Special

MmuINT0066450 @ mm10

Intron Retention

Gene
ENSMUSG00000028034 | Fubp1
Description
far upstream element (FUSE) binding protein 1 [Source:MGI Symbol;Acc:MGI:1196294]
Coordinates
chr3:152222829-152223365:+
Coord C1 exon
chr3:152222829-152222980
Coord A exon
chr3:152222981-152223285
Coord C2 exon
chr3:152223286-152223365
Length
305 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
GTTTTGTTCCCCACCCCTAGCGG
3' ss Score
8.13
Exon sequences
Seq C1 exon
GGCCCAGTAAATCCTTTAGGGCCACCTGTACCCCATGGGCCCCATGGGGTTCCAGGTCCTCATGGGCCTCCTGGACCTCCAGGGCCGGGAACTCCAATGGGACCATACAACCCTGCACCTTACAATCCAGGACCACCTGGCCCAGCTCCTCA
Seq A exon
GTAAGTACCACATTTGCTTGGTTCTGGGCTTTCCCTAAAGACCTAGGAATTGGGGGCTGGAGAGATGACGATGGCTCAGCAGTGCAGAGCACTTGTTCCTGTTGCAGAGGGACCTGAGCTCACTTCCCAGCACCACACGGGGGTTCGCAACCATTCGTGACAGGTTCCAGGGTATCTTTACAGCGACACTAGGCATACATAGCTGCATATACATACATGCAATACATGCAGAGGCAAAACCTACACATAAAATAAATAAAGCTGGCTTTTATTAATGGTATTTGTGTTTTGTTCCCCACCCCTAG
Seq C2 exon
CGGTCCTCCAGCCCCATATGCTCCCCAGGGATGGGGAAATGCGTATCCACATTGGCAGCAACAGGCTCCTCCTGACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028034:ENSMUST00000166984:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=0.975
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000143618





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000101727, ENSMUSP00000130145, ENSMUSP00000142638, ENSMUSP00000142990, ENSMUSP00000143019, ENSMUSP00000143101, ENSMUSP00000143354, ENSMUSP00000143370, ENSMUSP00000143478, ENSMUSP00000143686, ENSMUSP00000143729
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr1:77960264-77960343 
LOW PSI
HsaINT0066536
(FUBP1)
Human
(hg19)
chr1:78425949-78426028 
LOW PSI
HsaINT0066536
(FUBP1)
Rat
(rn6)
chr2:257440269-257440548 
ALTERNATIVE
RnoINT0062937
(Fubp1)
Cow
(bosTau6)
chr3:66980345-66980431 
LOW PSI
BtaINT0064425
(FUBP1)
Chicken
(galGal4)
chr8:17802758-17802840 
LOW PSI
GgaINT0039164
(FUBP1)
Chicken
(galGal3)
chr8:19602989-19603071 
LOW PSI
GgaINT0039164
(FUBP1)
Zebrafish
(danRer10)
chr2:8857959-8858062 
LOW PSI
DreINT0070516
(fubp1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCCCAGTAAATCCTTTAGGGCC

				
R: 
CCTGTTGCTGCCAATGTGGAT

				
Band lengths: 
216-521

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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