Special

MmuINT0084202 @ mm9

Intron Retention

Gene
ENSMUSG00000026971 | Itgb6
Description
integrin beta 6 [Source:MGI Symbol;Acc:MGI:96615]
Coordinates
chr2:60507159-60510768:-
Coord C1 exon
chr2:60510689-60510768
Coord A exon
chr2:60507364-60510688
Coord C2 exon
chr2:60507159-60507363
Length
3325 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
CCTCACCCCCACCCCCGCAGAAT
3' ss Score
8.55
Exon sequences
Seq C1 exon
GTGGCTGTGCCTGGGGTGGTGCAGAAAGCTGCTCAGACTGCCTGCTCACAGGACCCCACTGCGCCTGGTGCTCCCAGGAG
Seq A exon
GTAAATCCCTGGCTCTCACCCTGTTTCTAACACTGTTTCTACATCAGTTAGCATCCTCAGCGAAAGCGCTTCTCTCAGTGCGGTTGAATGAGTAACAAGTTTAAGAAAGGAACATGAGGGTCAGTGGACCAAAGTCGGATTCATCTATACTTTGGAAACAACTTACTGAAGGAACGGATGCCAAATTGTTCTTTAAAACCTGAACATCCTTTACTAAATCTAGACAGTTCTTTTATTTAACTTAATTACTTTATTTATTTATTTATTTTTATTTTTGAGACAAGGTCTCACTACATAGCCCTGGCTGTCCTGGGGCTCACTATGTAGACTAGGCTGCCCTGGAACTCACAGAGAGGTGGCTGCCTCTGCCTGGCCAGTGTTGCCAGCCACCTGGTTACTTCTCTTGCTATAAAGTCTTCCTAGTTGTTTGCTGGTGTAACATTCTGTCTGGATAATTGGTGGCCACAAAGATATTGTCCAAAGTGAAGCAGACATTGAATGTTGATACAATGTAGTTGTGTTCGCATCAGGGACCCGAGATCCGGTGTAAGTCTGTGCTAGGTACTTCGAGAAGGGAAATCTACGATTCAGCCATCAGCCAATTCCTGTACAAAGTCATGAACAGAGTGAGCACAGGAAACTCTCAAGTGGTGGTTCTCAACCTGTGGGTCAGGGTCCCTGTCAGGGTTGGATGACCTTTTCACGGGGGTCGCCTAAGATCATTGGAAAACACATGGATTTACATGACAATTCATAACAGCAGCAAAATTACAGCTGTGCAGTATAAACCAAAATAATTTTATGGGCGGGGCTCATCACAACACACTGTATTAAAGGGTTGTGGCATTAGGAAGGTTAAGAACCACTGCTTTAAAGAAATGGTCCTAGTCTGGTCAGAGTGAAACTTGCGTGAAGAAGTGTGGAGGCCATGAGGGCTAAATAACAAGACAGACCAAGTCCCAGCCTATGTTGTGATGAAGAGAGCAAGGTGTAGTGTAAATGATTCACACTAAGAAAAAGCAGTCTTGGTTTTCTGGATTTTTAAGTCCCATCCATTGGAAAGAATCTAAGTGCCAATCAAGGCTTACAAATGCCAACAGCAAAAGCCAAATAGCATGCAAAGGGAAAGGAATCTAGATGCCTGGATCAGACCTGGGCTGTAACTATTTGCACCCAAAGTCCCCACTTATTACACATCTGTGGAGGGTTGCATCACATGCAGAAGCATAAACCATGCACCCCGCCCCCCAGTGCCCCACACTACCTTAACTGCTTAGGCCACAAATAAAATTCAAGGCAATTATTCTCTTATAAGGTTTAACATGAAATGCAGGGTTGAGAATATTCAACAAGGAACAAGTCCATAGACTCTTTGGACACTGTCTAGAAGATAATATTAGCTTCATGGCAGAGACAAAGAATACTGTGTCAATCTGGAGTTTATGTTTACTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTACCCATGGAGGCCAGAAAACAAAATCAGATCCCCTGGAACTACACTTATAGGTAGTTGTGAGTTCCTTGACATGGTGCTGGGAACTGAACTTGGGTCTTCTAGAAGTATTGTTAGCTGTTGACCTCTCTCTCCAGCACACTAGAATGTATAATTAAATTCATTTTTTAGCATAATCGGGTGTTTCCTAAGGTGTTACTGAGGGTTTTAGTTGTAGCTGGTCAAGTGATCATCAAGTTTTAAGGCCAGATCATTTCAGAGGCCTCTCCAATAATAAAAGCAGTCATGAGTACGTCAGCTGAGGCAGGCAGATGTGGCCGTTAGCGCAAAAGATGAGCAAAACCGAGAGTATACACAGACTCACAAACTGCACGTCTCCAACTTTATTCTTTCTTTTTTTAAAAAGGATTTATTACTATATTTATATAAGTACACCATAGTTTTTTTTAGACATACCAGAAGAGGGCATCAGATCAGATGGTTGTGAGCTACCATGTGATCACTAGGATTTGAACTCAGGACCTTTGGAATAGCAAