Special

MmuINT0168115 @ mm9

Intron Retention

Gene
ENSMUSG00000001525 | Tubb5
Description
tubulin, beta 5 class I [Source:MGI Symbol;Acc:MGI:107812]
Coordinates
chr17:35973108-35973681:-
Coord C1 exon
chr17:35973573-35973681
Coord A exon
chr17:35973219-35973572
Coord C2 exon
chr17:35973108-35973218
Length
354 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
ATTGACTTGAATTCCTGCAGGTG
3' ss Score
7.96
Exon sequences
Seq C1 exon
TTCTGGGAGGTGATAAGCGATGAACATGGCATCGACCCCACCGGTACCTACCACGGTGACAGCGACCTGCAGCTGGACCGAATCTCTGTGTACTATAATGAAGCCACAG
Seq A exon
GTGAGGGCAGAAATCCCCACTTAACATTTATTCCCTGTCCCCTGTATTGGACAGTGAGCCCAGATGAATGCATCACTGGCTGCCCTGGAACTCCCATAGATCGTCTACCTCTCAAGTGCTGGGTTTAAGGAGAGCATCACCACGCCCTGTTTTTCCACACTTCTAAGTATCTATTACCCCTCTGCATGGTTCCCATTTTTTTTTCCCTAGACTCACACCCTAAGGGACTAAAGATTAGCTCTACTGCCACCAGGTGGTAGTGCCTGGAATGACAACTTTAGTGCTTTGTGGCTGATCTCCCACCCAGAGGTAATGCATTGCTGATCCGTCAAACATTGACTTGAATTCCTGCAG
Seq C2 exon
GTGGCAAGTATGTCCCTCGAGCTATCTTGGTGGATCTAGAACCTGGGACTATGGACTCCGTTCGCTCAGGTCCTTTTGGCCAGATCTTCAGACCAGACAACTTCGTTTTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001525-Tubb5:NM_011655:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.135 A=NA C2=0.026
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009120=Tubulin=FE(16.2=100)

							
A:
NA

							
C2:
PF0009120=Tubulin=PU(29.9=95.2)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000134598





     
                   









    
Main Skipping Isoform:
ENSMUSP00000001566





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr6:30722646-30722917 
LOW PSI
HsaINT1045695
(TUBB)
Human
(hg19)
chr6:30690423-30690694 
Rat
(rn6)
chr20:3424095-3424433 
LOW PSI
RnoINT0158244
(Tubb5)
Cow
(bosTau6)
chr23:28103352-28103608 
LOW PSI
BtaINT0155293
(TUBB5)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr2:67501136-67501386 
GgaINT0094212
(TUBB2B)
Zebrafish
(danRer10)
chr16:10431751-10432912 
LOW PSI
DreINT0169766
(tubb5)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCTGGGAGGTGATAAGCGATGA

				
R: 
ACGAAGTTGTCTGGTCTGAAGA

				
Band lengths: 
214-568

			

		

	





	
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"