Special

MmuINT0084061 @ mm9

Intron Retention

Gene
ENSMUSG00000025809 | Itgb1
Description
integrin beta 1 (fibronectin receptor beta) [Source:MGI Symbol;Acc:MGI:96610]
Coordinates
chr8:131230974-131234375:+
Coord C1 exon
chr8:131230974-131231059
Coord A exon
chr8:131231060-131234152
Coord C2 exon
chr8:131234153-131234375
Length
3093 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
GTATTTTATATTTCATTTAGACA
3' ss Score
5.71
Exon sequences
Seq C1 exon
ATAAAAATAGATGTTTAAAAGCAAATGCCAAATCTTGCGGAGAATGTATACAAGCAGGGCCAAATTGTGGGTGGTGTACAAATACG
Seq A exon
GTAAGATTTCTGATACTGTTCTATTTATTCTCTGATTTTTAGACTTATTCAGAGCCTTGTCCTTGGGAAGTGTCAGATAAGATATACCATTTTAATTAATGTTTATTGAATAGTGTATAGTAGTCAGAATTATGCTGTTTGACAAAATACTTGTCTTAGTTAATTTTATTTGTTGTGACAAAAAACCATTCTTAAGGTAACTTATAAAACAAACAAACAAAACATTTAATTTGCGGCTCAAAGCAGAGTGTCAGTCCATGGCCGTCATGGCTTTGAGCATTGCCCCAGACAGACAGACATGGAGCTGGGGCAGTAGTTAAAAGCTTACATCCTGATTGACACTATGAGGTAGAGAGAGCTAACTGGGAAAGTTGTGGGAATTTGAAAGCTCAAAGCCTAACTAACTTCAGTGAAAGGAAATATATGCAAATTTGAGTTCAGAGTTTGCTTAAAGATTAATGTACTTTGTCCCTTCTATAATGCTTACTAAAATTGTATTGAATTAATTTGAGGTTATGTTAGGTCAAAGGTTCTTTGTATATGTCTTCACTCAGCTGTTTGGACTTGTAAGATCAACTCTGACTAGGTAAGTTTCAACTATAGATTCAAACAATGATCCCATAAAAATGAATGCTGTTGGTGCCAGCAGCTGCCAGATAAATAGAACCTCTGAAGTAAACCTGTCATAACATGATCTGACAAAGTGAAATATAAAATGAGAAGTTTTTGTCTTATTTCAGATTTTTTTATACTACAAATGGTGCACTGGGGTGAAACTGGGGATATTTAGGAAAGTCCAATGGAAGCTCTTGCCTTCCTTCTTTGGAAAATGAGGAATAAGCTCATGCTTTACCAGTTGTTACAGTTAGAAATGCTGGATTAAAGAGAGGGGTTCATTTCAGAAGTTCTGTTTATCTGGAAGCTGCTGACACAGCGTTCATTTTATGGGTCCATAGTTTATCTATAGTTGAGACTTAGCTAGTCAAAGTTGAATACTATAGCTTCTGAAATCTAGGGCATAACTTCTCAATTACTAAAGGATCTTGTGGAATATGTTCAGTGGAATTTTATTTAGGTGTTATGAGGCTCCTTGATTGGTCAAATATTTGGGAATGGGCCAGGCATCGTGGCTCATGTCTTTAGTCCCAGTACTCAGGAGGCAGAAGCAGGCGATATCTGTGAGTTCAGTGCCATCCTAGTCGACAAAGCGAGTTCCAAGACAGCCAAGGCTACACAGAGAAACCCTGTCTTGAAACAACAACAACAAACAACAAACAACAAAAACAACAACAGCAACAACACCCAAACCCAAACAGAAGGAAAAGGATTCCCTCAGATCTTGTGCTTTGTTGGATTTTGAGATTTAAAAATAAACAAACAGATTTCAGTTTTGACCTTTCATCCTGGTCATTCTTTCCAGGTGTCTCTTTGTGTGGATACTCTTGCTATGTTACTTTTGCCTAAAAATATACTTTTACCAGCCATTATCTGTTCTTAGTCTTGTGCTGTATATGTACATTCATATGTGTCCATTGAAAGTGAGCAACAACAGGTTATCTTCTCCTATTGCTTTTTAACTTATTTTTTGTTACATTGAACCTCATTGAACCTCGGGCTTGCAATTTCAGCTAGATTGGTTGACCATTGGGTCCCCGTTCTGAGAACCCACTGTTTTTGTCCTCCATTATTGTGGGCCCAGGTTACAGATGTTCACTACCTTATGCAGCTTTTCTGTCAGTGCTAGGGAGCAAAACTAAGGTCCTCATGTTTGCAAAGCAAGCACTTTACCCATTAAGCCATCTCCTCAATCCCCACCTTGGGTTTTTGTGTATTTATTCGTACAGTATTAGGACCTTTAAAAAAGTTCAAGATTGTCTTAGGGTTTTACTGCTGTGAACAGACACCATGACCAAGGCAACTCTTCTAAGGACAACATTTAATTGGAGCTGACTTCTAGGTTCAGAGATTCAGTCCAGTATCAGGCAGGAGCATGGCAGTGTCCAGGTAGGCTGAGAGTTCTACATTTTCATCTGAAGGCTTCTAGGAGAAGATTGGCTCCCAGGGAGCTAAGATGAGGGTCTTAAAACCCATGCTTACAATGACATATTTCCTCTCACAAGACCATACCTACTCCCAACAAGGCCATATACTTCCTAATAGTGCCACTCCTTGGGCCAAACATATTTAAACCATCACAAATGTAAAATATAAAAATCTGGGGAGAAAGTTGTGAGAAAAGCATTGTCTGCCCTTCTAGTGCCTATTCTTAGCACCCACATCGTGGCTTACAGTCACAAGGTGTCTGACACCCTCTTCTGGCCTCTGTGGGTACTGCACACATGCGGTATAGGGATGTCCATGCAGGCAAGACACTCAAACAAATAAGATACAATTTAAGAAAAACAATAAAAATATCTCATTTAGTAGCAAGCATTTAAAAGATTTAGTAGCAAGCATTTAAAAGATTTTTAGCTCGTCAGTGATGGCACATGCATTTAATCTCAGCACTGGAAAGACAGAAACAGGCAGATGTCTGAGTTTGAGGATAGCCTGGTCTATATAGAGTTTCAGGACTACACATAGAAACCTTGTCTCAAAAAAGTTTTTATTCAGGAAAGTTTATGCTATGCTTTACACACACACACACACACACACACACTATTAATTGGGATGTATTTAGGCTAATGTGGTTTTCTTAAACGCCTAGTTGTTTAAAATGCTTTGCTGGGAAGTCCTTCAAAGGACTTTTCTAAGAGAAAATAATATTGTCTAATGTGTGGGCTTATCCATAATTAGGTGCTGCTAAGTATGCCAAACACTGAAGGATGTAGTTAGTATTGACATACTCTGAATTTGAAAGGTGAGGCTTCTAAAATATGCATAAAGCCTGGGGAAAGATAGGACTTTTTCAGTTGGTTTTACTTGTTTTTGTGTAAGAGCACACACATACCACGTTGTGGATTTTTGTTAAGAAGCTAGAAACGAACTACCTTAGATTAAGTCATTTGATTTTTGTAATTTGTTTACATGCAGTAAAAAACATCAAAATACTTGCTATACTTTTTTTGTTGATGTATTTTATATTTCATTTAG
Seq C2 exon
ACATTTTTGCAAGAAGGAATGCCTACTTCTGCACGATGTGATGATTTAGAAGCTTTGAAAAAGAAGGGTTGCCAGCCAAGTGACATAGAGAATCCCAGAGGCTCTCAAACTATAAAGAAAAATAAAAATGTCACCAATCGCAGCAAAGGGATGGCAGAGAAGCTCCGGCCAGAAGACATTACTCAGATCCAACCACAACAGCTGCTTCTAAAATTGAGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025809-Itgb1:NM_010578:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.467
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=FE(66.7=100),PF0036213=Integrin_beta=PU(70.8=58.6)

							
A:
NA

							
C2:
PF0036213=Integrin_beta=FE(17.2=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000087457





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:32930045-32932514 
LOW PSI
HsaINT0082795
(ITGB1)
Human
(hg19)
chr10:33218973-33221442 
LOW PSI
HsaINT0082795
(ITGB1)
Rat
(rn6)
chr19:61698778-61702232 
LOW PSI
RnoINT0076308
(Itgb1)
Cow
(bosTau6)
chr13:20267989-20271508 
LOW PSI
BtaINT0078135
(ITGB1)
Chicken
(galGal4)
chr2:13993583-13994968 
LOW PSI
GgaINT0095048
(ITGB1)
Chicken
(galGal3)
chr2:13977831-13979216 
LOW PSI
GgaINT0095048
(F1N8N7_CHICK)
Zebrafish
(danRer10)
chr24:1133964-1135358 
LOW PSI
DreINT0083219
(itgb1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"