Special

MmuINT0084216 @ mm9

Intron Retention

Gene
ENSMUSG00000001281 | Itgb7
Description
integrin beta 7 [Source:MGI Symbol;Acc:MGI:96616]
Coordinates
chr15:102054989-102058032:-
Coord C1 exon
chr15:102057829-102058032
Coord A exon
chr15:102055191-102057828
Coord C2 exon
chr15:102054989-102055190
Length
2638 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAAC
5' ss Score
4.14
3' ss Seq
AGCCTCCTCTTGGGGTACAGAAC
3' ss Score
3.41
Exon sequences
Seq C1 exon
GCCATGGTGGATTCATCAACTGTTCTCATTTTTCTGCTGGTTCTGGGCGGAGGTCAGAGTGAGTTAGATACCAAGATTACATCCTCTGGGGAGGCCGCAGAATGGGAGGATCCTGACCTGTCTCTGCAGGGATCCTGCCAGCCAGTTCCTTCCTGCCAGAAGTGTATTCTCTCACATCCCAGCTGTGCATGGTGCAAACAACTG
Seq A exon
GTAAACATGGGTGTGTGTGGTCCTGAACATGTGTGATGTGCGTTGTGTAGGTAGATTTGTGATTTTTTTTTGGGGGGGGGGGAATACTGTCCCTTCTCATGTGTGACTGAATTTGGACAGACAGGATTCCAATGTGTGACTCATATGCGTGTAAGTTTCTGAGCATACGTGAACAGAACCCGTGACCCATGAGCTCAGAGGAAGATGTCCTTGTGGGAGTTCGTGCTTCTGCATGTGAGAAAGTAGACTGGCCAGTTACGTATTCTGTGACAACATGCAACAGAAACATACTTCTTATGAATTGAAAGGCTTGGAATTCAAGAGCAAAGTGCTGGTTCATTTGGTTCTCTCTGGAGCATTTTTTCCTGGCTTAGAGATGGGCTACCTTCCTGCTGTATTACGACATGGGGTTAGGGTGTGGGGAGGAGACCCCTCTGCTGTTGACTCTCTCTCTCTCTCTTTAAAAGATTTATTGATTTTATTTATATGAGTACACTGTAGCTGTCCTCAGACACACCAGAAGAGGGCATCGGATCCCATTACAGATAGTTGAGAGCCACCATGTGGTTGCTGGGAATTGAAAGCAGGTCCTCTGGAAGAGCAGTCAGTGCTCTTAACCTCTGAGTCATCTCTCCAACCCTATTGATTCTTTATAAAAGATATTTATTTTATGTGCATGTGTGTTAGTGTGTGGATGTGCACCCCATGTCTGCAGGTACCTGTGGAGGTCAGAAGAGGGTGTTGGATCCCTAAGAACTGGAGTTACTGGTTGTAAACCATCACATGGGTGCTGGGAACTGAACTTGGGTCCTCTTAAAGCGCAGTAGGTGCTGTTAACTACTGAGCCACCTCTCCAGCCCCAGCTGTCACATCTTAAGGGGCACATCTCATCTCAAGGGTCTCACTCTCAGGACTTCACCTAAGCCTAACCTCCACCCAAAGGCCTCACCTCACATACCATCAAAGTGAGAGTTAAAAATTAAGCACAAGTCAGGAAATTATGGCATGTGCCTTTAATCCAAGCACTTGGGTGGCAGAGGCAGGCAGGTCTCTGTGAGTTCGAAACCGGCCTGTTCTATAATGTGAGTTCTAGGACAGACAGAGCTACATATTGAGGCTCTGTCTCAGACAGTAGATGGATAGACACATTGATAACAATAGATAATTTGGAGGGAGAATCCAGTCCATAACAGAACATGCATGATGAGGCTTCTGAGTCAGGCATGTATGTGCAGATTATGATTTCCCGGCATGCATTCTGGAGAGGGAAATATATGAAGGCTTCCAAAAACCTGTGGATTTATGTGAGTGTATGGGAGGAGGCCACTGGGAAGGTCTGGGGTACCTGAGGGGTAAGGATGCTGGGGAGTGTGTATTCCTTGCTGGTCAAAAGAGCTGTTCTTGGGCTGGAGAGATGGCTCAGGGGTTAAGAACACCGACTGTTCTTCCAGAGGTTCTGAGCTCAATTCTCAGCAACCACATGGTGGCTCACAACCCTCTGTAATGGGATTTGATGCACTCTTCTGGTGTGTGTCTGAAGACAGCTACAGTGTACTTATATACATAAAAATAAATAAAAAATTAGTTTTTTAAAAAAGCTGCTCTTTATGGATGCCTTAAAGAGGAAGTGCTCAGCCAGGCGTGGTAGCACACGCCTTTAATCCCAGCACTCGAGAGGCAGAGGCAGGTGGATTTCTGAGTTCGAGGCCAGCCTGGTCTATAAAGTGAGTTCCAGGACAGCCAGGGCTATAGAGAAACCCTGTCTCGAAAAACAAAAAAAAAAAAAAAAACAAAAATAAAAAAAAAAGAGGAAGTGCTCGTGGAAGGGCCTCTGAGGCAGTCTCTCACAGAAAGATGGAGATTTAGATAAGTGCAGGCTTGGTAAGATAGACACACTGACAGGCAGCCATGTTTACAGCTGCCTAGGGGGCCCAAGAAACTACTGATCATGAAACTCCGTAGTCAGGGAGGCAGAGGACCTAGACAGTGGCTAGAGAGATAAGCCCCTGGGAACAGCTGCTGGTCTGTATCTACCTCTTCCGTTCCCTAGGGGCTGGCACCATTGCCCACGGAGAAGCCACCTAGCCATTTCCTTCCCCTGCGGCTTGTCAGTCAGTGCAGGGTACCAGACGTCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTACGCGCGCGTGCGTGCACGTGTGTCTTTCTGTCGTCTTTATCGTCCTCCTTCCCAGAAACTGGTGTGACTGACCCCCTTCCTATTTTAATCTGGCCATGCAGGGGAAGATGGACTACGGGGTGGTTTTTCTGTAACCTTGAAGACCCTGAGATCTCAACGGAAGTTTGTAGCTCTAATGAGAAAGCATAGGTGGGAGACTTCGGGAAAGGGGACGTTGAGTTCCGGAAAGCGGGGAGGACTGCTACTGGAAGTGGGCGCTGATGAAGAAGAAAGTACTATAGGTTTTCCATAGTAGCTGTGGAGTGAGTGAACTGTAAGAATAAATCAGGGCTCATTGGAGGCTGGCTGAGAACAGACCGGGATGTGCAGGCGATTGCAGGCGGCAGGGTTTGCAGGGTGGTGTTGTTAGTCGGTTGAGGGGCCGTGGGGGCTGGGGTTCAGTGAGCCTCCTCTTGGGGTACAG
Seq C2 exon
AACTTCACTGCCTCGGGAGAGGCAGAGGCGAGGCGCTGCGCGCGGCGAGAGGAGCTACTGGCTCGCGGGTGCCCCGCGCAGGAGCTAGAGGAGCCGAGAGGCCGCCAGGAGGTGCTGCAGGACAAGCCGCTCAGCCAGGGAGATCGCGGCGAGGGGGCCACCCAGCTGGCCCCGCAGCGGATCCGCGTCACGCTGCGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001281-Itgb7:NM_013566:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.114 A=NA C2=0.477
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=PU(57.5=33.8),PF0036213=Integrin_beta=PU(50.0=25.0)

							
A:
NA

							
C2:
PF0036213=Integrin_beta=FE(15.7=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000001327





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000123227
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:53197952-53200242 
LOW PSI
HsaINT0082945
(ITGB7)
Human
(hg19)
chr12:53591736-53594026 
LOW PSI
HsaINT0082945
(ITGB7)
Rat
(rn6)
chr7:143830932-143833182 
ALTERNATIVE
RnoINT0076439
(Itgb7)
Cow
(bosTau6)
chr5:26964607-26966349 
ALTERNATIVE
BtaINT0078256
(ITGB7)
Chicken
(galGal4)
chr7:7181547-7181791 
LOW PSI
GgaINT0045903
(ITGB2)
Chicken
(galGal3)
chr7:7149477-7149721 
LOW PSI
GgaINT0045903
(F1NM67_CHICK)
Zebrafish
(danRer10)
chr9:45174499-45175513 
LOW PSI
DreINT0083259
(itgb2)
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"