCCCTCAGCCCCCCAGAGCCCAGCACAGAGGCCCCAGAGCCCCCCGAGAAGCCACTCCTGAGAGAGCTGATCGTGACAGACACCACACCCAACTCCCTGAGCCTCTCCTGGACAGTCTCCGAGGGACAGTTTGACCAGTTCGTGATCCAGTACAAGAACGGGGATGGGCAGCCCAAGGTGGTGCGGGTGCCAGGACACGAGGACCAGGTCACCATCTCCGGCCTGGAGCCAGACCACAAGTATAAGATGAACCTGTATGGCATCCATAGTGGCCAGCGTGTGGGCCCCGTGTCTGTTGTTGGTGTGACAG
Seq A exon
GTGAGTGGACTGTGGGACCCATCAGGAAGTGGGACCTGCTGTTCTTTGGTGACTAGTGACTAGGAAACAGTGGCCAAGGATTGGTCAGACCCACAGGTCTATTTTGGCTGAAGCCATGACCGACTATTATGTGCGCCGCCCCCTGAGCTGACCTGTCTCTCTGGGCAGGAGGGCTGTAGAGTCCGTGGCTATGTTGGTGGCTGTCTATGTCCCCTCAGCTGACCCAGGAGCTTGGGCATATTGGCCAGCTGTCAGATGACCAGGGACACTGCTCCTCATGGAGCAGCTCTAAACTGAGCCTAGGTCCCCTGGGAGCTATTGTTTCGTCCTCCTTCCCAAGGCCTGAGGACATCTGCTGGGGACCCTGCTCACCTCTCTGTCTCCTTCTCAG
Seq C2 exon
CTGCAGAGGAAGAACCCCCCAGCCCCACAGAGCCCAGCACAGAGGCGCCAGAACCCACTGAGGAGCCGCTCCTGGGAGAGCTGACAGTGACAGGATCGTCCCCAGACTCCCTGAGCCTCTCCTGGACCGTCCCCCAGGGAGACTTTGACTCCTTCACTGTCCAGTACAAGAGCAGTGATGGGCGGCCCCAGGTGATGCGTGTCGGGGGCCAGGAGAGGGAGGTCATCGTGAGAGACCTGGATCCTGGGCACAAATACAAGATGAACCTGTATGGACTCCATGAGGGGCATCGTGTGGGCCCTGTGTCCACTGTGGGCACAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.741 A=NA C2=0.798
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=WD(100=72.3)

							
A:
NA

							
C2:
PF0004116=fn3=WD(100=74.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084661





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000062808, ENSMUSP00000127487
  



Associated events






Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr6:32035762-32036166 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr23:27114388-27114745 
Chicken
(galGal4)
chr16:20915-21450 
ALTERNATIVE
GgaINT0123652
(FGA)
Chicken
(galGal3)
chr16:24839-25374 
ALTERNATIVE
GgaINT0123652
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GATCGTGACAGACACCACACC

				
R: 
GACGATCCTGTCACTGTCAGC

				
Band lengths: 
342-733

			

		

	





	
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"