Special

HsaINT0082795 @ hg19

Intron Retention

Gene
ENSG00000150093 | ITGB1
Description
integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12) [Source:HGNC Symbol;Acc:6153]
Coordinates
chr10:33218750-33221528:-
Coord C1 exon
chr10:33221443-33221528
Coord A exon
chr10:33218973-33221442
Coord C2 exon
chr10:33218750-33218972
Length
2470 bp
Sequences
Splice sites
5' ss Seq
TCAGTAAGT
5' ss Score
9.14
3' ss Seq
ATATTTTATATGTCATTTAGACA
3' ss Score
4.6
Exon sequences
Seq C1 exon
ATGAAAATAGATGTTTAAAAGCAAATGCCAAATCATGTGGAGAATGTATACAAGCAGGGCCAAATTGTGGGTGGTGCACAAATTCA
Seq A exon
GTAAGTAAGGTTGCTCAAGTCCTTTCCATTTGTTCTCTGGTCATTTAGTGTGGCTCAGTGCTGTATCCTTCAGAAGCACATATTAATTTTTATGTAAATCATAAAATGAATAACCTAATGGTTTGGAGCTATGTGGTTCAACACAGTAGCCACTAGGCAGATGTGGCTATTGAGCACTTTTGTACAAATTAGAATTGCTCTAAGTTTCAAAGATATACAAGATTTCAAAGACTTAGTATTAAATAAATAATAATGGTGAAATGATAATTTTTGTATATTTAAAAATAATGTTATAACAGTGTTAAAATTTTCTCTTTTTCTTTTTTTAGTGTGGCTACTAAACAATTTTAAAATACATATATTTGTAGCTCATCTTTGTGGCACATATTAGATTTTTATGGGAGAACCTTCAAAAAAATCCTAGTCATTTAGTTTGACTGTTTCAGATTTCCCCTTTTTTGATGGGGAGGTATAAATTAACCTTCTTAATTATATTTGAGTTAAACTACTGGAATTGATTTGCATCCCAATATAAGCTTATTGAGGTTAATTAGGGTTTGGATTTTATTCACTTTTGTCATCTCTATACTTTTGCTAATATGGTACCTTCCACAAAGCCTACTAAATGTTCAGTGAGTCAATGAATGAATGAATGAATATATCAAAAGAGAAGGTAAGGAGAAGTCATTTTGAGGTTGTATAGTTTATTCACAGAATGAATAACTAATATCAGAAGATCAAGGGGTTACTGATTTTGTTTTCATGCAGGCATTTGGGCCCAAGTTTCAAGTGCCTATTTTTGTATGCCTAAGTGGTCAAGTGTCAGATATGTCGTATGGTTTGACCACATGAAAGAAAAAATGAGAGGTTTTGTTGTTTTTCAAAAATTTTCTAATGGTGTTTTCTAAAAGTGGTGTGTTGGGATTACATTGGCAACAGTGGAGGAAATATGGAGTGTTGTGAGTTTGTCTCAGGCAAGGCTTATGTAACTGAAGCTCTTGGTTTTCATATCTGAAAATGAGGATGATAATATCCGCTTTATCTATTGTTACAATAATTAGAATTGATGAACTTAAAGCAGTTTCACTTAAAAACTTCTAAATAAGTGGTAGCTGCTATTATTGTTAACATATCCATTTTATGGGGACTACAGTTTATCTGTAGTTAAGGATTATCTTAGCCTTTGAGCTTTGGAGCATAATCCTTAAAATTTTAAAGGCTTTCTGAATATATTCAGTGAAATTGTATTTGGGTGTCATGATTGTAAATTTCGTGGATTGATTAGTATTTAGAAATGTGTAATTCACTAGGATCTTGTGCTTTGGTAGGTAGTAGTTTAGGTTTAATAAATAGTGCAGCTTTGAATTATCTGATTCTTGGTATTCCCTTCCAGTTGTTGATTACATAAATACTCTCATTAGTATGATGTTTCTCTTAAAAAATCTTATGTAAAAACTATTGTGTATTCTTTAAATTTAAATATCTTCACTTACTGTTACTTTATACAGCACCGTTAAATTGATATTTGATAAATAAATACCATATATAATGTCACTGTTTCCCCCACATTTTCACATTTCTTGAAACACCTTTATTCACAGTCTTTATATAGATCTTTAACAGCAGTGTTTTTGAATTCACTAAGGCACTTTTCAGTTATATGATTAAATTTTTATTTCTAAGTTGTTTGATGTATACCACATTTAAAATCTCTGTCATTACTAGAAATTTTACTACTGCAAATATCCATTCACCTGCCATTAAGAACTTTTTTTCCTTTTTTGAAATTTACCTGCCATTAGGACCTTTTACCCTTGTCATATACTTACTCCTTTTACCCTTGTCATATACTTACTATTTTGCTTTTTAAAAGTTTTTTAAAAACTTATTTACAATAATAGCTAATACTTAAAGTTTTTTCAAACCTGTGGGAATACTTATTTAATCGGTGCTAAATTTCGTGTTGTCCTTTTAAAAAATGCAATAATTAATTGAGATGTTTTTAAGCTCGTCTGTTTTCCCTAAACATCGGGTTGTTCAGCATATTGCGATGGGGAGAGTGCCACATAATATGAGACGCTTTGTAAGGACTTTTCAAAGGGAAATTTTGGAGAAATGATCTGATATTTGGGTGTATGTATACATTATTAGTAGCCATTAACCATGCTCAATTAGTGATTTCACTAAAGAAATTGCTTTTGATTAGATACTCTGAATTACAAGATAGAGCATTTACTGTGTACACTTGGGTCAGTTCTGGGAAAGGTATTACTTTCTTGGAAATGATTGTTTTTTAACAAGAACACTTACCACAGTTTGGATGAAGGGAGCATTTTGTTTAAAAGCCAGAATTGGGGTACATTAGATGTGATTTGATGTTTTGCAATTTAATTGCTTATTTGCAATTATTATGTAAAAAGGTTTGACCATTACAATTTTCATTTATACCTATATTTTATATGTCATTTAG
Seq C2 exon
ACATTTTTACAGGAAGGAATGCCTACTTCTGCACGATGTGATGATTTAGAAGCCTTAAAAAAGAAGGGTTGCCCTCCAGATGACATAGAAAATCCCAGAGGCTCCAAAGATATAAAGAAAAATAAAAATGTAACCAACCGTAGCAAAGGAACAGCAGAGAAGCTCAAGCCAGAGGATATTACTCAGATCCAACCACAGCAGTTGGTTTTGCGATTAAGATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000150093-ITGB1:NM_002211:3
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=0.546
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0143720=PSI=PU(46.3=86.2),PF0036213=Integrin_beta=PU(15.5=58.6)

							
A:
NA

							
C2:
PF0143720=PSI=PD(56.5=64.0),PF0036213=Integrin_beta=FE(71.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSP00000364094





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSP00000303351, ENSP00000303351f6407A, ENSP00000379350, ENSP00000388694, ENSP00000398029, ENSP00000400544, ENSP00000404546, ENSP00000417243, ENSP00000417537, ENSP00000420282, ENSP00000420416, ENSP00000420792, ENSP00000431326, ENSP00000436214
  



Associated events






Other assemblies


hg38




Conservation


Mouse
(mm10)
chr8:128707160-128710252 
LOW PSI
MmuINT0084061
(Itgb1)
Mouse
(mm9)
chr8:131231060-131234152 
LOW PSI
MmuINT0084061
(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
  • Autistic and control brains
  • Pre-implantation embryo development






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"