Special

MmuINT0084236 @ mm9

Intron Retention

Gene
ENSMUSG00000025321 | Itgb8
Description
integrin beta 8 [Source:MGI Symbol;Acc:MGI:1338035]
Coordinates
chr12:120409120-120411893:-
Coord C1 exon
chr12:120411759-120411893
Coord A exon
chr12:120409523-120411758
Coord C2 exon
chr12:120409120-120409522
Length
2236 bp
Sequences
Splice sites
5' ss Seq
GAAGTATGT
5' ss Score
6.97
3' ss Seq
TATTTTCCTTTGAAATTTAGGTT
3' ss Score
7.8
Exon sequences
Seq C1 exon
AAGATTATCTCAGAAGTAAAAGTGCAGCTGGAAAACCAGGTACACGGTGTCCATTTTAACATCACTGCCATCTGTCCAGATGGGGCCAGAAAGCCAGGCATAAGTGGGTGTGGAAACGTGACAAGCAATGACGAA
Seq A exon
GTATGTGGCAGTATGTTTTTCTTGTTTAAGACAATTTTTTGGTGTGCTTTCTTAAAAAAAAAAAACAAAAAAAAAAATTACTTTAAAAACATTGCTACTATTAGAATATTGTTTCAACTTTAAATGAGCCTTCCTGTTTCTTCTTAAAGTTACGTCTATACATAATTGACTTCTCTCAAACTTTCAAGTTAAAATAAATATGTATTGTGTTAAGTACTTATTAAATACTTAGTAGTAATATATTTTCTGAGAGGTTTTGCCTAATAAAAAAATAACATCCTTCCAAGCAAGTAGTATCTGTAGATGTAATAGTGACAAAGCCTTTATTGTTTCAAATCTGTTCATTCTCAGAGTATGAAAGGATGGTACAGTATATAAAAGCTACGAATTCCAAAATCTTTCATCTTGTGATGTCCAGGAAAAGGAGATGAAGAAATTTGTTAAAATCAGTCAAATCAGAGGGATGATACCATTTATATAATAACTAGAAAGAGTTGAGAGTCCAAGAGAACTCCAAGACCAGATGAAATGGTTATTCTCCAAGAACTGCCAGAATAGACTACATCATGTTCTCAGCAGGGGCTGGGTAGGGTGTCACTTCTTCAGTATCTCTTACTTCAGCTGTACCTGAATGAACTGGTACAGAGAAATTTTTGATTCTTTCCTCTTTCTTGTTCTAAGGTTCTGTAGTTTTATTACTCTATCCTGTATTGGGAAGAATTTTTCAAATGCAAAATCCTAAAGTTCTAAAATTAATTCAAAGAAAACACTTAAATTTTTTTTCCTCATAGGAACATTAGAAGCTGTGGGTAGTGTGATTGTGCCCACAAGCTGTGTATCTTTAATTAATTATCCTAAGCCTCTAATTCAGTAGTTTCCTCTATAATTTTTCCTTGGATATCATTCAAAAACGATCATATACTAGTTTATATAAGATACATTTGATTTCTGCTACAGAAAAGTTTTTGTAAATTTTTGTAAAAAAAATAAAAGGCTAAATTCTTAAAAACAAAGTGAGTCTTTAAAGACTCAAATATATAACAATGATTTACCTTCCTTAATTTTTTCTTTCTTTGACTATGCTCCTTTCAACTATAAACAGCTTGTCTCCCACGAGGAGTCAACCAGCCTTCAACTTTAGAAGGTCTGTTTTATTATACTAGTTTTAATAGCAGTGGCCACTCATCCTACACATCTGTGTATCCTTAAAATTCTTAGAGGCAAAAACAATTTGAGCACAAACTGACTCCAACCACACTGATTTTAATGTGACACATTTAAATAAAATGTCTTGTACATGGATGCCTAAATATAGATCTTTTATTTCATGCTACATAATTTCCAATTTAAAAGCCCAGCATCCATTATTTTAATGTTGGAATTTAATTACTGTAGTGAACTCATATATAACTGTATGTATATATAAGCTTCCCGATTTTCCAAAGCACCTGAAGCTGAAGTCAGAAAATATAGATATTAAATCAACCATATTATAAATAACAAGAAATTAAAGAACAAGGAAAAATTTTCAGGCAAATAAACTGTTGTTCTAGAGGGAAAAACAAACAAACAAACAAACAAACAAACCACTCCTTGCTACTAGTCCATTCTTTAGTTCTGGGATGACCCCACAGTAACAAGTGACTTTGGTGTGAGGTCTTGAAGCTGGAGAATAAGTCCTGAGCCTCTTTCTCAAGTAACATCAGAGATGGGGTTGTGTTTTCCTCCACTGAAAAACTGTATATGTATATACTAAAGATCATCTCTTGGTCTTTACCTTGAGCCTCTAAAAAGTAAAATACAAATAAATAAAATTGCCCATATGACTAAATCAGGGTTCTGACCCAGAAGATAAGAAACCATTTACTTAGGTTTATTGGTTCCTAATGCCAATTGTTCACTAACCTCATATGTCCAATTCAGAAAATAGAACATTGATTCAGCAGTTGTCCATGAAATCAGTTACCTAAGGTGACAGACACCTGAGGACAAATGGACACATGGTGATTTACAGGCCATTAGCAATTGTTACTTCCTTTAATTCTAATTAATCAGTTAGGCAAAAATGGAATTAAGTGGCAATTATGTACTTACATATTAGATTGCATGCACATGTGATTTATAAATATTGTTGGTATCTCTAAGATGTTCACCATTGATTTAAATATCATTACTTGATATACTGTTTACAGTATCCAAGGATATAAAGATATTTCTATTTTCCTTTGAAATTTAG
Seq C2 exon
GTTCTTTTCAATGTAACTGTTGTGATGAAAACATGTGATATCATGGGAGGAAAAAACTATGCAATAATCAAGCCTATTGGTTTCAATGAAACCACTAAAGTCCACATACACAGAAGCTGCAGTTGCCAGTGTGAGAACCACAGAGGACTCAAAGGACAGTGTGCGGAAGCTGCCCCAGACCCCAAGTGTCCACAGTGTGATGACAGCAGATGTCATTTTGATGAAGACCAGTTTCCTTCTGAAACTTGCAAGCCACAGGAGGATCAACCTGTCTGCAGTGGCCGAGGTGTTTGCATCTGTGGGAAATGTTTATGTCACAAAACCAAGCTAGGAAGAGTGTATGGCCAGTACTGTGAGAAGGATGACTTCTCCTGTCCCTATCTCCATGGGGATGTGTGTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000025321-Itgb8:NM_177290:9
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=FE(10.6=100)

							
A:
NA

							
C2:
PF0036213=Integrin_beta=PD(9.9=30.4),PF079748=EGF_2=WD(100=26.7),PF079748=EGF_2=PU(32.3=7.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000026360





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:20398995-20401720 
ALTERNATIVE
HsaINT0082964
(ITGB8)
Human
(hg19)
chr7:20438618-20441343 
ALTERNATIVE
HsaINT0082964
(ITGB8)
Rat
(rn6)
chr6:147102091-147104275 
RnoINT0076455
(Itgb8)
Cow
(bosTau6)
chr4:29204702-29207367 
LOW PSI
BtaINT0078276
(ITGB8)
Chicken
(galGal4)
chr2:30146514-30149322 
LOW PSI
GgaINT0090896
(ITGB8)
Chicken
(galGal3)
chr2:30036195-30039003 
LOW PSI
GgaINT0090896
(F1NE25_CHICK)
Zebrafish
(danRer10)
chr19:2463323-2464815 
LOW PSI
DreINT0083361
(itgb8)
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"