Special

MmuINT0012725 @ mm10

Intron Retention

Gene
ENSMUSG00000034254 | Agpat1
Description
1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha) [Source:MGI Symbol;Acc:MGI:1932075]
Coordinates
chr17:34611274-34611700:+
Coord C1 exon
chr17:34611274-34611449
Coord A exon
chr17:34611450-34611604
Coord C2 exon
chr17:34611605-34611700
Length
155 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TGTTTATGGCCTCCCATCAGGTG
3' ss Score
8.74
Exon sequences
Seq C1 exon
GAATGATGGAGGTCCTGCCAGATCGTTGTGTGCCCATTGCCAAGCGTGAGCTACTATGGGCTGGCTCTGCTGGGCTGGCCTGCTGGCTGGCAGGAATCATCTTCATTGACCGGAAACGCACAGGGGACGCCATCAGTGTCATGTCCGAGGTGGCTCAGACCTTGCTCACCCAGGAT
Seq A exon
GTGAGTCTTTCTCAGATGGGGACCTGGGGACCAGGGCATGAGTGGCTGCAAACCACAATAGTCAGTGCTGTGTCCTCTCAGTGCTGAGTTCTCTCAGTGCTGAGTCCTCTCAGCATGGCATGACCCCCCCTTGTGTGTTTATGGCCTCCCATCAG
Seq C2 exon
GTGAGAGTCTGGGTTTTTCCTGAAGGAACAAGAAACCACAATGGCTCCATGCTGCCCTTCAAACGAGGCGCCTTCCACCTTGCAGTACAGGCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034254:ENSMUST00000037489:4
Average complexity
IR
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:
PF0155316=Acyltransferase=PD(57.1=95.2)

							
A:
NA

							
C2:
PF0155316=Acyltransferase=FE(24.0=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000048573





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000109776, ENSMUSP00000133441, ENSMUSP00000133876, ENSMUSP00000133947, ENSMUSP00000134242, ENSMUSP00000134358
  



Associated events






Other assemblies


mm9




Conservation


Human
(hg38)
chr6:32170261-32170424 
LOW PSI
HsaINT1003187
(AGPAT1)
Human
(hg19)
chr6:32138038-32138201 
Rat
(rn6)
chr20:4376437-4376540 
LOW PSI
RnoINT0015236
(Agpat1)
Cow
(bosTau6)
chr23:27022378-27022526 
LOW PSI
BtaINT0015854
(AGPAT1)
Chicken
(galGal4)
chr17:7741278-7741385 
LOW PSI
GgaINT0124122
(AGPAT2)
Chicken
(galGal3)
chr17:8423869-8423976 
LOW PSI
GgaINT0124122
(AGPAT2)
Zebrafish
(danRer10)
chr21:7647602-7649723 
LOW PSI
DreINT0027820
(agpat2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CCAGATCGTTGTGTGCCCATT

				
R: 
CTGTACTGCAAGGTGGAAGGC

				
Band lengths: 
249-404

			

		

	





	
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
  • Ribosome-engaged transcriptomes of neuronal types
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types





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