Special

MmuINT0083786 @ mm9

Intron Retention

Gene
ENSMUSG00000027111 | Itga6
Description
integrin alpha 6 [Source:MGI Symbol;Acc:MGI:96605]
Coordinates
chr2:71691591-71694815:+
Coord C1 exon
chr2:71691591-71691720
Coord A exon
chr2:71691721-71693910
Coord C2 exon
chr2:71693911-71694815
Length
2190 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATT
5' ss Score
5.73
3' ss Seq
CTGTCCCCCACCCCTTCCAGTGT
3' ss Score
9.02
Exon sequences
Seq C1 exon
TGTGGCTTCTTCAAGAGAAATAAGAAAGATCATTACGATGCCACCTATCACAAGGCTGAGATCCATACTCAGCCGTCTGATAAAGAGAGGCTTACTTCCGATGCATAGTATTGATCTACTTCCATAATTG
Seq A exon
GTAATTGATCAATGTTTTTCATCGCTAGCTTTGGGACCTGCTGTGGTTGTGGTGGCTAACTTAAGAGCGACAGCTTGCTGTGTCTGTCCCATTAACAGTTGTTTCCAAGTGGCTTGCCTTGCTTGGATTTATTTATTTTTGTTATTTCACTTGATAGCTCAGTTGTTGTTGTTGTTGTTGTTGATGATGATGTTGTTTGTTGTTGCACAAAGAATCTTCTGTTGCAGGTGAGTTATTTTGTGTTCTTGTTAAACAACACCACAGCAATGAAGGCAGCCACACTGGTTTGTCTGATTAGGTTTTAAGAGCTCCGTAGCTGCCCTTTGCCATGTGTTTTTGTATCGTGTCCCACTCGGAATTTCAAAAGTGCATGAGAAATCGGCCCAGATTTCTTGTTCGTTTTGGAATTCCCTGGGGGCAGGAGCTTTTGTCGACTGCCTGCTTAACCTGTTGCATGTGGGAGAGTTTGTGTATCTCCTGGGAGGAGGCTCTCTTGTCCTTGTCTCCATGGTTGTCCTTGTTCTAGAGCGATGGCCAGGCTTGGGGCGCTTCTTACTGCCGCTTGGACGTGGTCCTGTGCTAGCTAAGCATGCGCCCTCCTTTTCCCTCCTTTCTCTCCTGGGCCAAAGCCATTACAACAAAGAATCCTTGTCAGCACGTGGGCTTCTTGAATACTTCAGGACATGGTCCTTTCCCCAAGTAACCACCAGCGTGCAAAAAATTCTAGCACCCAAGTACTGGGGTGGTTTCTACTTCAAGATGTTGTAATGGAGTTTGACCAGGTTTCGTGTTCTTAGCCCCTTTCTTCCACCTTGGCTCTCAGCTGATTTTAAGTTCGTATTTCTCTCCTATGATTTATAAACCCATGGAAACAGGAACTATTGTCAATTCCCTTTTCTTTCCCATGGGCAAGAGGGATTTCAGTTACTGCTACAGTTCCTTTCCAAGGTATTGACCCAGTGATCCCAACATGGCCATTTTGATTGTACATTTCAACTGCATTTTCTTCTGTTTTTAAATGGGGCAGACAGAAATCATATTTTATAATAAGTATATTGGCTTTTTCTGCACAGAATTACAAATGAGACCATAGAGAAATGGCCTATACCAAACTCCAGGCTCATTTGGGATTGGGATTTTTGCCTTGCCTTGTGGCAATTTTATAACACAACATTCTTCAATATAATTATTCTATTCCTGTTGCCGTCACAAAATAAGGACATTAAATGATCATTCTACATAGATCCCTCTTCTGAACTGCATTTTTAAATTTGAAAAGACTCCTTTGAAAAGAAAAAAAAACATGTAAATTCTTATTTATAACTTCTAAAAATCTGGTTCAAAAATCTTAGGCATATTTTTTAAGTGAACTTTTGTTTAGATCAAAATTTTTTAAGTAAATAAAGTTTAATAATTTGGCTTCTTTACTTACCCCTCCCCTCCACAAGCCCCCTCCCCCTTTCTTTCTTTCCTTCCTGTTTTTAAAGGAAGAGGAGAAATTGGGGAATGCTCCAAAATTCAGTGTAGTGATGCTGCCCGTGAGTCCTGTGAGGCTCCTGACTGACTGGTGTTCTTATGCAACAAATTACTTTGTAACTCATTAACAAAACAGCGTAATTGGAAGCACCCCACCGAGTCTCCCCAATGACTATTGATAGAGGATTGATTGGAGGATGAGAGGCCCAGGGGGGAGAGAATCATGTTAGAGGAACATGGCGCACCAAACAGCGTTTGTAAAATTACCTGTGATCTGATTCACAGCTTATTAATGGGTGAGAAATAGTGATTTTTTTTCTTTATACCCTTAGAGAAATCCTCTTAAGCTGGCCATGGTATGCACACGCCTATTATCCAGCACTAGGGAGCTTCAGACCAGATGATGTTGAGTTTGAGGCAAACCTTGGCTACAAAGCAAGCTCCAGTTCCCTACACACAAATACAAGATGTTTTATAATGAAATAGCTGAGGCTATAAAAAGTAAAGAAGGTGGACACTGACTTTTCTGTGGGGCCCACATCCGTTCTCCCTGCTTACCCCACTGCCTACTTTTTCTTAAAAGGAATCAGTGCCTTTTCCGAGCACTCCAGAGGGAGACCTAGCTGCACTGAGTGCTTACAAGTTCTGGTGTATGCACCAGGTCTTCAGATTAACTAACTTCCATCTTGTTTTTCTGTCCCCCACCCCTTCCAG
Seq C2 exon
TGTGGATTCTTTAAGCGCTCTAGGTACGATGACAGCATTCCCCGATACCATGCGGTGCGGATCCGGAAAGAAGAGCGAGAGATCAAAGATGAGAAACACATGGATAACCTCGAAAAAAAACAGTGGATCACCAAGTGGAATGAAAACGAAAGTTACTCATAGAGAGGAGGGCACAGGAAAGAACACCTCACACTACCCAAAGCCCCCCCTTATTTTTTCCAGCTCAGAAATTCAGGTGGCTTCAAAGCCTGCTCAGCTCCCCCATATATGATTTCAGACTGACGACACCCAGTATGGACCTACAGTTTCAACTGTGGATATTGTTACACCTAAGGCTCCTGTTTTGCACAGCCAAATTTAAGACTGGTAGAGTGGATTTTTCTTTAACTGCCTTAATTTAACTTTCCGGATTGCCTTTGTTTTTGACGTGGCTGACTTCCACACGCTGGGGCAGGGCCTGCCCATCTGCACTGCTGGGATGCTCTCCCCCAGGTCACCTGTGCTAACAGAGTGGCTATCCCAGCCTGCTCCCACAAGCATTCTTCTCATAAGATTGACCTTGGCTCAAGACTGCCAATGGATAGCTGTGCCTCTGGTGAAAGTTCTGTCTTAAATGTGCAATAGAAGGTGATGTTACCCTTTGGCCTTCTTTCTCCATCTCCTAGAAGTGAGGACCCTTGCTGACGCCAAATGCACACAGGTTCCCGTCTCCCTTGTCACTAAAGCACAGGGTCGACAGACTTGAATGCTAGTTACATTTGTTTGTATATGATATTTATTTTTTTCTTCAAGCCATCTTGCTGTTGACTAATAGGCCAAAGATGCTTCTGGGTGGTTTAAGCAATGAGAATGAGAACCTGGGAGGTCTTGTTGTTGTTGTTGTTCTGACCTTACTTATTTACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027111-Itga6:NM_008397:25
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
3' UTR





