Special

MmuINT0072177 @ mm9

Intron Retention

Gene
ENSMUSG00000002546 | Golga2
Description
golgi autoantigen, golgin subfamily a, 2 [Source:MGI Symbol;Acc:MGI:2139395]
Coordinates
chr2:32154406-32154645:+
Coord C1 exon
chr2:32154406-32154468
Coord A exon
chr2:32154469-32154551
Coord C2 exon
chr2:32154552-32154645
Length
83 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TGGTGGCCTTTTCTCCAAAGGTT
3' ss Score
8.84
Exon sequences
Seq C1 exon
GAGAAGAAGGATTATCAGCAGAAGCTGGCAAAGGAGCAGGGCTCTCTCAGGGAACAGCTGCAG
Seq A exon
GTGAGAGGTCTGGGCAGTGTCCCCGAGTTCTCTGGAGAGTGTTGCTCTCCCTTCTCTCAGCATTGGTGGCCTTTTCTCCAAAG
Seq C2 exon
GTTCACATTCAGACCATAGGCATCCTGGTGTCTGAGAAGGCAGAATTACAGACGGCCCTGGCCCACACTCAGCAAGCAGCCAGGCAGAAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002546-Golga2:NM_001080968:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.605 A=NA C2=0.408
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF090796=Cdc6_C=PD(3.3=9.5),PF106024=RPN7=FE(41.7=100)

							
A:
NA

							
C2:
PF106024=RPN7=PD(12.5=33.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000097768





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000080374, ENSMUSP00000109002, ENSMUSP00000109004, ENSMUSP00000109013, ENSMUSP00000114169, ENSMUSP00000114935, ENSMUSP00000115003, ENSMUSP00000121886, ENSMUSP00000133120
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:131028161-131028248 
ALTERNATIVE
HsaINT0070407
(GOLGA2)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:98886559-98886646 
LOW PSI
BtaINT0002398
([1])
Chicken
(galGal4)
chr17:5003949-5004188 
ALTERNATIVE
GgaINT0124936
([2])
Chicken
(galGal3)
chr17:5636011-5636250 
LOW PSI
GgaINT0124936
(GOLGA2)
Zebrafish
(danRer10)
chr5:1407597-1409811 
LOW PSI
DreINT0073794
(golga2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGAAGAAGGATTATCAGCAGAAGC

				
R: 
GCTTTCTGCCTGGCTGCTT

				
Band lengths: 
154-237

			

		

	





	
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






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