Special

MmuINT0007547 @ mm9

Intron Retention

Gene
ENSMUSG00000015243 | Abca1
Description
ATP-binding cassette, sub-family A (ABC1), member 1 [Source:MGI Symbol;Acc:MGI:99607]
Coordinates
chr4:53049745-53051163:-
Coord C1 exon
chr4:53051029-53051163
Coord A exon
chr4:53049849-53051028
Coord C2 exon
chr4:53049745-53049848
Length
1180 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTGTTTTATTCTAATTATAGGAT
3' ss Score
8.18
Exon sequences
Seq C1 exon
GTTGGTGAATGGGCAATTCGCAAACTGGGCCTGGTAAAGTATGGAGAAAAATATGCCAGTAACTACAGTGGCGGCAACAAACGAAAGCTCTCCACAGCCATGGCTTTGATTGGCGGACCTCCTGTGGTGTTTCTG
Seq A exon
GTGAGTGTGAGAGGGGTGTGAGTGAGTGGAGGGTGGAAATTGTTCTTCTGTCTTGAATAGACATCATGGCTTATCTGAAGTCACATGTAGGCCTTTGCGTACTTGGCATGGTGATAGCAAGTCCATCTGCTGGTCCAGAGCAGGCTTCTCCCTCACAGTTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGCTTCTCCCTCACAGGCTTCTCCCTCACAGCACGCTGGGTGGCTCGGCTGTACCTTTACAGGCTCCTGAGTAGACAAGCTCCACTCATCTTGTTTCCTTGCCTTAGATAATCCCTACAAACATGGCTGAAGGTGAAGGTGCTATTTGAATAGTCTCAGGAATATTCTTCATGACTCTATGTTGTTCATCCTCCAAAGGTAGAAGTGAGGACATGGCTTCTAGATGGACATAGTAGCCACAGATGACCATAGTAGCCACTGCATCATAGTTGCTCCCATACAGATGAATAAAAACCAGACCAGACTGGGCAGTGGTCCTTGATCCTCATTTTGTAGAGAACACTGGGAGTATGGGAAGAAGCCTTGGGTTGAAGCTTTAATTTTTATTGACCATGTGGATATGAAATTTCTCTATGATTAGCAAATGTAATAGAACAAGGAGAAAAATATGATGTAAGTTTCACTGCTCTGACTTCAAAAATAATTTTGGACAAAAAGTTTTGGGGTTTTTGTTTTGCTGTTGTTGTTGTTTTGCTATAAGGTTTCACTATGTAGCCCTGGGTGGCCTAAAACTTCCTATGTGGACTAGGCTGACTTTGAGCTCATAGAAATCCACATGTCTCACCCCACCCCCACTCTGGGAAACCCGGCATGATCATTAGCATTGAAAAAAAATTGTCTTGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACTGACTGCTCTTCTGGAGACCCTGAGTTCAATTCCCAGAAATCACATGGTGGCTCACAACCTTCTGTATTCTGTAATGGGGTCTGATGCCCTCTTCTACAGTGTACTCACATATATAAAATAGATAAATAAATCCTTTTAAAAAATTGTCCTTGACATTTTTTTTCCAGCAAATAAACTTGTTTTATTCTAATTATAG
Seq C2 exon
GATGAACCAACCACAGGCATGGACCCTAAAGCCCGGAGATTCTTGTGGAATTGTGCCCTAAGCATTGTCAAGGAGGGGAGATCTGTAGTCCTTACATCTCATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015243-Abca1:NM_013454:46
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=0.029
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0000522=ABC_tran=PD(17.2=54.3)

							
A:
NA

							
C2:
PF0000522=ABC_tran=PD(2.8=11.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000030010f450A





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000030010
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr9:107549258-107550200 
ALTERNATIVE
HsaINT0000403
(ABCA1)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr8:96276553-96278221 
LOW PSI
BtaINT0010831
(ABCA1)
Chicken
(galGal4)
chrZ:54551180-54551794 
LOW PSI
GgaINT0064467
(ABCA1)
Chicken
(galGal3)
chrZ:53603475-53604089 
LOW PSI
GgaINT0064467
(E1C619_CHICK)
Zebrafish
(danRer10)
chr1:51983734-51986720 
ALTERNATIVE
DreINT0023541
(abca1a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTTGGTGAATGGGCAATTCG

				
R: 
TATGAGATGTAAGGACTACAGATCTC

				
Band lengths: 
238-1418

			

		

	





	
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






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"