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.171 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF151761=LRR19-TM=PD(45.7=88.9),PF153471=PAG=PD(47.8=91.7),PF0035715=Integrin_alpha=PD(86.7=36.1)

							
A:
NA

							
C2:
PF151761=LRR19-TM=PD(56.3=90.7),PF0035715=Integrin_alpha=PD(83.3=18.5)

						

					

				








    
Main Inclusion Isoform:
ENSMUSP00000118086





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000028522
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:172501902-172504090 
ALTERNATIVE
HsaINT0082515
(ITGA6)
Human
(hg19)
chr2:173366630-173368818 
ALTERNATIVE
HsaINT0082515
(ITGA6)
Rat
(rn6)
chr3:58510353-58512597 
LOW PSI
RnoINT0076063
(Itga6)
Cow
(bosTau6)
chr2:24132287-24134475 
LOW PSI
BtaINT0077907
(ITGA6)
Chicken
(galGal4)
chr7:17214670-17216174 
ALTERNATIVE
GgaINT0047790
(ITGA6)
Chicken
(galGal3)
chr7:19091308-19094349 
ALTERNATIVE
GgaINT0047790
(ITA6_CHICK)
Zebrafish
(danRer10)
chr9:3508562-3514098 
ALTERNATIVE
DreINT0083050
(itga6a)
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"