Special

MmuINT0163678 @ mm9

Intron Retention

Gene
ENSMUSG00000033327 | Tnxb
Description
tenascin XB [Source:MGI Symbol;Acc:MGI:1932137]
Coordinates
chr17:34831111-34832650:+
Coord C1 exon
chr17:34831111-34831401
Coord A exon
chr17:34831402-34832329
Coord C2 exon
chr17:34832330-34832650
Length
928 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TCCATGTCTCTCTGAACCAGACC
3' ss Score
7.69
Exon sequences
Seq C1 exon
AGCCCACGAATGCTGCGGACCACACAAAATCTCGACTGGGAGAGGAACTGCGGGTGACTGGTGTGACTCAAAACTCCGTGGACCTCTCCTGGACAGTCTCCGAGGGCCAGTTTGACTCCTTTGTGGTCCAGTACAAGGACAGGGATGGGCAGTCCCAGGTGGTGCCTGTGGACGGAAGCCATAGAGAGGTTAGAGTCTCTGGTCTAGACCCAGGTCGCAGGTATAAGCTGCTACTCTACGGCCTCCGAGACAGCAAGCGTGTGGGTCCCCTTTCAGTCATTGCTGTGACCG
Seq A exon
GTGAGTGTGACAGGCCACCTAACTGGACCACTTCTTTTGGGGGAGGCTTTATCGAGGCAACATTTACATATAGTACCAAATGGGCTTGGCAAATGTATAAGTCACAGAACGATGGCTCAGGGAGGCACAAGAAAGTTCCCTCACCCCTGTATCCAGGATCAGTAGACCAAAGAAACAGATAAGAAGAAAAGAGTGATTTATTCACTGTGGCCATGTTGGGAAGAGGAGCAAAGAGTGAACCCCTCAAGTCCATCTTTGAAGTCTTGGCAGGCATGAGGTTTAGTTTTAAATGGATATACATGTATATATGTATATACATATATATATTATGCACTCACACATAATATACATATACATATATACACACATATATGCACACGCATAACATACACAATACACATATATGCATATATGTGTACATATACATATATATGTAAGCAACCCCTGGCAAGAGGCGGTTCCACCCATCAGCTCCGCTCTCCTGCACGGTGGGCTGATGAATTGTGAAATCTCTTTCCTGAAGACATGTTTCCCCTCTGACTGTACCAAGCTTTATCCCTCCCCCCATGAGATTCCTGCGTAACTTGGCATGGACTGGGTGGAGTTTGTTTCAATGGTCTGACAGTCCATTGGATGGGCACAAGGTTCCATTGGGATGGCTTCATTCCTGCTGGGAGCTTTCGAGGTCCTCTTTGCCCTCACCTCCCCAGGCCCTAGCAGACACTGAGGTGCCTTCTGTCCTTCAGGGTTTGCCTGCCTCTGCATCTCATTTTGGAGCATCTTCTACTTCAAACGCTTTTGCCAACCCTCCGGCCTCTGCCTCCCTCCCTTCTTCCCCACACCCTTTCTCCCTCCTATCCCCCACCACTCTTCAACATATCAATTCTGCAACAGAGCAGCCATTTCTCTCCATGTCTCTCTGAACCAG
Seq C2 exon
ACCCCAGAGAAACAACAGAAGCTTGGACAGAGGTCCCCACAACTTCAACTCCTGCAGCTGTGCCCCGCCTCGGGGAGCTGAGAGTGGAGGAAGCCACGCCTCACAGCCTGCATCTCTCCTGGGTGGTGACTGAGGGAGAATTTAACTCCTTCGAGGTCCAGTACACTGACAGAGATGGGCAACTCAGAGTGGCCAGTACAGAGGGTGACCAGACTGACATTACCCTTACTGGCCTGGAATCGAACCACAGATACCTGATAACCCTATATGGCTTCCATGATGGGCAGCCTGTAGGCTCTGCTCAAATTGAGGCCCTGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033327-Tnxb:NM_031176:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.367 A=NA C2=0.519
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=WD(100=80.6)

							
A:
NA

							
C2:
PF0004116=fn3=WD(100=73.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000084661





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000062808, ENSMUSP00000127487
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:32069137-32069552 
ALTERNATIVE
HsaINT1044833
(TNXB)
Human
(hg19)
chr6:32036914-32037329 
Rat
(rn6)
chr20:4450302-4450669 
ALTERNATIVE
RnoINT0004972
(AABR07044388.2)
Cow
(bosTau6)
chr23:27105801-27106349 
LOW PSI
BtaINT0151333
(TNXB)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr16:25677-26033 
HIGH PSI
GgaINT0123653
([1])
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGTGGGTCCCCTTTCAGTCAT

				
R: 
GCCTCAATTTGAGCAGAGCCT

				
Band lengths: 
345-1273

			

		

	





	
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"