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCACCACCTTCCCAACTTTATTCTTTTGGCAAAGGCTGAGCAGAGCTGATAGCCATTGTACTGTGTTAAGAAGCATTCTGAGGCCTTGGGCAGCTACTGCTTGCCTTTATTACACCACAGGAAGTTGCATTTTACCAGACCCAAGTTATAGCTGTAAATCTGTATGGGTCTGATTGGCAGGGAACAAATCGTATTTTTGAAAGTCAATTTCAGAAGAAGTGTATCTTTCCTAGTTGGTGAAAATGACAGTAATGGCTTAGAATCCTAAGGTGGCAAGAAACTGGTTTCTATGTGCACATCACACACACACACACACACACACACACACACACACACACACCACACCACACCACACCACACCACACCATACCACACCAGAGTCCAAGGGCCTCGGGTCAATTCAGCTCAGGACCAGCTTTGCCTTTCCTGTCAGTAGCACCTGTTCTGTCCATGCCTTGGCTCCATCTCCCTGCTCTGGGTACTGCAAGATTAGAATGGCCACATCTCTGCTGAGCCCTACACCTCCCCACCTTCTCTCTGGATGGATCTGAAGGACTGGGACTTTCTGAAATCTCAGACAGAATGTGTATCTTTAAAGCATCTTCTCTTTCAGCCTCCAGACCTGGGTGGTGGAGGGAGCTCTAAGACCTTGAACTAGAATCTGTTAAGACACCGAGCTTAACGTCCTTGAGAGGTCAATTCAAGTGAAGGGATGCTGTAGTCGAAGGGAACACACCATCCCGTAAAAGCAGCAGAGTGCCAGACAGGGAGATGCCAGGAGCCCTGTCCTTTGGGAACCCACAGCAAACATCTCTCTGGGTTGGTTGACAGTCCTAGGCTAGGAGTCCAGCCATTCATCTGGAACAAATAAATTCTCAGGAAAATATCAACTTTGGGAACTCAGACATTTAAAAGGTCCACTCAGATCACTGAAGAAATTTTACAACATGGGCTTTAGGAAGAAAAAAAAAACCTGTTAGATGAATTTGACTGAATGTAGTAAGAAGAAAAAAGAAAGAAGAAGAAGAAGAAGAAGAAGCTCAGGTTTATTCAAAAATATTGCTGGCTAAATTCTCCAGTTATTCAGCTATCACAGAACTCCATCTGTCAATCACCACCAGTCGTGTAGGGGATGTGATGTTCCTAGCATGTATTTATTTCACAAAGCACATACAAGTTTAATGTCTGGAATCTTACAAAGAGATGCAGATTTGTCTTTTCCTCCTTGTTATCTTCCCCTCACCCCCACCCCCGCAG
Seq C2 exon
AATTTCACCCACCTGTCTGGAGCTGGCGAGAGGTGCGACACCCCAGCGAATCTTTTAGCCAAAGGATGTCAACTACCCTTCATTGAAAACCCTGTCTCCCGCATAGAAGTCCTTCAAAATAAGCCTCTCAGCGTGGGCCGACAGAAGAACAGTTCTGACATTGTTCAGATTGCTCCTCAAAGCTTGGTTCTTAAATTGAGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026971-Itgb6:NM_021359:2
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=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0036213=Integrin_beta=PU(4.0=63.0)

							
A:
NA

							
C2:
PF0036213=Integrin_beta=FE(16.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000028348





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000054944, ENSMUSP00000108136, ENSMUSP00000117815
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:160196421-160199178 
ALTERNATIVE
HsaINT0082929
(ITGB6)
Human
(hg19)
chr2:161052932-161055689 
ALTERNATIVE
HsaINT0082929
(ITGB6)
Rat
(rn6)
chr3:46722584-46725970 
LOW PSI
RnoINT0076426
(Itgb6)
Cow
(bosTau6)
chr2:36257475-36260010 
LOW PSI
BtaINT0078243
(ITGB6)
Chicken
(galGal4)
chr7:21294513-21296864 
ALTERNATIVE
GgaINT0049593
(ITGB6)
Chicken
(galGal3)
chr7:23383087-23385438 
LOW PSI
GgaINT0049593
(E1C6K8_CHICK)
Zebrafish
(danRer10)
chr11:11002529-11003884 
LOW PSI
DreINT0083341
(itgb6)
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"