Special

MmuINT0072174 @ mm9

Intron Retention

Gene
ENSMUSG00000002546 | Golga2
Description
golgi autoantigen, golgin subfamily a, 2 [Source:MGI Symbol;Acc:MGI:2139395]
Coordinates
chr2:32153041-32153354:+
Coord C1 exon
chr2:32153041-32153097
Coord A exon
chr2:32153098-32153273
Coord C2 exon
chr2:32153274-32153354
Length
176 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CCTCTCTGCATGCGCCTCAGAAC
3' ss Score
5.88
Exon sequences
Seq C1 exon
TCTACATCCTACATCAACGGGGAGGGCCTCACATCTTCCAACATGAAGGAACTGGAG
Seq A exon
GTGAGTGGCCTGGACTCATGGCCCAGCAACCCTTTACGCCAACAGCCTATCTCCTCCTACAGGGACCTGGGTGCCCGCTGCCAGCTGAGACAGCCCACCACCCCCACCCCTAATGATGCTCTCTCTACCTTTCCCCCCATCCCTCCTCCAACTCCTCCTCTCTGCATGCGCCTCAG
Seq C2 exon
AACCGGTACCAAGAGCTAGCAGTAGCCCTGGACTCCAGCTATGTAACAAACAAACAACTCAGTAGCACGATAGAGGAATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000002546-Golga2:NM_001080968:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.909 A=NA C2=0.362
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF090796=Cdc6_C=PU(26.7=84.2),PF053776=FlaC_arch=PU(10.9=26.3)

							
A:
NA

							
C2:
PF090796=Cdc6_C=FE(43.3=100),PF053776=FlaC_arch=FE(56.5=100),PF106024=RPN7=PU(12.5=22.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000097768





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000080374, ENSMUSP00000109002, ENSMUSP00000109004, ENSMUSP00000109013, ENSMUSP00000114935, ENSMUSP00000117476, ENSMUSP00000133120
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:131029554-131029736 
HsaINT0070404
(GOLGA2)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr11:98888116-98888305 
LOW PSI
BtaINT0002395
([1])
Chicken
(galGal4)
chr17:5000916-5001365 
ALTERNATIVE
GgaINT0124933
([2])
Chicken
(galGal3)
chr17:5632978-5633427 
LOW PSI
GgaINT0124933
(GOLGA2)
Zebrafish
(danRer10)
chr5:1410254-1413344 
LOW PSI
DreINT0073791
(golga2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TCTACATCCTACATCAACGGGGA

				
R: 
CAATTCCTCTATCGTGCTACTGAGT

				
Band lengths: 
138-314

			

		

	





	
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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