Special

MmuINT0007716 @ mm9

Intron Retention

Gene
ENSMUSG00000054746 | Abca15
Description
ATP-binding cassette, sub-family A (ABC1), member 15 [Source:MGI Symbol;Acc:MGI:2388709]
Coordinates
chr7:127540113-127540644:+
Coord C1 exon
chr7:127540113-127540238
Coord A exon
chr7:127540239-127540449
Coord C2 exon
chr7:127540450-127540644
Length
211 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TTTGTGTATTTTTTTTAAAGATA
3' ss Score
7.34
Exon sequences
Seq C1 exon
GATATAATTTCTAAGGAATTATCTGGGACTTCTGAAGATAATGATGTAGAAAATGAGAGAAGAGAAATTTTGTACCAGCCTGAAAAGTTTCTGAATTGCCCAGTTCTTATTAAGGAGCTCACGAAG
Seq A exon
GTAAGCCATTTCATGGCTTTCATAGTCTGCCCTCCACCTCCTGGGGGGGGGGGTGTCAAAGTCTCACTGTGGTTCTTCAGGAGCCTTGAAAACACTTCTCTAAAGTTCTTGTGACACTATCTAAGGGAGTGACCACTTTGTCCACAATATTTTTTGTATATAACCTAAACATGTCCTTTACTAAATTGTGCTTTGTGTATTTTTTTTAAAG
Seq C2 exon
ATATACTTTAAGTCTCCACTAATTCTGGCTGTGAAAAATATCTCCCTTGCTATCCAAGAGAGGGCGTGCTTTGGGTTACTTGGATTCAATGGAGCAGGTAAAACAACTACTTTTCAAATTTTGACTGGAGAAAATATTCCTACCGCCGGGGATGTGTTCATTGATGGCATTAGCCTCACCAAGAACATCGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054746-Abca15:NM_177213:25
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:
NO

							
A:
NA

							
C2:
PF0000522=ABC_tran=PU(37.2=83.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000075621





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000112821
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr16:2331223-2331381 
LOW PSI
HsaINT0000646
(ABCA3)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr25:19561523-19561743 
BtaINT0001338
([1])
Chicken
(galGal4)
chr14:13571494-13571611 
LOW PSI
GgaINT0016432
(ABCA3)
Chicken
(galGal3)
chr14:14336877-14336994 
LOW PSI
GgaINT0016432
(E1BVQ5_CHICK)
Zebrafish
(danRer10)
chr3:12529983-12537124 
LOW PSI
DreINT0023644
(abca3b)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGGAATTATCTGGGACTTCTGAAGA

				
R: 
ACGATGTTCTTGGTGAGGCTA

				
Band lengths: 
304-515

			

		

	





	
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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