Special

MmuINT0007824 @ mm9

Intron Retention

Gene
ENSMUSG00000026944 | Abca2
Description
ATP-binding cassette, sub-family A (ABC1), member 2 [Source:MGI Symbol;Acc:MGI:99606]
Coordinates
chr2:25301958-25302227:+
Coord C1 exon
chr2:25301958-25302061
Coord A exon
chr2:25302062-25302134
Coord C2 exon
chr2:25302135-25302227
Length
73 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
CCTGAGCTGTCTGTCCACAGCAT
3' ss Score
7.92
Exon sequences
Seq C1 exon
GATGAGCCCACCACTGGCATGGACCCTAAGGCCCGGCGCTTCCTGTGGAACCTCATTCTGGACCTCATCAAGACGGGACGTTCGGTGGTGCTGACGTCACACAG
Seq A exon
GTGTGCCCCTCCCCCACCCCTCCGTGGGCCTCTGGCAGCCCCTCTGGTACCAGCCTGAGCTGTCTGTCCACAG
Seq C2 exon
CATGGAGGAGTGTGAGGCTCTGTGCACACGCTTGGCCATCATGGTGAACGGGCGGCTGCGCTGCCTGGGCAGCATCCAGCACCTTAAGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000026944-Abca2:NM_007379:43
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:
PF0000522=ABC_tran=PD(2.8=11.4)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099983f2032A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000092742, ENSMUSP00000099983, ENSMUSP00000109908
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:139903915-139903992 
LOW PSI
HsaINT0000616
(ABCA2)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:45180924-45181079 
ALTERNATIVE
BtaINT0011212
(ABCA7)
Chicken
(galGal4)
chr17:422250-422548 
ALTERNATIVE
GgaINT0125096
(ABCA2)
Chicken
(galGal3)
chr17:803427-803725 
ALTERNATIVE
GgaINT0125096
(E1C8X7_CHICK)
Zebrafish
(danRer10)
chr5:24592670-24592753 
LOW PSI
DreINT0023629
(abca2)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
ACCACTGGCATGGACCCTAAG

				
R: 
CTTAAGGTGCTGGATGCTGCC

				
Band lengths: 
183-256

			

		

	





	
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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